A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses.HOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FThe cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.The online version contains supplementary material available at 10.1186/s12864-022-08384-0. Since cattle domestication, which occurred around 10,000 years ago , 3 have One effect of these concentrations of homozygous alleles is the emergence of ROH. A ROH is defined as the continuous length of homozygous genotypes that are present in an individual genome due to the progenitors transmitting identical haplotypes to their descendants . The ideHeterozygosity-enriched regions, also known as runs of heterozygosity, consists on the identification of genomic regions with high variability, and can provide information about the population diversity and evolutionary history . For insGenetic diversity is not static, being a continuous process of creation and loss according to evolutionary and selection changes in a population. The maintenance of sufficient genetic diversity is important for the long-term sustainability of livestock populations , 8, 16. The main objectives of this study were to: 1) characterize the population structure of 16 cattle populations from 15 pure or composite breeds selected for different breeding goals; 2) quantify and classify ROH and HER in each population based on their length and alternative detection parameters; 3) perform functional annotation analyses to identify candidate genes and pathways involved in the genomic regions with higher concentration of ROH and HER; 4) estimate inbreeding coefficients and effective population size based on genomic information; and, 5) compare the results obtained from the analyzes of SNP and WGS.The group that presented the highest number of ROH is the SEN breed Fig.  with 419In total, 24,187 ROHs were identified, distributed throughout the autosomal chromosomes. The majority of ROHs were classified as 2-4 Mb, representing 55% of all ROHs found. In summary, only 14% of the ROHs were larger than 8 Mb; of these, 24% were larger than 16 Mb. The distribution and classification of ROHs by chromosome and population can be visualized in Additional file ROH method . The Hereford (HFD) population showed the highest inbreeding rate for the methodologies FHOM1 (0.086), FGRM (0.087), FHOM2 (0.087), and FUNI (0.087), while the SEN population showed the highest inbreeding rate (0.075) when FROH was used.The ANGSIM population showed the lowest inbreeding rate (− 0.026), except for the Fod Table . For FROHOM1 and FHOM2, FHOM1 and FUNI, and FGRM and FUNI  was found between FThe effective population size (Ne) for each population from the 54th to 13th generation ago is shown in Fig. The longest ROH island was found on BTA16 of the BRM breed Table , with anThe ROH island present in the highest proportion (92%) of the population was found in the BTA5 for the GIR breed. This island was also present in the BRM breed, in a lower proportion of animals (51.43%). An overlap of ROH islands were observed in the BTA1, BTA16, and BTA19 in both GIR and BRM breeds. These breeds also showed the highest number of ROH islands (5 islands in each breed). In total, the ROH islands in these breeds contain 556 and 863 genes in the GIR and BRM breeds, respectively, which are involved in key biological processes, cellular components, and molecular functions, as detailed in Additional file Two methods were used to detect HER: the windows method, and the consecutive-SNP method . DespiteIn total, 3576 HERs were found for all populations and the highest number of HERs was found in the MON population 1702 runs). The smallest number of HER was found in the CGU population (2 HERs). In general, the highest percentage of HER was classified as having a length of 0.5-1 Mb (45.13%) and 1-1.5 Mb (41.11%). The percentage of HER higher than 2 Mb were only detected in 1% of HER. The HER distribution by chromosome in each population indicated that the BTA5 had the highest number of HER, with 12% of all HER  was found on BTA1 in NEL50. This region harbors 28 genes , DVL1 in BTA16, and FZD2 and WNT3 in BTA19.In summary, 1662 positional genes were found in the ROH islands and 850 genes in the HER. The genes found in ROH islands are related to 379 pathways, 389 cellular components, 400 biological processes, and 319 molecular functions. The genes found in HER islands are related to 217 pathways, 180 cellular components, 373 biological processes, and 224 molecular functions ; in the GIR breed, three genes are involved , while for Jersey (JER) and SEN, only the genes MPK10 and PRLR were involved, respectively. Another pathway in common between groups was the calcium signaling pathway in ANGSIM and JER, where the CACNA1E and DRD5 genes were found related to this pathway.Prolactin signaling was another important pathway observed in this study. Four genes identified for BRM are involved in this pathway , with the selection of SNPs with higher MAF in Zebu cattle populations and designed to optimize equidistant spacing of markers [The difference in the SNP panel density affected the number of ROHs detected. For NEL35 and NEL50 (same breed but genotyped using different SNP panels), there was a considerable discrepancy between the amount of ROH detected Fig. : Fig. S1 markers . These fSome studies reported that the SNP panel density affect ROH detection , 19, 34.HOM1, FHOM2, FGRM) are dependent on genotype allele frequency different to the methodology by uniting gamete [In general, the inbreeding estimates of the first four methodologies showed similar results. Each one of the methodologies used in the present study has their particularities regarding inbreeding estimation and are dependent on some factors. For example, the first three methods  is responsible for the development and differentiation of mammary gland cells in different life stages [MAPK10 gene (mitogen-activated protein kinase 10) is linked with the inflammatory response and immunity of epithelial cells in the mammary gland. According to Silva et al. [MAPK10 is a candidate gene to somatic cell score (SCS). The PRLR gene (prolactin receptor), also known as the SLICK gene, was associated with heat tolerance [Another pathway found to be in common in four populations that presented the homozygosity islands was the prolactin signaling pathway, which is responsible for many biological processes. Various genes in this pathway were previously associated with important traits in cattle. For example, the e stages . The MAPa et al. , MAPK10 olerance , becauseolerance .CACNA1E . Hay and Roberts [CACNA1E as a candidate gene for growth and carcass-related traits. In JER breed, the DRD5 gene (dopamine receptor D5) was associated with the calcium signaling pathway, which has been associated with feed intake regulation and energy homeostasis [The calcium signaling pathway found in the common islands was observed in ANGSIM and JER. In the ANGSIM breed, the gene related to this pathway is  Roberts  reportedeostasis . Other pDifferent from ROHs, it is expected that the HER occur in regions under balancing selection or with high recombination rate, as low linkage disequilibrium leads to high region diversity. Normally, HER are concentrated in genomic regions associated with disease resistance, where higher levels of diversity can help the population to deal with novel (and changing) potential infirmity issues . DespiteBos taurus indicus and Bos taurus taurus [The population that showed the highest amount of HER was MON (a composite population), which represented more than 47% of HER found in this study. This result was expected as the MON population is a composite breed that combines different biological groups, including breeds from s taurus .It is also important to point out the difference found between NEL35 and NEL50 groups for HER, mostly because the difference on the density among SNP panels. The length classification of HER was different between SNP panels: the NEL50 group presented a smaller length of HER compared to the NEL35 group. As the same regions were detected based on both SNP panels, this result suggests that many of the long HER regions are composed of small HER, broken by regions with homozygous SNPs.KHDRBS2 . This gene has been associated with fertility and reproductive performance in Sanmartinero cattle [IFNG (interferon-gamma), which was found in the HER island for MON breed. IFNG has been previously associated with tick resistance in taurine and zebu cattle [ANXA1 gene (Annexin A1), a protein regulated by glucocorticoids, which was identified for SEN, plays an inhibitory role in the synthesis of arachidonic acid, a precursor of inflammatory processes.Only one gene was found in the smaller HER – o cattle . Howeveru cattle . The ANXThese high heterozygosity concentrations in the region of immune response control are an interesting point to be investigated in these populations, as they can contribute to disease resilience . AdditioAlthough only few studies have focused on identifying HER islands, it seems that the use of the consecutive approach is preferred, as the case of Biscarini et al ., Marras Currently, some WGS studies have been used to detect population structure and identify the regions influencing economically-important traits in livestock . The preSLICK gene, already discussed previously and originally found in SEN animals. Recent studies have already shown that the SLICK gene has been introduced into some HOL populations in a selection process to control heat stress [One interesting observation in the comparison between breeds and SNP panels that was not previously identified with the analysis only with SNP panels, was a small ROH concentration observed in the WGS analysis for Holstein breed close to an island region found in SNP panel analysis of the SEN population. This region contains the t stress .As found in our study, the number of ROH and HER regions differ among populations and provide insights on their differences in selective breeding and evolutionary histories. These differences are expected once the events that acted in each population are different or show different intensity . Some paThe comparison between the 35 K and 50 K SNP panels in the Nellore breed evidenced a divergence in the identification and classification of ROH and HER  from 16 worldwide cattle populations selected for different purposes were used in this study. The sample size of each breed and the density of the SNP panels used are presented in Table http://widde.toulouse.inra.fr/widde/) provided the data of Angus (ANG), Borgou (BOR), Brahman (BRM), Creolo from Guadalupe (CGU), Charolais (CHL), Gyr (GIR), Hereford (HFD), Holstein (HOL), Jersey (JER), Limousin (LMS), Senepol (SEN), and Santa Gertrudis (SGT). To increase the sample size for some breeds, datasets from high-density and 50 K SNP panels were merged for the ANG, BRM, GIR, HFD, JER, and LIM breeds. This was done on the WIDDE platform prior to downloading the data. All SNP coordinates were updated to the ARS-UCD 1.2 [Genomic datasets n = 241 from 16 -UCD 1.2  referenc− 6) parameters were also used to filter out SNPs. The density of genotype panels and the amount of discarded SNP in each QC are shown in Table The genotype quality control (QC) was done separately for each analysis. For ROH and HER, we removed SNPs with call rate lower than 0.90, duplicated position, non-autosomes, or without a defined position. For the other analyses, the minor frequency allele (MAF < 0.05) and Hardy-Weinberg equilibrium , number of homozygous SNPs allowed in a HER (0 to 5), and number of missing SNPs allowed in a HER (0 to 5). In this case, the two population with the highest amount of HER were used to test the impact of parameters alterations on HER results (MON and NEL50).HOM1), calculated as [Hexp is the expected value for homozygous genotypes and Hobs is the observed value for the homozygous genotypes.Five models of inbreeding coefficient estimates were analyzed. The first method was based on the homozygous genotypes observed and expected (Flated as :\documenGRM), using the following model [i is the number of reference allele copies of ith SNP, pi is the reference allele frequency in the population. Similar to the first method, the methodology FHOM2 was based on homozygous genotype following the model:The second method was based on genotype additive variance (Fng model :\documenUNI) using the following model [The above models are all dependents of genotype allele frequency, for this reason, a fourth model was a test based on the correlation between uniting gametes (Fng model :\documenROH) using the following eq. [f(ROHi) is the ROH length of individual ith, n is the total intact homozygous genomic regions of each individual, h(j) is the length of chromosome jth, and A is the number of autosomal chromosomes (A = 29). Still, for each class of ROH , inbreeding estimates were made dividing the total sum of ROH segments by the total length of the cattle autosomal genome covered by SNPs. All the genomic inbreeding coefficients were calculated using the PLINK v1.9 software [The last method was based on the sum of ROH individual length divided by the total length of the autosomal genome  was investigated with the relationship method between linkage disequilibrium variances and the effective population size using the SNeP software  and the Bos taurus from the Ensembl database (https://www.ensembl.org/Bos_taurus/Info/Index), version ARS-UCD1.2 [The genomic regions considered as ROH and HER islands were used for genomic annotations. The GALLO package  was usedS-UCD1.2 . SubsequS-UCD1.2  was usedBos taurus taurus and Bos taurus indicus and their crosses. In our analyses, we only considered breeds in common for the analyses in the SNP panel, this configured a sum of 914 animals. We removed SNPs with call-rate lower than 0.90, duplicated positions, non-autosomes, or without a defined position for the quality control. The analyses were made separately for each chromosome. The parameters used to identify both ROHs and HER in the WGS data was basically the same than those used in the SNP panel analyses, except the number of heterozygous/homozygous SNPs (3) and missing SNPs (5). These parameters were adapted from Ceballos et al. [The results of the SNP panel analysis, for both ROH and HER analyses were also carried out using WGS data. The WGS data was obtained from the “The 1000 Bull Genomes Project – Run 8” database . A totals et al. .Additional file 1: Figure S1. Classification of runs of homozygosity according to length size by chromosome in the different breeds.Additional file 2: Figure S2. Classification of heterozygous-enriched regions according to length size by chromosome in the different breeds.Additional file 3: Figure S3. Comparison between runs of homozygosity SNP panel and whole-genome sequence (WGS) analyzes.Additional file 4: Figure S4. Comparison between heterozygous-enriched regions SNP panel and whole-genome sequence (WGS) analyzes.Additional file 5: Table S1. Genes found in Brahman’s runs homozygosity islands and the processes that are involved.Additional file 6: Table S2. Genes found in AngusxSimmental crossbreed’s runs homozygosity islands and the processes that are involved. Additional file 7: Table S3. Genes found in Gyr’s runs of homozygosity islands and the processes that are involved.Additional file 8: Table S4. Genes found in Montana’s heterozygous-enriched regions and the processes that are involved.Additional file 9: Table S5. Genes found in Nellore 50 K’s heterozygous-enriched regions and the processes that are involved.Additional file 10: Table S6. Genes found in Jersey’s runs of homozygosity islands and the processes that are involved.Additional file 11: Table S7. Genes found in Angus’ heterozygous-enriched regions and the processes that are involved.Additional file 12: Table S8. Genes found in Hereford’s heterozygous-enriched regions and the processes that are involved.Additional file 13: Table S9. Genes found in Nellore 35 K’s heterozygous-enriched regions and the processes that are involved.Additional file 14: Table S10. Genes found in Senepol’s heterozygous-enriched regions and the processes that are involved.Additional file 15: Table S11. Genes found in Senepol’s runs of homozygosity islands and the processes that are involved.Additional file 16: Table S12. Genes found in Santa Gertrudis’ heterozygous-enriched regions and the processes that are involved.


The objective of this study was to investigate whether the use of live attenuated varicella zoster virus (VZV) MAV vaccination can efficiently induce VZV antibody production in naive rhesus monkeys as an approach to prevent simian varicella virus (SVV) reactivation in animals immunosuppressed for transplantation studies.Clinically available human VZV vaccine was used to induce the production of anti-VZV antibodies in rhesus monkeys. A vial of the vaccine was subcutaneously injected at 0 week, and the second and third vaccination was performed at 5 and 6 weeks by intratracheal inoculation. The titer of anti-VZV IgG was assessed at 0, 2, 4, 6, and 7 weeks. At 2 weeks, 3/16 were seropositive for VZV IgG. At 6 weeks, 9/16 were shown to be seropositive. At 7 weeks, 16/16 were found to be seropositive.The VZV vaccine via intratrachael inoculation was shown to induce VZV IgG humoral immunity in rhesus monkeys and may be important immunosuppressed macaques for transplantation studies. Although the humoral immunity produced is an important finding, further studies will be necessary to confirm possible protection and it could protect probably against SVV infection in rhesus monkey. Simian varicella virus (SVV) in Old World monkeys causes epizootic erythematous disease, which is characterized by fever, vesicular skin rash, hepatitis, and high morbidity and mortality . OutbreaR1 (ID of rhesus monkey number 1), an immunosuppressed rhesus monkey, for porcine islet transplantation among 14 rhesus monkeys , housed in Nonhuman Primate Research Center at Seoul National University Hospital exhibited clinical symptoms, such as systemic vesicular rash, fever, anorexia, and vomiting  were seropositive at 2 weeks. At 6 weeks , 9 out of 16 monkeys (56.2%) were shown to be seropositive. At 7 weeks , 16 out of 16 monkeys (100%) were found to be seropositive , especially via intratracheal inoculation, was able to induce VZV IgG production. Meyer et al. demonstrated a lack of varicella and viral replication in either the lungs or whole blood by wild type VZV intratracheal inoculation in rhesus monkeys. All four rhesus monkeys generated an immune response characterized by the generation of VZV-specific antibodies and T-cells in their study. VZV-immune rhesus monkeys displayed no varicella rash and had lower SVV viral loads as well as earlier and stronger humoral and cellular immune responses than controls in the SVV challenge . Our datThe seropositivity of SuduVax (VZV MAV vaccine) by subcutaneous inoculation in humans was shown to be 51 ~ 69% in 1- to 6-year-olds , and theThere were a few limitations of this study. We were not able to did not confirm that VZV IgG could neutralize the SVV antigen due to the absence of the SVV antigen. The SVV IgG level could not be measured because an ELISA kit, which measures only SVV, was not available. A challenge test of SVV in VZV-vaccinated rhesus monkeys was not performed due to lack of pathogenic SVV. In the future, SVV can be obtained from leaders in the SVV field for the needed challenge studies. However, because various studies, especially Meyer et al.’s report , have coWe used 0.7 ml of SuduVax as an intratracheal inoculation. This volume might be negligible in terms of safety concerns. A typical volume of 1–2 mL/kg body weight was safely used to avoid any potential coughing (> 2 ml/kg) and subsequent loss of instilled test material .Our results showed that clinically available SuduVax was able to induce VZV IgG production, especially after two intratracheal inoculations at one-week intervals. These data show a strong humoral immune response was produced by VZV vaccination via intratracheal inoculation. They suggest further efficacy testing against SVV challenge is needed to confirm the use of VZV vaccination to protect against SVV reactivation and disease in rhesus monkeys utilized for immunosuppressive and organ transplantation studies.All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of the Biomedical Research Institute at the Seoul National University Hospital, an AAALAC accredited facility .After the SVV outbreak and follow-up in our NHP facility, we planned to immunize newly imported macaques using clinically available human VZV vaccine. SuduVax  was used to immunize rhesus monkeys. Sixteen naïve female rhesus monkeys (age: 3–5 years) were used. Sedation of the monkeys was induced with medetomidine  and ketamine . The injection site was prepared aseptically. A vial of the vaccine solution 0.7 ml, 1400 pfu) was subcutaneously injected at week 0 and administered via intratracheal inoculation at week 5 and 6 due to poor VZV IgG seropositive after 0 week subcutaneous VZV inoculation. The trachea of the rhesus monkey was grasped by the thumb and index finger of the nondominant hand. The needle was inserted into the trachea in a 30-degree cephalad or caudal orientation to the skin and directed cranially or caudally after penetration of the anterior tracheal wall. Before inoculation, air was aspirated to ensure that the needle was in the proper position. The complications related to subcutaneous or intratracheal injection were monitored by observer’s subjective judgement for pain  and observer’s objective judgement for swelling and redness at the injection site, fever, and rash by systemic reaction. VZV IgG titers were monitored at week 0, 2, 4, 6, and 7 . VZV IgG titers greater than 150 mIU/ml were considered seropositive VZV IgG titers greater than 150 mIU/ml were considered seropositive which is suggested by chemiluminescent immunoassay  for human VZV , cutoff To determine how the VZV IgG antibody titer waned over time, we analyzed five monkeys among 16 at one of three time points among 19, 23, 31, and 55 weeks.


The Kemp’s ridley sea turtle is an endangered species that is susceptible to a tumor disease called fibropapillomatosis (FP) and its associated virus, chelonid alphaherpesvirus 5 (ChHV5). The goal of our study was to describe FP in Kemp’s ridley turtles, including estimated disease prevalence and pathologyg, and case demographics and outcomes, to better understand the risk posed by FP to Kemp’s ridley population recovery. During 2006–2020, we identified 22 cases of Kemp’s ridley turtles with FP, including 12 adult turtles, a reproductively valuable age class. Molecular diagnostics were used to identify ChHV5 DNA in blood (7.8%) and tumor (91.7%) samples collected from free-ranging Kemp’s ridley turtles. Genomic sequencing was conducted to identify ChHV5 variants in tumor samples collected from Kemp’s ridley turtles with FP. Along with case data, phylogenetic analysis of resultant sequences suggests increasing, spatiotemporal spread of ChHV5 infections and FP among Kemp’s ridley turtles in coastal areas, including the Gulf of Mexico and the southwestern Atlantic Ocean, where they share habitat with green sea turtles (in which FP is enzootic). This is concerning because FP has an uncertain pathogenesis, is potentially related to anthropogenic environmental degradation, and can cause suffering and/or death in severely afflicted turtles.Lepidochelys kempii). With this study, we describe FP and the associated chelonid alphaherpesvirus 5 (ChHV5) in Kemp’s ridley turtles encountered in the United States during 2006–2020. Analysis of 22 case reports of Kemp’s ridley turtles with FP revealed that while the disease was mild in most cases, 54.5% were adult turtles, a reproductively valuable age class whose survival is a priority for population recovery. Of 51 blood samples from tumor-free turtles and 12 tumor samples from turtles with FP, 7.8% and 91.7%, respectively, tested positive for ChHV5 DNA via quantitative polymerase chain reaction (qPCR). Viral genome shotgun sequencing and phylogenetic analysis of six tumor samples show that ChHV5 sequences in Kemp’s ridley turtles encountered in the Gulf of Mexico and northwestern Atlantic cluster with ChHV5 sequences identified in green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtles from Hawaii, the southwestern Atlantic Ocean, and the Caribbean. Results suggest an interspecific, spatiotemporal spread of FP among Kemp’s ridley turtles in regions where the disease is enzootic. Although FP is currently uncommon in this species, it remains a health concern due to its uncertain pathogenesis and potential relationship with habitat degradation.Fibropapillomatosis (FP), a debilitating, infectious neoplastic disease, is rarely reported in endangered Kemp’s ridley sea turtles ( Lepidochelys kempii) is an endangered (United States Endangered Species Act 1970)/critically endangered  species that primarily lives in the Gulf of Mexico (GoM) and in waters off the eastern coastal United States of America (USA) . To. To14]. Lk11FPT1, Lk17FPT2, and Lk9FPT3 all cluster closely  and compared to the reference ChHV5 HP32 gene.  closely , and areP32 gene .Our study summarizes case data, including epidemiology, molecular diagnostics, and phylogenetics analysis, on Kemp’s ridley sea turtles with FP in the United States during 2006–2020. Although the current study spans a period of 14 years, nearly half  of these cases were reported in 2019–2020, suggesting a potential for increasing disease prevalence over time, increased reporting, or both. Of the 22 cases, 16 (72.7%) were encountered on the GoM (Texas and western Florida), and six 27.3%) were found stranded on the coasts of the western Atlantic Ocean , corresponding to the known range of Kemp’s ridley turtles in coastal United States waters ,50. Nota.3% were Overall, the FP cases reported here were generally less severe than those reported in sympatric green turtles, including low numbers of mostly small tumors . FP presented as one to multiple smooth, pedunculated tumors in 50% of cases, and as verrucous-type tumors in 45.5% of cases. This is similar to descriptions of FP in loggerhead turtles, which typically present with few small tumors at very low prevalence , and difAdditionally, most (68.1%) of the Kemp’s ridley turtles with FP were classified as adults based on SCL ≥60.0 cm , includiLk17FPT2). Furthermore, enrichment was based on centrifugation and extraction from supernatant, and thus intracellular latent ChHV5 DNA may have been underrepresented.The qPCR assay used herein was successful in amplifying ChHV5 DNA in all but one (91.7%) of the tumor samples tested. This is promising because although this qPCR assay was developed based on a consensus sequence intended to target ChHV5 UL30 gene segments in green turtle samples, it also provides reliable results when used on samples from other sea turtle species including loggerhead and Kemp’s ridley turtles  current, the widLk14FPT8 and Lk15FPT5 (from New England and southwest Florida) had the same or a very closely related variant to known Florida variants A–C [Globally, there are four major clades of ChHV5: eastern Pacific, midwestern Pacific, western Atlantic/eastern Caribbean, and Atlantic . To dateants A–C . This shThe evidence presented here suggests that, while currently uncommon, fibropapillomatosis may be increasing in endangered Kemp’s ridley sea turtles. This is concerning since the disease has an uncertain pathogenesis, is potentially related to anthropogenic environmental degradation, and can cause suffering and/or death in severely afflicted turtles. Phylogenetic analysis of ChHV5 sequences isolated from Kemp’s ridley turtles with fibropapillomatosis suggest interspecific, spatial, and temporal spread of this disease among Kemp’s ridley turtles in regions where the disease is enzootic, including the Gulf of Mexico and the southeastern Atlantic coast of the United States.


Edward's syndrome (ES) occurs as a result of trisomy of chromosome 18 and is associated with multisystem congenital anomalies. The association of ES with various gastrointestinal malformations but Hirschsprung disease (HD) is well documented.A female infant on her 5th day of life presented with episodes of bilious vomiting along with abdominal distension and no passage of stool. The child had a small head and prominent occiput, low set abnormal ears, small jaw, upturned nose, widely spaced eyes, small neck with widely spaced nipples, clenched hands with overlapping fingers, flexed big toe, and prominent heels.Edward syndrome is associated with multisystem congenital abnormalities of which gastrointestinal abnormalities make up the most part. The condition can be identified by fetal ultrasound screening. Surgical correction of associated congenital anomalies at different times along with lifelong supportive management is important.Edward syndrome can present as Hirschsprung disease as a part of associated gastrointestinal Malformation. Often, early identification and termination of the pregnancy in antenatal life can reduce the suffering. Surgical correction of associated anomalies along with supportive care forms the cornerstone of management. However, the prognosis remains poor. •Association of Edward syndrome (Trisomy 18) with Hirschsprung disease is still not clear.•Although prognosis is poor, surgical correction of associated anomalies along with supportive care is the crucial in management. HD has 22P1L1 mother by spontaneous vaginal delivery at 39+2 period of gestation was brought to the emergency department with a complaint of multiple episodes of bilious vomiting along with abdominal distension and unable to pass stool since birth. There was no history of fever, lethargy, inconsolable cry, and irritability. The female had no history of spontaneous abortion and her first child is healthy and normal.A Five-day-old female infant, born to a 23-year GOn examination, the child was conscious and ill-looking with a small head but prominent occiput, low set abnormal ears, small jaw, upturned nose, widely spaced eyes, small neck with widely spaced nipples, clenched hands with overlapping fingers, flexed big toe, and prominent heels; features suggestive of Edward's syndrome . She wasAll the hematological parameters were within normal limits. X-ray abdomen supine view revealed marked dilatation of large bowel with no gas in the rectum . USG abd3Edward syndrome is a rare chromosomal disorder that occurs due to non-disjunction or translocation of chromosome 18 with a live prevalence of 1/3600 to 1/10,000 . Multior3.1Major clinical manifestations of the syndrome are represented by prenatal growth deficiency, specific craniofacial features in the postnatal period collectively associated with other major and, minor anomalies along with noticeable psychomotor and cognitive developmental delay in later days of life . Among mOf various gastrointestinal abnormalities that can occur with ES as previously mentioned, however, HS is not one of them. Although chromosomal abnormalities account for 12% of the syndromic association of HD, Down's syndrome is the commonest. Other syndromes like multiple congenital anomalies-Mental retardation syndrome, Mowat Wilson Syndrome, DiGeorge Syndrome, Mosaic trisomy 8, XXY chromosomal constitution, partial duplication of chromosome 2q, tetrasomy 9p should be considered in the vicinity [Presentation of HD in neonates is early with symptoms suggesting intestinal obstruction, marked by distention of the abdomen, the passage of meconium after 48 h, feeding intolerance, and bilious vomiting [3.2Anatomical malformations associated with trisomy 18 can be detected by prenatal ultrasound and amniocentesis or cordocentesis tests can be carried out for karyotyping or fluorescent in situ hybridization . Early d3.3Surgical intervention with resection of aganglionic bowel is the principal treatment for Hirschsprung disease. Colostomies were performed readily to prevent the development of enterocolitis . Dependi3.4From an ethical point of view, it is necessary for a physician to identify those children who would actually benefit from an interventionist approach, consider factors like overall survival, long term quality of life, and not simply deny an interventionist approach based solely on a diagnosis of trisomy 18. Simultaneously, it is of paramount importance to respect parental values, consider parental decisions, and also the right to parental authority . After m4HD can occur with Edward syndrome. More understanding of the association of HD with syndromic diseases including Edward's can provide insights into the condition. Additionally, termination of pregnancy once diagnosed with trisomy 18 as previously thought no longer holds true and all the necessary interventions have to be provided with a consensual decision of treating physician and the parents. Proper counseling at different points of time along with intensive supportive treatment is necessary for optimal survival of the child.Written informed consent was obtained from the patient's parent for publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal on request.Not required.None.Bibek Man Shrestha.None.Dinesh Prasad Koirala (DPK), Diwan Shrestha (DS), and Bibek Man Shrestha (BMS) = Study concept, Data collection, and surgical therapy for the patientBMS and Suraj Shrestha (SS) = Writing - original draft preparationAnil Bist (AB) and Sanjeev Kharel (SK) = Editing and writingDPK and DS = senior author and manuscript reviewer.All the authors read and approved the final manuscript.None to declare.


However, the expression and clinical significance of BMPs/BMPRs in lung adenocarcinoma remain unclear due to a lack of systematic studies.Bone morphogenetic proteins (BMPs) regulate tumor progression via univariate and multivariate Cox regression analyses. LASSO was performed to construct an initial risk model. Subsequently, after weighted gene co-expression network analysis (WGCNA), differential expression analysis, and univariate Cox regression analysis, hub genes co-expressed with differentially expressed BMPs/BMPRs were filtered out to improve the risk model and explore potential mechanisms. The improved risk model was re-established via LASSO combining hub genes with differentially expressed BMPs/BMPRs as the core. In the testing cohort including 93 lung adenocarcinoma patients, immunohistochemistry (IHC) was performed to verify BMP5 protein expression and its association with prognosis.This study screened differentially expressed BMPs/BMPRs (deBMPs/BMPRs) in a training dataset combining TCGA-LUAD and GTEx-LUNG and verified them in four GEO datasets. Their prognostic value was evaluated p: 3e-04) but low prognostic accuracy . Seventy-nine hub genes co-expressed with BMP5 were identified, and their functions were enriched in cell migration and tumor metastasis. The re-established risk model showed greater prognostic correlation  and value . IHC results revealed that BMP5 protein was also downregulated in lung adenocarcinoma and higher expression was markedly associated with better prognosis .BMP2, BMP5, BMP6, GDF10, and ACVRL1 were verified as downregulated in lung adenocarcinoma. Survival analysis identified BMP5 as an independent protective prognostic factor. We also found that BMP5 was significantly correlated with EGFR expression and mutations, suggesting that BMP5 may play a role in targeted therapy. The initial risk model containing only BMP5 showed a significant correlation (HR: 1.71, 95% CI: 1.28−2.28, BMP5 is a potential crucial target for lung adenocarcinoma treatment based on significant differential expression and superior prognostic value. Bone morphogenetic proteins (BMPs) were initially identified as factors that induce ectopic bone formation . Since tvia the phosphorylation of the type II receptor and subsequent phosphorylation of Smad family and other signaling proteins . The normalized gene expression level of the TCGA-LUAD cohort was utilized to evaluate the expression of BMPs/BMPRs in lung adenocarcinoma tissues (n = 526) compared with normal lung tissues (n = 59). The GTEx (https://commonfund.nih.gov/GTEx/) project provided us the RNA-seq data of normal lung tissue , which effectively reduced the bias resulting from the large gap of sample sizes between lung adenocarcinoma and normal lung tissues in TCGA-LUAD (The gene expression profile data in the current study combined the RNA-seq transcriptome data of lung adenocarcinoma (LUAD) cohort from The Cancer Genome Atlas (TCGA) and lung tissue from the Genotype-Tissue Expression (GTEx) from the University of California Santa Cruz (UCSC) Xena platform  and osteogenic proteins (OPs). To avoid confusion, only the terms “BMP” and “GDF” are used in this study. As for BMPRs, there are four type I receptors and three type II receptors. We extracted the expression matrix of 11 BMPs and 7 BMPRs and the clinical information of the samples for subsequent bioinformatics analysis.p <0.05 as the DEGs.To screen the differentially expressed genes among 11 BMPs and 7 BMPRs in lung adenocarcinoma, the package “Limma” in R/Bioconductor software was applied to analyze the expression of 18 genes in 526 tumor tissues and 347 normal lung tissues. The results of the differentially expressed gene (DEG) analysis are presented in the form of a heatmap, and the violin plot was used to visualize the overall expression levels of BMPs/BMPRs in lung adenocarcinoma and normal lung tissues. We defined the genes with logFC value (the logarithm of fold change) >1 or ≤1 and Although the amount of data combining TCGA-LUAD and GTEx-LUNG was large, the DEG analysis between no paired cancer and normal tissues could be affected by individual differences. To further validate the ubiquity of differential expression of BMPs/BMPRs between lung adenocarcinoma and normal lung tissues, four gene expression profile datasets [GSE10072 , GSE4079http://kmplot.com/), an online database capable of assessing the association of genes on survival in four types of cancer , was also applied to verify the prognostic value of BMPs/BMPRs in lung adenocarcinoma patients (n = 719)  . Next, tTo predict the clinical outcomes of lung adenocarcinoma patients using BMPs/BMPRs, the R package “glmnet” was utilized to construct the risk model using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm in the TCGA-LUAD dataset. Based on the minimum criteria, part of the differentially expressed BMPs/BMPRs was selected out and the risk scores were calculated from the coefficients of the risk model. Then, the TCGA-LUAD dataset was separated into low- and high-risk groups based on the mean risk score. The prognostic value of the risk model was evaluated through Kaplan–Meier survival analysis, ROC curve, and univariate and multivariate Cox regression analyses.To explore the potential mechanism of BMPs/BMPRs involved in the risk model, the weighted gene correlation network was constructed using the weighted gene correlation network analysis (“WGCNA”) package in R . In TCGAp < 0.001) from the module genes. Finally, the hub gene prognostic value was weighted via LASSO regression, and the risk model was re-established.We selected the genes in the module that were highly relevant to the expression of BMPs/BMPRs in the risk model. Next, the “ClusterProfiler” R package was utilized for Gene Ontology (GO) enrichment analysis of the module genes . Then, DA total of 93 lung adenocarcinoma patients who received surgical resection at Tongji Hospital of Huazhong University of Science and Technology, Tongji Medical College  and who accepted medical follow-up that continued until July 2021 were included. Paraffin specimens from these patients were collected at Tongji Hospital between 2014 and 2018. All 93 patients were histologically diagnosed with primary lung adenocarcinoma. The study was approved by the Institutional Ethics Committee of Tongji Medical College, Huazhong University of Science and Technology, and written informed consent was obtained from all of the patients before surgery.Immunohistochemistry (IHC) staining was performed for the tissue microarrays (TMA) which contain 93 paired paraffin-embedded lung adenocarcinoma tissues and adjacent normal tissues together with 122 metastatic lymph nodes. The IHC kit  was used according to the instructions of the manufacturer. Primary antibody of rabbit anti-BMP5 antibody (dilution 1:200) was purchased from Cusabio Co. Ltd. . We evaluated BMP5 expression levels in each specimen with a semiquantitative immunoreactivity scoring system, which ranged from 1 to 8 and was equal to the sum of the intensity of IHC staining  and the percentage of positive cells . The mean IHC score was chosen as the cutoff value to define low and high BMP5 expression. Protein expression levels of BMP5 were independently scored by two pathologists with the blind method.t-test, and non-normally distributed data were analyzed using Mann–Whitney tests, after a normality check. The Pearson test was employed to evaluate the correlation among BMPs/BMPRs, and Kendall rank correlation coefficient tests were used to check the correlation of these DEGs with clinicopathologic features. The prognostic value of BMPs/BMPRs was evaluated using Kaplan–Meier survival analysis and Cox multivariate regression analysis. Differences were considered to be statistically significant at p <0.05.Normally distributed data were analyzed using Student’s In the lung adenocarcinoma gene expression profile dataset, 526 cases were tumor tissues  and 347 cases were normal tissues (288 from GTEx-LUNG and 59 from TCGA-LUAD). To explore the differential expression of BMPs/BMPRs, we extracted and compared the expression levels of 18 BMPs/BMPRs between tumor and normal tissues in the above datasets Table 1,p-values showed that the four downregulated BMPs  and ACVRL1 were verified among four GEO datasets, and the trend of GDF10 downregulation was the most stable . Among eight deBMPs/BMPRs, only BMP5  and GDF10  had prognostic value, and the higher expression of both indicated a better prognosis in lung adenocarcinoma (p: 9e-10 < 0.001) and GDF10  from TCGA-LUAD (p: 0.00016 < 0.001) suggested the short OS in the Kaplan–Meier plotter, but its expression  did not have significant prognostic value in TCGA-LUAD. Compared with GDF10, the above results both suggested that BMP5 has high prognostic value and its increased expression has a high association with better prognosis in lung adenocarcinoma.For differentially expressed BMPs/BMPRs (deBMPs/BMPRs), survival analysis was performed with prognostic information from the tumor samples of TCGA-LUAD . The lower the expression of BMP5, the shorter the OS, and the poorer the prognosis in lung adenocarcinoma   (p = 0.0372) (p = 0.942)  and a low-risk group (n = 291) to investigate the association with the clinicopathological features and prognostic roles of the risk model. Since treatment information was not available from the database for the 513 patients included, survival analysis was performed without taking into account the treatment differences.To predict the clinical outcomes of lung adenocarcinoma using deBMPs/BMPRs, we applied the LASSO Cox regression algorithm to the eight genes in the TCGA-LUAD dataset. Only BMP5 was selected to build the risk model based on the minimum criteria, and its coefficient obtained from the LASSO algorithm was −0.1697154 for calculating the risk score for TCGA-LUAD (p < 0.001) and N-stage (p < 0.001) in lung adenocarcinoma ; however, the receiver operating characteristic curve (ROC curve) found that the AUC was generally small , and its diagnostic value was not satisfactory  and was chosen as the focus of subsequent research. The positive coefficient indicated a positive correlation between the screened module and BMP5, and a higher coefficient with a statistically significant p-value indicated a stronger correlation with BMP5 and prognosis in lung adenocarcinoma. As the above results show, the genes in the brown module may be regulated by BMP5 and play an important role in the prognosis of patients with lung adenocarcinoma.Based on the correlation between modules and clinicopathologic features, the modules significantly associated with BMP5 expression were selected  in comparing tumor tissues with normal tissues in TCGA-LUAD . In cell component terms (p < 0.0001). Although the molecular function “receptor regulator activity” is very common, the enriched DEGs under cell components such as “actin cytoskeleton” and “membrane raft” were associated with cell migration and tumor invasion. Interestingly, in terms of biological processes (p < 1e-11). The above results of the function enrichment analysis suggested that the DEGs associated with BMP5 may play an important role in invasion and metastasis and affect prognosis in lung adenocarcinoma.The 537 DEGs were analyzed for GO function enrichment. In molecular function terms of GO  in lung adenocarcinoma  was 5.27, which was lower than the score in adjacent normal tissues . Metastatic lymph nodes (n = 122) showed even lower BMP5 expression (average IHC score = 4.49) than primary tumor. Overall, BMP5 expression was higher in adjacent normal tissues than primary tumor tissues and was the lowest in metastatic lymph nodes  based on mean IHC score of BMP5 as the cutoff value in their primary tumors. Kaplan–Meier survival curve revealed that BMP5 expression levels were significantly associated with overall survival in lung adenocarcinoma patients. The overall survival was longer in patients with high BMP5 expression compared with patients with low expression  . To evaluate the prognostic value of these five deBMPs/BMPRs, a series of survival analyses including Kaplan–Meier curve and univariate and multivariate Cox regression analyses were carried out, and BMP5 was identified as an independent protective prognostic factor in lung adenocarcinoma. We found that BMP5 expression was significantly correlated with EGFR expression and mutations, suggesting that BMP5 may play a role in targeted therapy. Based on BMP5 and closely related hub genes such as CHRDL1, GIMAP8, and KAL1, we constructed and improved a prognostic risk model that effectively evaluated the prognosis of lung adenocarcinoma. Subsequently, we verified the protein expression of BMP5 in TMA by IHC staining. The results showed that BMP5 expression was low in primary lung adenocarcinoma compared with adjacent normal tissues, and was even lower in metastatic lymph nodes. Consistent with public database analysis, higher expression of BMP5 protein in lung adenocarcinoma indicated better prognosis.BMP5, as a tumor suppressor, has been previously studied in myeloma, adrenocortical carcinoma, breast cancer, and colorectal cancer . RegardiDevelopmental studies confirmed that BMP signaling could be suppressed by cysteine-rich domain proteins that sequester ligands from the BMPRs such as chordin . ChordinCurrently, immunotherapy based on immune checkpoint PD-L1 (programmed death ligand 1) has made remarkable progress in the treatment of advanced lung cancer, accompanying the problem of limited beneficiaries . The GIMThe unified nomenclature for Kallmann syndrome 1 gene (KAL1) and anosmin-1 is ANOS1 . At presCompared with other studies focused on BMPs/BMPRs in lung cancer, the present research is a systematic screening study of BMPs/BMPRs based on large-sample RNA-seq data. On the premise of fully considering the influence of histology types in this study, we focused on lung adenocarcinoma to explore the expression differences and prognostic correlation of BMPs/BMPRs. Finally, we identified BMP5 as having significantly differential expression and superior prognostic value, rather than BMP2, BMP4, and BMP7, which have been extensively explored in lung cancer. To some extent, the current results provide a direction for the subsequent studies on the mechanism of BMPs in lung adenocarcinoma. In addition, the WGCNA identified hub genes co-expressed with BMP5 and, for the subsequent, puts forward an important series of thoughts. First, CHRDL1 as a BMP signaling antagonist suppresses tumor metastasis but co-expressed with BMP5 in lung adenocarcinoma. Therefore, exploration of the regulatory mechanisms of both will further the understanding of lung cancer metastasis. Second, GIMAP8 is a potential immunotherapy target and will be the focus of subsequent studies to improve the efficacy of immunotherapy on the basis of fully understanding the relationship between GIMAP8 and BMP5. Third, the diagnostic value of KAL1 as a mature diagnostic biomarker in gastric cancer is also worthy looking forward to in lung adenocarcinoma.The current research completed a systematic screening of BMPs and preliminary functional exploration in lung adenocarcinoma; however, the biggest deficiency is that the above results are mainly based on bioinformatics analysis of public databases. Although the sample size included is large and the results have been repeatedly verified by different cohorts, these conclusions still lack necessary experimental evidence. Subsequent studies will conduct experiments on the detailed mechanisms of BMP5 in lung adenocarcinoma, especially on the regulatory relationship between BMP5 and the three hub genes. Based on significant differential expression and superior prognostic value, BMP5 has the potential to become a crucial target for the treatment of lung adenocarcinoma.We screened and verified four differentially expressed BMPs  and one BMPR (ACVRL1), which all were downregulated in lung adenocarcinoma tissues. BMP5 was identified as an independent protective prognostic factor, and higher BMP5 expression indicated better clinical outcomes in lung adenocarcinoma. The correlation between BMP5 and EGFR expression and mutations suggests that BMP5 may affect EGFR-targeted therapy in lung adenocarcinoma. Based on the co-expression network of BMP5, 79 hub genes were selected, and their functions were enriched in cell migration and tumor invasion. The risk model was established around BMP5 and its hub genes and constantly improved. Subsequently, the risk model combining 20 hub genes including CHRDL1, GIMAP8, KAL1, and BMP5 as the core showed significant prognostic correlation and excellent prognostic value. Finally, IHC staining in TMA revealed that the expression level and prognostic value of BMP5 protein were consistent with public database analysis. In conclusion, BMP5 is differentially expressed and can accurately evaluate prognosis as an independent protective factor in lung adenocarcinoma. BMP5 is expected to become an important target for the treatment of lung adenocarcinoma. Future research will focus on the detailed mechanisms of BMP5, especially the regulatory relationship with the three hub genes.The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/The studies involving human participants were reviewed and approved by the Institutional Ethics Committee of Tongji Medical College, Huazhong University of Science and Technology. The patients/participants provided their written informed consent to participate in this study.HX: ideas incubation, study design, workflow construction, data analysis, data interpretation, writing—original draft, and writing—review and editing. YL: ideas incubation, study design, and writing—review and editing. WM: study design, data collection, data analysis, writing—original draft, and writing—review and editing. RZ: literature search, data collection, writing—original draft, and writing—review and editing. DL: study design, workflow construction, figures, data interpretation, and writing—review and editing. KL: literature search, data collection, and writing—original draft. YM: data collection and writing—review and editing. JC: data collection and writing—review and editing. YW: data collection and writing—review and editing. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


The health and growth of children less than two years of age can be affected by the poor quality of complementary foods and poor feeding practices even with optimal breastfeeding. In Ethiopia, empirical evidence on the minimum acceptable diet and its associated factors is limited. Therefore, this study was aimed to assess the level of minimum acceptable diet and its associated factors among children aged 6–23 months in Addis Ababa Ethiopia.p-value < 0.05.An institution-based Cross-sectional study was conducted among a total of 575 mother-child pairs. A simple random sampling technique was used to recruit participants. For infant and young child feeding practices, the data collection tools were adapted from world health organizations’ standardized questionnaire which is developed in 2007. Data entry and analysis were performed using EPI data version 3.1 and SPSS version 20 respectively. Bivariable and multivariable logistic regression analyses were performed to determine predictor variables. Statistical significance was declared at In this study, the level of minimum acceptable diet was found to be 74.6%.. About 90.6 and 80.2% of the children received minimum meal frequency and dietary diversity respectively. Having a husband secondary and above educational level [AOR = 4.789(95%CI:1.917–11.967)], being a housewife [AOR = 0.351(95% CI: 0.150–0.819)], having a history of more than three postnatal follow-ups [AOR = 2.616], being male child [AOR = 1.585(95%CI:1.052–2.388)] and having children age between 18 and 23 months [AOR = 3.026(95%CI:1.786–5.128)] were some of the factors significantly associated with a minimum acceptable diet.In this study, the minimum acceptable diet among children aged 6–23 months was significantly associated with the educational status of the husband, mother’s occupation, history of postnatal follow-up, age of the mother, sex of the child, and age of the child. Thus, attention should be given to educating the father, empowering mothers to have a job, promoting gender equality of feeding, and counseling on the benefit of postnatal care visits. In addition, the ministry of health should work on educating and advocating the benefit of feeding the recommended minimum acceptable diet to break the intergenerational cycle of malnutrition. Improving nutrition through appropriate complementary feeding practices is crucial for the achievement of healthy growth, development, and survival of young children and is one of the most cost-effective approaches to address many of the societal, environmental, and economic challenges worldwide –3. The WInsufficient quantities and inadequate quality of complementary foods, poor child feeding practices, and high rates of infections harm health and growth in children less than 2 years of age . Any damGlobally, ensuring optimal complementary feeding can avert a substantial proportion of childhood deaths . WorldwiIn many low-income countries including Ethiopia, meeting MDD and MMF standards has been a serious challenge, especially in areas where household food security is poor . Culturehas been made in the development of complementary feeding and the provision of national nutrition programs by defining standards for appropriate feeding through the notable publication of different guiding principles. However, the strategies for breaking the inter-generational cycle of malnutrition were not well focused and not complete, particularly in addressing the critical window of opportunities “the first 1000 days” and critical elements of efforts such as encouraging and supporting appropriate complementary feeding for children aged 6–23 months [In Ethiopia, considerable progress 3 months .Empirical evidence on minimally acceptable diet and associated factors are limited in Ethiopia and they are in the rural communities and district level . TherefoAn institution-based cross-sectional study was conducted from June 01 to June 30, 2019, in the city of Addis Ababa Ethiopia. The city comprises 10 sub-cities (Kifle Ketemas). Yeka sub-city, Bole sub-city, and Arada sub-city were three of the ten sub-cities with a total population of 454,850, 406,059, and 279,020 respectively. The expected number of children aged 6–23 months was 21,872 . Yeka sub-city had 14 districts and 15 health centers and one governmental hospital, Bole sub-city had 10 health centers and 15 districts and Arada sub-city had 9 health centers and 10 districts .All children aged 6–23 months who came for the expanded program on immunization (EPI) at the government health facility in Addis Ababa, Ethiopia were the source population whereas those children aged 6–23 months and came to the Expanded Program on Immunization (EPI) during the data collection period at the selected governmental health centers were taken as the study population.All children aged 6–23 months with a permanent residence of the mother (lived for at least six months) who came for the Expanded Program on Immunization (EPI) only. Children aged 6–23 months whose mothers had (permanent residents) in the study area during data collection. While those children aged 6–23 months with known medical or surgical problems were excluded.Minimum dietary diversity: was taken as an achieved if the children were received four or more food groups from of the seven food groups such as grains, roots and tubers; legumes and nuts; dairy products ; Flesh foods ; eggs; vitamin A-rich fruits and vegetables; and other fruits and vegetables –21.Minimum meal frequency: The children who received solid, semisolid, or soft foods is taken as minimal meal frequency and was measured when the infant feeds twice for breastfed infants 6–8 months, three times for breastfed children 9–23.9 months, and four times for non-breastfed children 6–23 months , 21.Minimum acceptable diet: For breastfed children, it is achieved if the child meets both the MDD and MMF criteria. For non- breastfeed children, the child has to receive at least four food groups excluding dairy products, two milk feeds, and MMF .Satisfactory exposure to media: If Women aged 15–49 years read a newspaper or magazine or listen to the radio, or watched television at least once a week [Household income: consists of all receipts whether monetary or in-kind (goods and services) that are received by the household or by individual members of the household at annual or more frequent intervals, but exclude windfall gains and other such irregular and typically one-time receipts .Household food security: households who experience none of the food insecurity (access) conditions, or just experience worry, but (one or two times in the last 4 weeks) are labeled as “Food secured” , 24.Household food insecure: in the ability of households to access sufficient food at all time to lead to an active healthy life  without eating), even as infrequently as rarely (one or two times in the last 4 weeks) .Maternal decision making: if the mother has the right to decide on the amount of food type of food and the right to buy food for the baby, then the mother is said to be involved in the decision making. However, if she doesn’t involve in any of the above criteria, then the mother is said to be not involved in the decision-making.Timely introduction of complementary feeding: the Introduction of solid, semi-solid, or soft foods, minimum meal frequency, minimum dietary diversity, and consumption of iron-rich or iron-fortified foods and started at six months of age , 26.Appropriate:-if the mother responds correctly to all four indicators .Inappropriate:-among the four indicators if at least one indicator was not fulfilled .The minimum sample size was determined using a single and the double population proportion formula for the first and the second objectives respectively and was calculated using Epi Info™ version 7 stat calc. The final required sample size (large sample from the two objectives) for this particular study was obtained using the second objective and it was 575 .Out of 10 sub-cities in the city, 30% of them  were selected by lottery method. From each sub-city 30% of their health centers (HC) were again selected by lottery method . The eligible total number of children aged 6–23 months from each sub-city were selected using population size to proportional allocation based on their medical record number as sampling frame  was performed to check the consistency or reduce data entry error.P < 0.25 in the bivariate analysis were included in the final model of multivariable analysis. To see the correlation between independent variables multi-collinearity test was carried out by using collinearity statistics. Values with the standard error > 2 were dropped from the analysis. In a multivariable model adjusted odds ratio determined with a 95% confidence level was used to assess the strength of association. In this study P-value < 0.05 was deemed to declare statistical significance. Then, the finding was presented by using simple frequencies, summary measures, tables, texts, and figures.The collected data were coded, cleaned, edited, and entered into Epidata version 3.1 and exported to SPSS version 20.0 for statistical analysis. The presence of an association between explanatory and outcome variables was ascertained using binary logistic regression analysis. The goodness of fit was tested by the log-likelihood ratio (LR). To control all possible confounders all variables with (See Table 1).In this study, 562 respondents participated with a response rate of 97.7%). The median age of the mothers was 28 (SD ±6 years). More than half (50.7%) of the children were males. The majority (37.4%) of the children were in the age group of 18 and 23 months. The median age of the children was 16 (±4 years) months. All most all, (95.4%) of mothers were married, 406 (72.2%) and 339 (60.3%) of their husbands had a secondary and above level of education and were private workers respectively. Four hundred thirty-five (77.4%) were orthodox Christian religious followers. Four hundred six (72.2%) of fathers had an educational level of secondary and above, and 70.8% of the mothers had been working as a housewife (See Table 2).The majority, (90.4%) of the mothers had a history of antenatal care (ANC) follow-up (≥four times). Five hundred fifty-four, (98.6%) of children were delivered to a health facility. About 94.7% of mothers received postnatal care and 82.6% of children were breastfeeding at the time of the survey Nearly three-fourth, 419 (74.6%) of the children fulfilled the recommended minimum acceptable diet criteria. Five hundred six (90.6%) of children received minimum meal frequency and 80.2% of them were received minimum dietary diversity. Four hundred twenty (74.6%) of children started complementary feeding practice in a timely manner, and 55.7% of them had started complementary feeding at an appropriate time .The age of the mother between 25 and 34 years , being a male child , having a postnatal visit of ≥3 , age child between 18 and 23 months  and fathers education level secondary and above  were approximately 2 times, 1.6 times, 2.6 times, 3 times and 4.8 times respectively more likely to have achieved minimal acceptance rate than their counterparts Achieving a minimum acceptable diet among infants and young children of 6–23 months of age is one of the strategies currently used to break the intergenerational cycle of malnutrition. The study findings showed that the proportion of children who received minimum dietary diversity is higher than studies conducted in Addis Ababa (59.9%) , DembechSimilarly, the minimum meal frequency of the study was higher than that reported in studies coducted in Ethiopia such as Dabat District (72.2%), Dangla Town (50.4%) and Wolaita Sodo town (68.9%) , 15, 29 In this study much amount of the children who received minimum acceptable diet, which is much higher than findings in Dembecha, North West Ethiopia, Wolaita Sodo town, Northern Shoa (Oromia region), and EDHS 2016 , 28, 31.In this study, we have found some factors associated with a minimally acceptable diet. These included; educational status of the father, maternal occupation; history of postnatal care visit, gender, maternal age, and age of the child. Mothers who had a history of more than three postnatal care visits were two times more likely to provide the recommended minimum acceptable diet than their counterparts. This finding is supported by a study done in Northern Shoa, Ethiopia . This isThose children with the age group of 18–23 months had higher odds of having a minimum acceptable diet than those children whose ages were 6–11 months old. This finding is supported by a study done in Afghanistan, rural Ghana, Wolaita Sodo, EDHS 2016 , 32, 33.Children born from fathers who had a secondary and above level of education were four times more likely to meet the recommended minimum acceptable diet than those fathers who have no formal education. This study is supported by EDHS, 2016 . This miChildren born from mothers who were government employees were 64.9% more likely to receive a minimum acceptable diet than housewives. This finding is in line with EDHS, 2016 . But it children who were born from mothers whose ages were in between 25 and 34 years were two times more likely to practice the recommended minimum acceptable diet than the age group of 15–24 years. This finding was similar to a study done in Dabat District, North West Ethiopia . This miFinally, male children were more likely to achieve the minimum acceptable diet than female children. The finding was supported with the study done in Ethiopian adolescents , West GuIn this study, the practice of minimum acceptable diet in children aged between 6 to 23 months is relatively high in Addis Ababa. Being 18–23 months old child fathers educational level of secondary and above, having more than three postnatal care visits, being a housewife, being male gender, and maternal age between 25 and 34 years were some of the factors associated with the practice of minimum acceptable diet. More efforts should be needed to educate and advocate the benefit of the feeding of recommended minimum acceptable diet for all children to break the intergenerational cycle of malnutrition. On the other hand, it is important FMOH encourage postnatal care service utilization and health professionals who give postnatal care service should also provide education and counseling on the benefit of the feeding of the recommended minimum meal frequency and meal diversity to the child, advise the mother to avoid traditional believes that inhibit the practice of child feeding. Additionally, it is important to do on the gender equality of feeding practice of the mother. A strong study design (cohort) should be recommended.Being a health facility-based study particularly governmental health facilities ignored the entire community and those who had served in private health facilities, might overestimate the finding. In addition to this, as the study considered only 24 h recall dietary method, it might not accurately reflect participants’ past feeding dietary habits. Moreover, there might be a recall bias, and being a self-reported study might not give the exact figure of the minimum dietary diversity practice .


Geological data integration and spatial analysis for structural elucidation are more assertive approaches for reconnaissance scale mineral exploration. In this study, several methods involving Fry analysis, distance correlation analysis, prediction area plots as well as knowledge driven predictive models including TOPSIS, ARAS and MOORA were systematically employed for unravelling the spatial geological attributes related to gold mineralisation. Additionally, statistical validation of knowledge driven predictive models were implemented using the Receiver Operating Characteristic/Area Under Curve analysis (ROC/AUC). The evidence from Fry and distance correlation analysis suggests that gold occurrence within parts of the Malumfashi schist belt of Nigeria is defined by a strong spatial association with the ENE-WSW as well as the NNE-SSW trending structures. The prediction area plot also revealed a robust spatial correlation between mineral occurrence and spatial data related to geological structures. The application of knowledge driven predictive models suggest a high favourability for gold occurrence within the southern, central, and north-eastern parts of the study location, while statistical validation using the ROC/AUC curves suggest a high prediction accuracy greater than 70% for all models. The geospatial analysis for mineral exploration within the Malumfashi area has unveiled an invaluable geological criterion for gold targeting with a considerable level of certainty. Gold, Mineral Deposit, Schist belt, Malumfashi, Predictive modelling. In many cases, several methods consisting of geochemistry, mineralogy, petrology, geophysics, and remote sensing/Geographic Information System (GIS) are employed for feasibility assessment and target delineation of mineral resources across a wide range of geological environments , 6, 7, 8The choice of exploration method employed is usually dependent on the ore deposit character, its geological attributes and more specifically, the scale of geological prospecting. Although geochemistry and geophysical methods have been widely used for mineral exploration, recent developments from remote sensing/GIS approaches have been invaluable for exploring a wide range of mineralisation across numerous mineral belts around the world , 10, 11.On a regional scale, the use of remote sensing and GIS remains the best alternative as it has been credited with enormous success with respect to time efficiency, prediction accuracy and ability to explore inaccessible areas. The practical applications of remote sensing/GIS methods to mineral exploration are often centred on three main aspects consisting of satellite mapping of hydrothermal alteration, structural investigation of ore geometry and spatial data integration for prospectivity map development , 14, 15.The implementation of data integration techniques is generally based on sufficient knowledge of mineral deposit evidence. According to Carranza , the appIn exploring for gold within the Nigerian basement complex, remote sensing/GIS dataset remains the most suitable technique owing to its ability to map and delineate hydrothermal alterations as well as geological structures associated with gold occurrence , 21, 22.2The Nigerian basement complex forms a part of the Pan-African mobile belt and lies between the West African and Congo Cratons, and south of the Tuareg Shield a 28]. T. T28]. Tsensu stricto accounting for about 30% of the total surface area of Nigeria. It constitutes heterogeneous assemblages of rock suits including the migmatites, gneisses of various origin and basic and ultra-basic rocks such as amphibolite and talc schists . A. A29]. A schists . The occ schists  as ancie schists . The lit schists , consist schists . Radiome schists .2 between latitudes 12⁰ 18ʹ and 12⁰ 24ʹ 30ʹʹ N and longitudes 8⁰00ʹ and 8⁰ 6ʹ 30ʹʹ E In this study, spatial data used for gold prospectivity analysis include:A basic summary of the spatial data used in gold predictive analysis is illustrated in The study area is underlain by lithologies of Pan-African granites and metasedimentary rocks as shown in The digitized lineaments shown in 3.3Gold occurrence within the Nigerian schist belts are mesothermal, with origin linked to metamorphic processes of devolatilization and dehydration of subducted crustal materials along a collisional sutured zone . The hydIn Nigeria, metasedimentary rocks are generally considered the most viable lithological units for gold mineralisation , 52. By The environmental dynamics associated with rock magnetism validates the use of aeromagnetic data for gold prospecting . Usually4A spatial illustration of methods used in the study is shown in 4.1The detailed information on directional anisotropy of spatial distribution of mineral deposits at different scales can be obtained using Fry analysis . The Fry4.2Establishing a proximal relationship between mineral deposit occurrence and a set geological structure can be accomplished using a plethora of spatial and statistical tools , 62, 63.4.3Optimal prediction via application of knowledge driven predictive models are usually influenced by sufficient information on spatial association between exploration data and known mineral deposit occurrence. In most cases, the prediction ability for every spatial data is computed as weight values using a variety of statistical tools including Shannon entropy, information value, Chi-Square analysis or prediction area plot. The prediction area plot first proposed by Yousefi and Carranza , have be4.4, et al. [The TOPSIS model initially developed by Hwang and Yoon , can be , et al. , the cor, et al. . The sys, et al. .Step 1: Generation and creation of a decision matrix as shown in Step 2: Calculation of a normalised decision matrix using the formula in Step 3: Calculation of weight normalised value calculated using the formula in Step 4: Determination of ideal and negative ideal solution (solution .(4)A+={vStep 5: Consist of:i) separation of each alternative from the positive ideal solution using ii) separation of each alternative from the negative ideal solution using Step 6: Consist of calculating the relative closeness to the ideal solution as well as ranking the performance order using 4.5, et al. [The ARAS model first proposed by Zavadskas and Turskis  represen, et al. , the ARAStep 1: Determination of optimal performance rating for every criterion. This step is usually applied when the decision making does not have a preference. Thus, the optimal performance is computed using Step 2: Consists of calculating the normalised decision matrix using Step 3: Involves computing a weighted normalised decision matrix using the formula on Step 4: Consist of calculating the overall performance rating for every alternative within a given criteria. The application of Step 5: The degree of unity for every alternative is calculated using the formula on Step 6: Consist of ranking the various alternatives and selecting the most effective ones. Considered alternatives are ranked in ascending order based on their computed 4.6, et al. [Multi-criteria decision making with the MOORA technique is generally considered an invaluable tool for optimising the best alternatives and identifying the most viable substitute within a given number of options , 77. It , et al. , the enh, et al. . StatistStep 1: Involves the creation and generation of a decision matrix designated by an Step 2: Involves the normalisation of the decision matrix using the formula computed in Step 3: Consists of optimising the different attributes by adding the normalised performance in case of maximisation (for favourable attributes) and deduction in case of minimisation . The optimisation of different criteria is implemented using the formula in Step 4: Because some attributes are usually more important in predicting a given event, it is essential to incorporate a weight factor illustrated in The output value 4.7Performance assessment of every GIS model is generally considered invaluable in predicting future events , 81 as i5The effective structural control for gold mineralisation within the Malumfashi area is illustrated using the Fry plot and distance correlation analysis plots as shown in Figures A statistical correlation analysis amongst predictive variables is shown in A total of seven datasets consisting of geology, geophysical, structural, and remote sensing data were effectively integrated for gold predictive mapping using three multi-criteria decision models consisting of TOPSIS, ARAS and MOORA . SpatialA visual analysis of the spatial association between known gold occurrence and every predictive model suggests a significant association with zones of high favourability. Within these models, approximate estimate of 77% of all gold mineralisation appears to fall within the most favourable predicted zones. The statistical validation using the ROC/AUC tool shown in Geological evidence from several studies in the open literature , 86, 87 Bonham-Carter  have sugThe application of multi-criteria methods for predicting mineral deposit occurrence are well suited for green field programs . In most6Regional structural mapping and data integration methods are important tools for mineral exploration at regional extents. The assessment of prediction competence for every geospatial data and the incorporation of derived weights into GIS models have been invaluable in augmenting prediction accuracy of multi-criteria models. Positive spatial association of gold deposits with the NNE-SSW as well as the ENE-WSW may suggest the genesis of gold mineralisation involved two distinct orogenic episodes. The close spatial similarity amongst the TOPSIS, MOORA and ARAS models as well as the high prediction accuracy above 70% are reliable indicators that these models could be effective in prospecting gold mineralisation within the study area.Andongma W. Tende: Conceived and designed the experiments; Performed the experiments; Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data; Wrote the paper.Mohammed D.Aminu, Abdulgafar K. Amuda and Jiriko N. Gajere: Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data.Hadiza Usman and Fatima Shinkafi: Analyzed and interpreted the data.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Data will be made available on request.The authors declare no conflict of interest.No additional information is available for this paper.


The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds.Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds.Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large The online version contains supplementary material available at 10.1186/s12711-021-00640-3. Bos indicus cattle breeds [Bos indicus cattle are renowned for their heat tolerance and adaptation to harsh conditions, making them the predominant type of cattle in tropical countries. Apart from ancient movements of zebu cattle into Africa between 4500 and 700 BCE [Bos indicus cattle in the rest of the world have been imported from the Indian sub-continent in the past 200 years and may deviate genetically from their original Indian breeds, e.g. Brazilian Nelore or Guzerat [Bos primigenius nomadicus [The Indian subcontinent is the center of domestication and current home to most of the world’s e breeds . Bos ind 700 BCE , 3, mostomadicus ; howeveromadicus . Archaeoomadicus –12.http://www.nbagr.res.in/nbagr.html) listing 50 registered Indian cattle breeds to date. Five of these registered breeds—Sahiwal, Gir, Red Sindhi, Tharparkar, and Deoni—are pure milking breeds, whereas the others are dual purpose or pure draught animals [The number of registered cattle breeds in India has increased steadily over time, with Sukhatme  reportin animals , 15. OnlBos indicus cattle are still lacking. Among the studies reported in the literature, some have used limited numbers of mitochondrial DNA markers [Detailed studies on the genetic diversity of  markers , 16, 17, markers –20, and  markers , or indi markers . Thus, rIn this paper, we present the results of the largest sampling of Indian indigenous cattle breeds so far, which includes 15 pure breeds and a population of non-descript animals genotyped on the 777 k SNP BovineHD chip. We analyzed the within- and between-breed genetic diversity and derived past and present estimates of effective population sizes. In addition, we performed comparisons of the Indian breeds sampled here with other indicine breeds and populations outside of India and with taurine breeds.The BAIF Development Research Foundation sampled 699 Indian indigenous cows and bulls in 2017 from different locations across India  and a minimal quality control (QC) was run using the SNPQC pipeline  to proviIn addition, 345 animals from reference breeds were included in the analyses, i.e. six exotic dairy breeds including Holstein, Jersey, Canadian Ayrshire, British Friesian, Guernsey, and Brown Swiss, and 18 indicine breeds including Achai, Bhagnani, Cholistani, Dajal, Dhanni, Gabrali, Gir, Guzerat, Hariana, Hissar, Kankraj, Lohani, Nelore, Ongole, Red Sindhi, Rojhan, Sahiwal, and Tharparkar  were calculated based on the genomic relationship matrix (GRM) which was derived using two approaches. The first approach constructed the GRM according to VanRaden . MissingBos taurus ancestry, as estimated by admixture analysis. To remove potential bias due to a limited number of SNPs with a low minor allele frequency (MAF), we applied a cut-off threshold so that only SNPs with a MAF higher than 0.05 were used.Allele frequencies , We calculated the correlation of the observed allele frequencies between each breed-pair, entclass1pt{minimaThe variance of the true SNP allele frequencies in one breed that was explained by the true SNP allele frequencies in another breed was estimated as:Ancestral breed proportions of the Indian indigenous animals were estimated by using either the reduced 35 k SNP set when all reference breeds were included for a supervised admixture analysis, or the full 700 k marker set when only the 16 BAIF indigenous populations were used in an unsupervised admixture analysis . The unsBreed diversity was measured based on allele frequencies, the GRM (described above according to VanRaden ), and \dg to Nei  and Weirg to Nei , respectg to Nei ), we setRuns of homozygosity (ROH) were also analyzed in the Indian indigenous animals to assess inbreeding, using the R-package detectRUNS with a sliding-window approach similar to that of Purcell and Neale . AccordiPhylogenetic trees were constructed with the TreeMix v.1.72.0 software . MaximumThe f4 statistic , 31, as th marker was retained, was used to calculate LD between markers separated by 1 to 50 Mb in order to speed up computing time without losing too much accuracy. The LD calculations are described in Material and Methods S3  and by less than 0.34% for PC2. Many livestock-related studies use GRM for genome-wide association studies (GWAS) or genomic prediction purposes based on VanRaden’s method rather than only for genetic diversity studies. Thus, our study focuses on the results from the first approach based on VanRaden’s method , to makeBos indicus from Bos taurus breeds. Several of the Indian indigenous breeds in our study, especially Sahiwal, Red Sindhi, and the non-descript population, were distributed towards the taurine reference breeds  that had more than 1% taurine content from the PC analysis, all the Indian indigenous and indicine reference breeds clustered tightly together Fig. b. In ther et al. . To creaBos taurus breeds  and 20 Bos taurus breeds . However, selection of markers was heavily biased towards SNPs that have a high MAF within and across breeds and put much more emphasis on Bos taurus data, such that a bias against diversity of Bos taurus rather than between Bos indicus breeds is expected. Thus, these results also point strongly to much less molecular genetic variation between Bos indicus breeds than between Bos taurus breeds.Using only the Indian indigenous animals (700 k data) sampled for this study, the first six PC were obtained with up to 20 animals per breed and by removing all admixed animals Fig. b and  breeds and were misclassified in the field as Malnad Gidda and Khillar.For all the breeds genotyped on both the 35 k and 700 k SNP sets, the average allele frequency was lower than 0.5, with the largest bias being observed for the 35 k SNP set and for the indicine breeds , the high correlation values indicate that individual breeds are well represented in the average frequency across all indigenous animals.The correlations of each breed’s allele frequencies with the average allele frequency across the whole sample of 586 Indian indigenous animals ranged from 0.967 to 0.990 for all SNPs. Because the ascertainment bias of the SNP assay resulted in more markers with a low MAF in the Bos taurus reference breeds, based on 700 k data. This table shows that whereas expected correlations of 0.902 and 0.864, respectively above and below the diagonal, were obtained based on a sample size of 20 randomly chosen animals for each breed, all the observed correlations were much lower, which indicates that substantial differences exist between breeds. The Bos taurus dairy breeds, about 60% of the variance in SNP allele frequency is within breeds and about 40% between breeds.For a comparison with the correlations of each breed’s allele frequencies with the average allele frequency across all indigenous animals, Additional file Bos indicus breeds can be treated as belonging to a single population for the purpose of designing an SNP assay, while the Bos taurus breeds that show substantial differences in SNP allele frequency between breeds should be taken into account separately for an optimal assay design.Thus, in conclusion the Indian indigenous Bos indicus reference samples and the Indian indigenous animals in our dataset. However, given the very large genetic distance between the Bos taurus and Bos indicus breeds, the admixture analyses do provide an accurate estimate of the proportion of Bos taurus versus Bos indicus admixture.For assigning ancestral proportions, unsupervised admixture analyses use the information directly from the target population. Thus, the composition of the target population affects the admixture estimates, which makes a direct comparison of ancestral proportions between studies difficult. However, unsupervised admixture analyses are not intended to indicate true ancestral breed composition but are useful to indicate the diversity between and within breeds and the degree of affinity between the various Bos taurus and 16 Bos indicus reference breeds are set as a possible ancestral breed. This analysis found that 109 of the Indian indigenous samples contained more than 1% Bos taurus admixture . The proportion of animals with more than 1% Bos taurus admixture ranged from 0 (Ongole and Red Kandhari) to 0.63  and the proportions for the other breeds were the following: Red Sindhi (0.32), Sahiwal (0.26), Malnad Gidda (0.26), Haryana (0.24), Krishna Valley (0.23), Tharparkar (0.06), Gaolao (0.05), Dangi (0.04), Khillar (0.04), Hallikar (0.04), and Gir (0.02). Among the remaining 588 Indian indigenous animals with less than 1% Bos taurus admixture, 578 were estimated to have less than 0.01% Bos taurus admixture. This strong dichotomy between animals with and without Bos taurus admixture and the large variation in admixture proportion for animals with more than 1% Bos taurus admixture is consistent with admixture being of very recent origin. An ancient admixture in the history of the development of breeds post-domestication would have led to a near equal Bos taurus proportion in all the animals of breeds that had an ancient admixture.Figure Bos taurus admixture > 1%) from a supervised admixture analysis when only the indicine reference breeds are set as possible ancestral breeds. The proportion of each ancestral reference breed (columns) is shown for each Indian indigenous breed sampled in our study. A number of Indian indigenous breeds appear to have a high affinity with individual indicine reference breeds. For example, the origin of the indigenous Gir and Red Sindhi samples appears to be primarily of the reference Gir and Red Sindhi breeds, respectively. The origin of the Khillar and Hallikar animals appears to be mostly of the reference Ongole breed and that of the indigenous Tharparkar sample appears to be mostly of the reference Kankraj breed, with a small contribution from the reference Tharparkar breed. In addition, a number of the Indian indigenous breeds in our sample include small contributions from many reference breeds. Consistent with its name, the origin of the non-descript population showed little affinity with any of the reference breeds.Figure The heatmap patterns in Fig. Figure The f3 test determines whether a population A shows admixture based on populations B and C . Significant Z-scores (< −3) were found only for the non-descript population, which shows admixture from ten of the other Indian indigenous breeds , which agrees with the results of the admixture analysis  were smaller than 6 Mb in all of the Indian indigenous breeds sampled here. This abundance of short ROH confirms that recent inbreeding levels are low. However, the inbreeding coefficient derived from ROH  samples that both include 20 animals, cluster together. Similarly, the reference Nelore (from Brazil) and reference Ongole (from India) samples, each with 20 animals, also cluster together.Figure  indicus , 26, 42.Figure The f4 statistic was used to test whether two clusters of four populations  have a significant gene flow between them. Most often, the Hallikar breed closely followed by the non-descript population are included in the clusters that show a significant gene flow, whereas the Gaolao and Malnad Gidda breeds are less commonly included in clusters with gene flow. Gene flow is mostly observed between the non-descript population and the Dangi breed, i.e. 122 times in 1498 clusters, followed by Khillar and Hallikar 108 times), Hallikar and Krishna Valley (83 times), and Gir and Red Kandhari (77 times), which is in concordance with the maximum likelihood tree and the identified migration edges .Additional file 12: Figure S7. Decay of the linkage disequilibrium with increasing distance between SNPs for a six indigenous breeds (N > 2f0) and b eight indigenous breeds (N < 20).