Genome-wide association studies and whole-genome prediction reveal the genetic architecture of KRN in maize.
BACKGROUND
Kernel row number (KRN) is an important trait for the domestication and improvement of maize. Exploring the genetic basis of KRN has great research significance and can provide valuable information for molecular assisted selection.


RESULTS
In this study, one single-locus method (MLM) and six multilocus methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB and ISIS EM-BLASSO) of genome-wide association studies (GWASs) were used to identify significant quantitative trait nucleotides (QTNs) for KRN in an association panel including 639 maize inbred lines that were genotyped by the MaizeSNP50 BeadChip. In three phenotyping environments and with best linear unbiased prediction (BLUP) values, the seven GWAS methods revealed different numbers of KRN-associated QTNs, ranging from 11 to 177. Based on these results, seven important regions for KRN located on chromosomes 1, 2, 3, 5, 9, and 10 were identified by at least three methods and in at least two environments. Moreover, 49 genes from the seven regions were expressed in different maize tissues. Among the 49 genes, ARF29 (Zm00001d026540, encoding auxin response factor 29) and CKO4 (Zm00001d043293, encoding cytokinin oxidase protein) were significantly related to KRN, based on expression analysis and candidate gene association mapping. Whole-genome prediction (WGP) of KRN was also performed, and we found that the KRN-associated tagSNPs achieved a high prediction accuracy. The best strategy was to integrate all of the KRN-associated tagSNPs identified by all GWAS models.


CONCLUSIONS
These results aid in our understanding of the genetic architecture of KRN and provide useful information for genomic selection for KRN in maize breeding.
['An|Yixin|Y|', 'Chen|Lin|L|', 'Li|Yong-Xiang|YX|', 'Li|Chunhui|C|', 'Shi|Yunsu|Y|', 'Zhang|Dengfeng|D|', 'Li|Yu|Y|', 'Wang|Tianyu|T|']
D002523:Edible Grain D018745:Genome, Plant D055106:Genome-Wide Association Study D040641:Quantitative Trait Loci D019655:Quantitative Trait, Heritable D003313:Zea mays
Genome-wide association study Whole-genome prediction Maize Kernel row number Quantitative trait nucleotide