A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum.
BACKGROUND
Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping.


RESULTS
In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL.


CONCLUSION
A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of 'stable QTL' found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs.
['Ali|Iftikhar|I|', 'Teng|Zhonghua|Z|', 'Bai|Yuting|Y|', 'Yang|Qing|Q|', 'Hao|Yongshui|Y|', 'Hou|Juan|J|', 'Jia|Yongbin|Y|', 'Tian|Lixia|L|', 'Liu|Xueying|X|', 'Tan|Zhaoyun|Z|', 'Wang|Wenwen|W|', 'Kenneth|Kiirya|K|', 'Sharkh|Abdalla Yousef Ahmed|AYA|', 'Liu|Dexin|D|', 'Guo|Kai|K|', 'Zhang|Jian|J|', 'Liu|Dajun|D|', 'Zhang|Zhengsheng|Z|']
D002874:Chromosome Mapping D016000:Cluster Analysis D032561:Cotton Fiber D018744:DNA, Plant D015723:Gene Library D018745:Genome, Plant D003368:Gossypium D021141:Nucleic Acid Amplification Techniques D010641:Phenotype D020641:Polymorphism, Single Nucleotide D040641:Quantitative Trait Loci D017422:Sequence Analysis, DNA
Genetic map Single nucleotide polymorphism marker Specific locus amplified fragment sequencing (SLAF-seq) Fiber quality traits Quantitative trait loci mapping Upland cotton (Gossypium hirsutum L.)