A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum

BMC Genomics

Abdalla Yousef Ahmed Sharkh¹  Kai Guo¹  Zhengsheng Zhang¹  Lixia Tian¹  Dajun Liu¹  Yuting Bai¹  Kiirya Kenneth¹  Dexin Liu¹  Zhonghua Teng¹  Qing Yang¹  Yongbin Jia¹  Xueying Liu¹  Zhaoyun Tan¹  Juan Hou¹  Jian Zhang¹  Yongshui Hao¹  Wenwen Wang¹  Iftikhar Ali¹ 

[1]College of Agronomy and Biotechnology, Southwest University

关键词: Upland cotton (Gossypium hirsutum L.);    Genetic map;    Fiber quality traits;    Quantitative trait loci mapping;    Specific locus amplified fragment sequencing (SLAF-seq);    Single nucleotide polymorphism marker;   

DOI  :  10.1186/s12864-018-5294-5

来源: DOAJ

【 摘 要 】

Abstract 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.

【 授权许可】

Unknown