Genetic dissection of QTLs linked with seedling, yield and fiber quality traits of upland cotton under salt stress field conditions

Gossypium hirsutum is extensively cultivated due to its wide adaptability to environment, high production and better yield potential. The saline soil inhibited the emergence and seedling stage, and then effect on the production of upland cotton. In this study, a recombinant inbred lines (RIL) population was developed from a salt-sensitive variety (Zhong G5) and a salt-tolerance variety (Zhong 07). Using GBS-sequence technology, a genetic linkage map was constructed with 1,154 bin markers, which included 4,077 single nucleotide polymorphisms (SNPs) covering the 1796.067 cM of genome length. We performed QTL mapping controlling field emergence rate, seedling age, yield and fiber quality traits under salt stress and normal conditions in 2017-2019 years, to explore genetic basis of salt stress in upland cotton. There were 162 QTLs identified for seedling, yield and fiber quality traits from RIL population in field conditions. In the yield-related, five stable QTLs, qBNP-ChrA13-1, qBW-ChrD12-1, qBW-ChrD12-2, qLP-ChrA01-1 and qLP-ChrD05-1, were identified under different conditions in different years. Three stable loci, qFL-ChrD11-3, qFM-ChrA13-2 and qFM-ChrD05-1, were detected in fiber quality traits under multiple conditions in two years. These results could be useful in understanding the genetic basic of the salt tolerance mechanisms of cotton, and facilitating cotton salt tolerance breeding.