6th Global Summit on Plant Science
Institute of Cotton Research-CAAS, China
Title: Single nucleotide polymorphism associated with salinity stress tolerance in upland cotton (Gossypium hirsutum L.)
Biography: Xiongming Du
Although much studies have been done on salinity tolerance in cotton crop, but little is known about genetic control based on single nucleotide polymorphism (SNPs) underlying salt tolerance of cotton plants at seedling stage. To gain an understanding of the genetic basis of upland cotton tolerance to salinity at seedling stage, a genome wide association study (GWAS) was conducted for salinity stress tolerance traits in a core collection of genetically diverse population comprising of 419 accessions. While a genetic map of 5178 SNP markers were developed from 277 F2:3 populations. The map spanned 4768.098 cM with an average distance of 0.92 cM. Next generation high throughput Illumina HiSeq platform was used for genome sequencing, which resulted in 6.45 Tb raw sequences with 150 -bp read length. After sequence quality and filtering process 6.35 Tb high quality SNPs were finally used for subsequent analysis. A total of 5655 SNPs associated with different traits were found. Finally, 15 candidate genes containing key SNPs, involved in different biological pathways for salt tolerance were found for further omics studies. We identified 18 single nucleotide polymorphs (SNPs) significantly associated with relative electrolyte conductivity ratio, 13 SNPs were found high association with REC, 5 SNPs with relative water content and 5 SNPs were found significantly associated with fresh weight. A total of 66 QTLs (quantitative-trait loci) for 10 traits related to salinity were detected in three environments (0, 110 and 150 mM salt treatment). Only 14 QTLs were consistent, accounting for 2.72% to 9.87% of phenotypic variation. Parental contributions were found to be in the ratio of 3:1, 10 QTLs from the sensitive and four QTLs from the resistant parent. Five QTLs were located in At and nine QTLs in the Dt sub-genome. Moreover, eight clusters were identified, in which 12 putative key genes were found to be related to salinity. The GBS-SNPs-based genetic map developed is the first high-density genetic map that has the potential to provide deeper insights into upland cotton salinity tolerance. The 12 key genes found in this study could be used for QTL fine mapping and cloning for further studies. The findings of our GWAS study provides new knowledge about genetic control of salt tolerance at seedling stage, which could aid in elucidation of genetic and molecular mechanism of salinity stress tolerance in cotton crop.