Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

Abstract

Background: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. Results: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. Conclusions: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing Upland cotton varieties with high yields and salt stress tolerance.

Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

“…In total, 102 quantitative trait nucleotides (QTNs) on 26 chromosomes were identified as significantly associated with the traits (Additional file 7: Table S3). We define the flank 200 Kb regions of QTN as an initial QTL and merge the overlapped QTLs to obtain the final QTLs as described previously [14]. In total, 81 QTLs were detected 413 times under different environments and a best linear unbiased predictors (BLUP) by six multi-loci MLM models.…”

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum

“…The identification of salt tolerance genes is of key importance for improving cotton yield in salt affected lands [24,25]. Limited number of salt tolerance genes have been identified in cotton as compared to other model plants [26,27].…”

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

“…Recent years, association mapping as an important method for the identi cation of complex quantitative traits has been widely used in cotton for various traits including salt tolerance [35][36][37][38][39][40]. Jia et al [21] identi ed 3 simple sequence repeats (SSR) markers signi cantly associated with the relative survival rate under salt stress through association mapping methods using 323 G. hirsutum germplasms.…”