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 quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

“…BN is a major yield component that significantly contributes to the individual plant yield of cotton [ 22 ]. In a previous study, we have also found that BN is the most important factor in cotton fiber yield [ 20 ]. However, the high CV value and low heritability of BN (72.92%) indicate that the trait is greatly influenced by the environment and is difficult to be controlled in genetic improvement.…”

“…It is of great significance to discover QTLs and candidate genes related to yield traits for genetic improvement of cotton to develop high-yielding cultivars. With the release of genome-wide sequence information, lots of QTLs and genes associated with cotton yield traits were identified by GWAS analysis [ 12 , 20 – 22 ]. Nevertheless, the yield components are complex quantitative traits controlled by multiple genes and affected by environments.…”

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 identification of complex quantitative traits has been widely used in cotton for various traits including salt tolerance [ 35 – 40 ]. Jia et al [ 21 ] identified 3 simple sequence repeats (SSR) markers significantly associated with the relative survival rate under salt stress through association mapping methods using 323 G. hirsutum germplasms.…”