Identification of SSR markers linked to the abscission of cotton bolls traits and mining germplasm in Cotton

Abstract Background: Cotton is one of the most important economic crops. To effectively improve yield of cotton, an urgent way is decreasing the abscission of cotton bolls and buds. However, unclear genetic and molecular mechanism underlying cotton bolls abscission traits hindered the genetic improvement of cotton. Methods: In this study, the correlation analysis between abscission traits and other agronomically important traits were carried out by Pearson correlation analysis. Then, a genome-wide association study for these traits were performed based on 145 alleles locus with highly polymorphism and uniformly distributed on 26 chromosomes by TASSEL V2.1 software. The loci of elite allelic variation and typical materials carrying elite alleles were determined by association study. Results: The Pearson correlation analysis showed a significant positive correlation among AR1 (boll abscission rate 1) and AR2 (boll abscission rate 2). There were 18, 46 and 62 markers significantly associated with abscission traits, fiber quality traits and yield traits (P < 0.05), and explaining 1.75% ~ 7.13%, 1.16% ~ 9.58% and 1.40% ~ 5.44% of the phenotypic variation respectively. Among these markers, MON_CGR5732aand MON_CGR5732b markers were associated with cotton abscission traits, fiber quality traits and yield traits loci, and 13 marker loci have been reported by previous studies. In addition, based on phenotypic effects six typical materials with elite allele loci related to fiber quality traits were identified and they will be widely used in practical breeding. Conclusions: Phenotypic analysis of 238 accessions showed that the traits were relatively stable under four environmental conditions, and AR2 was an important indicator of abscission. Association analysis based on SSR markers provides two excellent allelic variants associated with low abscission rate and the six typical materials with excellent alleles.