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

Abstract

Abstract Background Cotton is an economically important crop. It is crucial to find an effective method to improve cotton yield, and one approach is to decrease the abscission of cotton bolls and buds. However, the lack of knowledge of the genetic and molecular mechanisms underlying cotton boll abscission traits has hindered genetic improvements. Results Pearson’s correlation analysis revealed a significant positive correlation between boll abscission rates 1 (AR1) and boll abscission rates 2 (AR2). A genome-wide association study was conducted on 145 loci that exhibited high polymorphism and were uniformly distributed across 26 chromosomes (pair). The study revealed 18, 46, and 62 markers that were significantly associated with boll abscission, fiber quality, and yield traits (P < 0.05), explaining 1.75%–7.13%, 1.16%–9.58%, and 1.40%–5.44% of the phenotypic variation, respectively. Notably, the marker MON_SHIN-1584b was associated with the cotton boll abscission trait, whereas MON_CGR5732a was associated with cotton boll abscission and fiber quality traits. Thirteen of the marker loci identified in this study had been previously reported. Based on phenotypic effects, six typical cultivars with elite alleles related to cotton boll abscission, fiber quality, and yield traits were identified. These cultivars hold great promise for widespread utilization in breeding programs. Conclusions These results lay the foundation for understanding the molecular regulatory mechanism of cotton boll abscission and provide data for the future improvement of cotton breeding.