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Genome-wide association study of yield components using a 40K SNP array and identification of a stable locus for boll weight in upland cotton (Gossypium hirsutum L.)

LI Yi-Qian2,XU Shou-Zhen1,LIU Ping1,MA Qi1,XIE Bin1,CHEN Hong1,*   

  1. 1 Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, Xinjiang, China; 2 College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China
  • Received:2024-12-03 Revised:2025-04-27 Accepted:2025-04-27 Published:2025-05-14
  • Supported by:
    This study was supported by the Science and Technology Innovation 2023-Major Project (2023ZD0404106).

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Abstract:

Cotton yield is primarily determined by key yield components, including boll number per plant, boll weight, and lint percentage. Understanding the genetic basis of these traits is essential for advancing molecular breeding strategies. In this study, a natural population of 612 upland cotton (Gossypium hirsutum L.) accessions was genotyped using a 40K SNP array based on liquid-phase probe hybridization technology. Phenotypic data for boll number per plant, boll weight, lint percentage, and seed cotton yield were collected across five different environments. A genome-wide association study (GWAS) identified six significant loci: two associated with boll number per plant (on chromosomes A03 and A05), one with boll weight (on chromosome A07), one with lint percentage (on chromosome D01), and two with seed cotton yield (on chromosomes A05 and D07). Notably, a stable QTL located between 89.01 and 90.45 Mb on chromosome A07 was consistently associated with boll weight across all five environments (P=5.3646×10?8). Haplotype analysis of this region revealed two major haplotypes, with accessions carrying the favorable haplotype exhibiting a significant increase in boll weight of 0.64 g. By integrating whole-genome resequencing and transcriptome data, seven candidate genes were identified within this region, and a key SNP variant was pinpointed for potential use in molecular marker development. These findings enhance our understanding of the genetic architecture of cotton yield traits and offer valuable molecular resources for high-yield cotton breeding programs.

Key words: upland cotton, yield components, GWAS, boll weight, high-yield breeding

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