Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Gossypium hirsutum L.) via GWAS

• DOI: 10.3389/fpls.2023.1254365
• Publication Date: 2023-09-01T07:17:32Z
• Authors: Libei Li; Yu Hu; Yongbo Wang; Shuqi Zhao; Yijin You; Ruijie Liu; Jiayi Wang; Mengyuan Yan; Fengli Zhao; Juan Huang; Shuxun Yu; Zhen Feng
• Keywords: Quantitative trait locus; 0301 basic medicine; Candidate gene; Genotype; Trait; Germination; Plant Science; germination rate; Gene; SB1-1110; Cotton Genomics; Agricultural and Biological Sciences; 03 medical and health sciences; Genetics; GWAS; seed vigor; Genomic Studies of Cotton Fiber Development and Improvement; Biology; 2. Zero hunger; Single-nucleotide polymorphism; Gossypium; Plant culture; Life Sciences; 15. Life on land; Computer science; Agronomy; Programming language; upland cotton; FOS: Biological sciences; Marker-assisted selection; candidate genes; Biotechnology

Seed vigor (SV) is a crucial trait determining the quality of crop seeds. Currently, over 80% of China’s cotton-planting area is in Xinjiang Province, where a fully mechanized planting model is adopted, accounting for more than 90% of the total fiber production. Therefore, identifying SV-related loci and genes is crucial for improving cotton yield in Xinjiang. In this study, three seed vigor-related traits, including germination potential, germination rate, and germination index, were investigated across three environments in a panel of 355 diverse accessions based on 2,261,854 high-quality single-nucleotide polymorphisms (SNPs). A total of 26 significant SNPs were detected and divided into six quantitative trait locus regions, including 121 predicted candidate genes. By combining gene expression, gene annotation, and haplotype analysis, two novel candidate genes (Ghir_A09G002730 and Ghir_D03G009280) within qGR-A09-1 and qGI/GP/GR-D03-3 were associated with vigor-related traits, and Ghir_A09G002730 was found to be involved in artificial selection during cotton breeding by population genetic analysis. Thus, understanding the genetic mechanisms underlying seed vigor-related traits in cotton could help increase the efficiency of direct seeding by molecular marker-assisted selection breeding.