AUTHOR=Li Libei , Hu Yu , Wang Yongbo , Zhao Shuqi , You Yijin , Liu Ruijie , Wang Jiayi , Yan Mengyuan , Zhao Fengli , Huang Juan , Yu Shuxun , Feng Zhen 

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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1254365

DOI=10.3389/fpls.2023.1254365

ISSN=1664-462X

ABSTRACT=<p>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 (<italic>Ghir_A09G002730</italic> and <italic>Ghir_D03G009280</italic>) within <italic>qGR-A09-1</italic> and <italic>qGI/GP/GR-D03-3</italic> were associated with vigor-related traits, and <italic>Ghir_A09G002730</italic> 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.</p>