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ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #432954
Research Project: Effective Cotton Genetics and Management Practices for Improved Cotton Quality and Production

Location: Coastal Plain Soil, Water and Plant Conservation Research

Title: Genome-wide association study of yield-component traits in U.S. upland cotton (Gossypium hirsutum L.)

Author
item GOWDA, RAKESH J - North Carolina State University
item GOWDA, S - North Carolina State University
item FANG, H - North Carolina State University
item BOURLAND, FRED - University Of Arkansas
item Campbell, Benjamin
item DEVER, JANE - Clemson University
item ZHANG, JINFA - New Mexico State University
item JONES, DON - Cotton, Inc
item KURAPARTHY, VASU - North Carolina State University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2026
Publication Date: 7/14/2026
Citation: Gowda, R.L., Gowda, S.A., Fang, H., Bourland, F.M., Campbell, B.T., Dever, J., Zhang, J., Jones, D.C., Kuraparthy, V. 2026. Genome-wide association study of yield-component traits in U.S. upland cotton (Gossypium hirsutum L.). Crop Science. 66(4). Article e70334. https://doi.org/10.1002/csc2.70334.
DOI: https://doi.org/10.1002/csc2.70334

Interpretive Summary: Genetic improvement of cotton yield is challenged by the complex and polygenic nature of yield and its underlying component traits. In this study, an elite diversity panel of 348 upland cotton accessions, genotyped using the CottonSNP63K array, was evaluated across 10 environments in the U.S. Cotton Belt for four yield-component traits: lint percent (LP: %), seed index (SI: g), boll weight (BW: g), and lint index (LI). All traits exhibited high broad-sense heritability (>60%), and all except SI showed high genomic heritability. Positive correlations were observed among BW, SI, and LI, whereas SI was negatively correlated with LP. Our genome-wide association analysis identified 19 genomic regions putatively containing genes associated with yield component traits. Notably, this study confirmed the pleiotropic region influencing SI and BW on chromosome D11 and identified a novel co-localized group on chromosome D12 associated with LP and LI. The genomic insights identified in this study provide valuable resources for harnessing genetic diversity to achieve targeted genetic improvement and facilitate the discovery of genes associated with yield in cotton.

Technical Abstract: Genetic improvement of cotton yield is challenged by the complex and polygenic nature of yield and its underlying component traits. In this study, an elite diversity panel of 348 upland cotton accessions, genotyped using the CottonSNP63K array, was evaluated across 10 environments in the U.S. Cotton Belt for four yield-component traits: lint percent (LP: %), seed index (SI: g), boll weight (BW: g), and lint index (LI). All traits exhibited high broad-sense heritability (>60%), and all except SI showed high genomic heritability. Positive correlations were observed among BW, SI, and LI, whereas SI was negatively correlated with LP. Genome-wide association study (GWAS) of the four traits identified 308 significant marker-trait associations (MTAs), including 80 stable MTAs distributed across 19 genomic regions, of which 15 are novel associations. These 19 genomic regions included MTAs detected in at least three environments. The phenotypic variation explained by MTAs within these regions ranged from 7.23 to 11.46%. Notably, this study confirmed the pleiotropic region influencing SI and BW on chromosome D11 and identified a novel co-localized group on D12 associated with LP and LI. Haplotype analysis further revealed superior allele combinations associated with LP, showing a high trait value (LP: 39.77%). The genomic insights and favorable haplotypes identified in this study provide valuable resources for harnessing genetic diversity to achieve targeted genetic improvement and facilitate the gene discovery of yield traits in cotton.