Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.)

Authors: GOWDA, S - North Carolina State University; FANG, H - North Carolina State University; TYAGI, P - North Carolina State University; BOURLAND, F - University Of Arkansas; DEVER, J - Texas A&M University; Campbell, Benjamin - Todd; ZHANG, J - New Mexico State University; ABDELRAHEEM, A - New Mexico State University; SOOD, S - North Carolina State University; JONES, D - Cotton, Inc; KURAPARTHY, V - North Carolina State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2024
Publication Date: 9/3/2024
Citation: Gowda, S.A., Fang, H., Tyagi, P., Bourland, F., Dever, J., Campbell, B.T., Zhang, J., Abdelraheem, A., Sood, S., Jones, D.C., Kuraparthy, V. 2024. Genome-wide association study of fiber quality traits in US upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 1374. Article 214. https://doi.org/10.1007/s00122-024-04717-7.
DOI: https://doi.org/10.1007/s00122-024-04717-7

Interpretive Summary: In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the U.S. Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. Genome-wide association analyses of these six traits identified 380 significant marker trait associations including 143 on 30 genomic regions. These 30 genomic regions included marker trait associations identified in at least three environments and 23 of them were novel associations. Phenotypic variation explained for the marker trait associations in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality associated genomic regions were mapped in the D subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (upper half mean length, fiber strength, and fiber uniformity), and identified novel co-localized regions on D04 (fiber uniformity, short fiber content), D05 (upper half mean length, fiber uniformity), and D06 (upper half mean length, fiber uniformity). Marker haplotype analysis identified superior combinations of fiber quality associated genomic regions with high trait values for upper half mean length, fiber strength, and fiber elongation. Genomic analyses of traits, haplotype combinations, and candidate gene information described in the current study could help leverage genomics, and genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.

Technical Abstract: In this study, an elite diversity panel of 348 upland cotton accessions was evaluated in 10 environments across the U.S. Cotton Belt and genotyped with the cottonSNP63K array, for a genome-wide association study of six fiber quality traits. All fiber quality traits, upper half mean length, fiber strength, fiber uniformity, fiber elongation, micronaire and short fiber content, showed high broad-sense heritability. All traits except fiber elongation showed high genomic heritability. Upper half mean length, fiber strength, and fiber uniformity were all positively correlated with each other and negatively correlated with fiber elongation, micronaire, and short fiber content. Genome-wide association analyses of these six traits identified 380 significant marker trait associations including 143 on 30 genomic regions. These 30 genomic regions included marker trait associations identified in at least three environments and 23 of them were novel associations. Phenotypic variation explained for the marker trait associations in these 30 genomic regions ranged from 6.68 to 11.42%. Most of the fiber quality associated genomic regions were mapped in the D subgenome. Further, this study confirmed the pleiotropic region on chromosome D11 (upper half mean length, fiber strength, and fiber uniformity), and identified novel co-localized regions on D04 (fiber uniformity, short fiber content), D05 (upper half mean length, fiber uniformity), and D06 (upper half mean length, fiber uniformity). Marker haplotype analysis identified superior combinations of fiber quality associated genomic regions with high trait values for upper half mean length, fiber strength, and fiber elongation. Genomic analyses of traits, haplotype combinations, and candidate gene information described in the current study could help leverage genomics, and genetic diversity for targeted genetic improvement and gene discovery for fiber quality traits in cotton.