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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience and Utilization Research » Research » Publications at this Location » Publication #417744

Research Project: Genomic Dissection and Molecular Characterization of Fiber Quality Traits for Cotton Variety Improvement

Location: Cotton Fiber Bioscience and Utilization Research

Title: A GWAS Identified Loci and Candidate Genes Associated with Fiber Quality Traits in a New Cotton MAGIC Population

Author
item MOHAMMED, JAMAL - Oak Ridge Institute For Science And Education (ORISE)
item Thyssen, Gregory
item Hinze, Lori
item ZHANG, JINFA - New Mexico State University
item Zeng, Linghe
item Fang, David

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/9/2024
Publication Date: 12/23/2025
Citation: Mohammed, J., Thyssen, G.N., Hinze, L., Zhang, J., Zeng, L., Fang, D.D. 2025. A GWAS Identified Loci and Candidate Genes Associated with Fiber Quality Traits in a New Cotton MAGIC Population. Theoretical and Applied Genetics. 138. Article 10. https://doi.org/10.1007/s00122-024-04800-z.
DOI: https://doi.org/10.1007/s00122-024-04800-z

Interpretive Summary: In this research, we analyzed a new multiparent population consisting of 372 progeny plant in order to identify genetic loci controlling cotton fiber quality traits. The population derived from inter-crosses among 16 parental lines including 12 exotic germplasm lines and 4 Upland cotton cultivars. Both progeny and parental lines were evaluated at three locations between 2016 and 2023. Fiber quality from all progeny lines were measured using a High Volume Instrument. We sequenced the genomic DNAs of all progeny and parental lines. We identified significant DNA markers for elongation, length and uniformity index while strength and micronaire (maturity and fineness) were location dependent. These results suggest an important role of genotype by environment interaction in a genome wide association study of fiber traits. Twenty possible novel fiber QTLs were identified. The QTLs for elongation (Chr.D04: 53-Mb), length (Chr.D11: 24-Mb), and uniformity index (Chr.D04: 34-Mb) were stable across multiple environments and may be useful for marker assisted selection to improve fiber quality. For strength, we found candidate genes Gh_A07G1574 and Gh_A07G1581 to be present in the previously identified QTL region (Chr.A07: 77-Mb) on chromosome A07. Identified loci and their corresponding candidate genes will be useful to improve fiber quality via marker-assisted selection in a cotton breeding.

Technical Abstract: Identification of loci and underlying genes for fiber quality traits will facilitate genetic improvement of cotton fiber quality. In this research, a genome-wide association study (GWAS) was carried out for fiber quality attributes using a new multiparent advanced generation inter-cross (MAGIC) population consisting of 372 recombinant inbred lines (RILs). Sixteen parents including 12 exotic germplasm lines derived from five tetraploid Gossypium species and 4 Upland cotton cultivars were intercrossed to develop the population. Both RILs and parental lines were evaluated at three locations, College Station, TX, Las Cruses, NM and Stoneville, MS from 2016 through 2023. Fiber length (UHM) had positive correlation with strength (STR) and uniformity (UNI) and a negative correlation with micronaire (MIC) and elongation (ELO). By combining all the data from all locations, we identified significant SNPs for ELO, UHM and UNI while STR and MIC were location dependent. These results suggest an important role of genotype by environment interaction in a GWAS of fiber traits. Twenty possible novel fiber QTLs were identified: 10 for STR, three for UNI and seven for MIC. The QTLs for ELO (Chr.D04: 53-Mb), UHM (Chr.D11: 24-Mb), and UNI (Chr.D04: 34-Mb) were stable across multiple environments and may be useful for marker assisted selection to improve fiber quality. For STR, we found candidate genes Gh_A07G1574 and Gh_A07G1581 to be present in the previously identified QTL region (Chr.A07: 77-Mb) on chromosome A07. Identified loci and their corresponding candidate genes will be useful to improve fiber quality via marker-assisted selection in a cotton breeding.