Abstract
Key message
Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Abstract
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.
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Data availability
The datasets employed in this study will be deposited in the CottonGen database.
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Acknowledgements
The authors acknowledge and appreciate the funding support provided by Cotton Incorporated (CI) and North Carolina Cotton Producers’ Association for the current research. We thank Kelli Kochan of Texas A&M University for her help with genotyping the cotton accessions using the CottonSNP63K array. We thank Josh Udall, James Frelichowski and Janna Love of the Crop Germplasm Research, USDA-ARS, College Station, Texas for providing the Upland cotton accessions used in this study.
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Cotton Incorporated (core projects 18–231 and 19–969) and NC Cotton Producers Association (project 17-588NC) provided funding support for this research.
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SAG: Data curation, Formal analysis, Software, Methodology, Validation, Visualization, Writing—original draft; FB: Resources, and Writing—review and editing; BK- Investigation, Resources; DJ- Resources; Funding acquisition, and Writing—review and editing; VK: Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, and Writing—original draft, review and editing.
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Gowda, S.A., Bourland, F.M., Kaur, B. et al. Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.). Theor Appl Genet 136, 230 (2023). https://doi.org/10.1007/s00122-023-04477-w
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DOI: https://doi.org/10.1007/s00122-023-04477-w