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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 #382288
Research Project: Effective Cotton Genetics and Management Practices for Improved Cotton Quality and Production

Location: Coastal Plain Soil, Water and Plant Conservation Research

Title: Population structure and genetic diversity of the Pee Dee cotton breeding program

Author
item BILLINGS, GRANT - North Carolina State University
item JONES, MICHAEL - Clemson University
item RUSTGI, SACHIN - Clemson University
item Hulse-Kemp, Amanda
item Campbell, Benjamin - Todd

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2021
Publication Date: 4/29/2021
Citation: Billings, G., Jones, M., Rustgi, S., Hulse-Kemp, A.M., Campbell, B.T. 2021. Population structure and genetic diversity of the Pee Dee cotton breeding program. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkab145.
DOI: https://doi.org/10.1093/g3journal/jkab145

Interpretive Summary: Since 1935, the Pee Dee cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. In this study, we conducted a detailed genetic survey of the program’s eight historical breeding cycles to evaluate genetic diversity across and within breeding groups relative to the global upland cotton gene pool. Overall, the pairwise genetic diversity varied, ranging from 0.55 to 0.97, while 99% of the program’s genetic diversity was introduced within the first four breeding cycles. In addition, we identified a small core collection (n <20) of germplasm resources representing 99% of the program’s genetic diversity. The results of this study will steer future utilization of the program’s germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.

Technical Abstract: Accelerated marker-assisted selection and genomic selection breeding systems require genotyping data to select the best parents for combining beneficial traits. Since 1935, the Pee Dee cotton germplasm enhancement program has developed an important genetic resource for upland cotton (Gossypium hirsutum L.), contributing alleles for improved fiber quality, agronomic performance, and genetic diversity. To date, a detailed genetic survey of the program’s eight historical breeding cycles has yet to be undertaken. The objectives of this study were to evaluate genetic diversity across and within breeding groups, examine population structure, and contextualize these findings relative to the global upland cotton gene pool. The CottonSNP63K array was used to identify 17,441 polymorphic markers in a panel of 114 diverse Pee Dee genotypes. A subset of 4,597 markers was selected to decrease marker density bias. Identity by state pairwise distance varied substantially, ranging from 0.55 to 0.97. Pedigree-based estimates of relatedness were not very predictive of observed genetic similarities. Few rare alleles were present, with 99.1% of single nucleotide polymorphism (SNP) alleles appearing within the first four breeding cycles. Population structure analysis with principal component analysis, discriminant analysis of principal components, fastSTRUCTURE, and a phylogenetic approach revealed an admixed population with moderate substructure. A small core collection (n <20) captured 99% of the program’s allelic diversity. Allele frequency analysis indicated potential selection signatures associated with stress resistance and fiber cell growth. The results of this study will steer future utilization of the program’s germplasm resources and aid in combining program-specific beneficial alleles and maintaining genetic diversity.