Population structure and genetic diversity of the Pee Dee cotton breeding program
Open Access
- 29 April 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 11 (7)
- https://doi.org/10.1093/g3journal/jkab145
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 (IBS) 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 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.Keywords
Funding Information
- Clemson University Experiment Station
- NIFA (SC-1700561)
- U.S. Department of Agriculture
- U.S. Department of Agriculture
This publication has 50 references indexed in Scilit:
- Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvementNature Genetics, 2020
- A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cottonTheoretical and Applied Genetics, 2019
- Evaluation of a Chromosome Segment from Gossypium barbadense Harboring the Fiber Length QTL qFL‐Chr.25 in Four Diverse Upland Cotton Genetic BackgroundsCrop Science, 2019
- Second-generation PLINK: rising to the challenge of larger and richer datasetsGigaScience, 2015
- Genetic Improvement of the Pee Dee Cotton Germplasm Collection following Seventy Years of Plant BreedingCrop Science, 2011
- Using Environmental Correlations to Identify Loci Underlying Local AdaptationGenetics, 2010
- Ascertainment Biases in SNP Chips Affect Measures of Population DivergenceMolecular Biology and Evolution, 2010
- Using molecular markers and field performance data to characterize the Pee Dee cotton germplasm resourcesEuphytica, 2009
- PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCRNucleic Acids Research, 1996
- The Origin of American Tetraploid Gossypium SpeciesThe American Naturalist, 1940