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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #410177
Research Project: Genetic Resource and Information Management for Pulse, Temperate Forage Legume, Oilseed, Vegetable, Grasses, Sugar, Ornamental, and Other Crops

Location: Plant Germplasm Introduction and Testing Research

Title: Effective population size estimation in field pea (Pisum Sativum L.)

Author
item JOHNSON, JOSEPHINE - North Dakota State University
item PICHE, LISA - North Dakota State University
item WORRAL, HANNAH - North Dakota State University
item ATANDA, SIKIRU - North Dakota State University
item Coyne, Clarice - Clare
item McGee, Rebecca
item MCPHEE, KEVIN - Montana State University
item BANDILLO, NONOY - North Dakota State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2024
Publication Date: 7/16/2024
Citation: Johnson, J., Piche, L., Worral, H., Atanda, S., Coyne, C.J., McGee, R.J., McPhee, K., Bandillo, N. 2024. Effective population size estimation in field pea (Pisum Sativum L.). BMC Genomics. 25:695. https://doi.org/10.1186/s12864-024-10587-6.
DOI: https://doi.org/10.1186/s12864-024-10587-6

Interpretive Summary: Crop improvement through genetics and breeding deliver superior cultivars to USA farmers and producers. An important tool in delivering these new cultivars is understanding the population genetics of the specific crop under improvement for important traits like increased yields, improved seed or fruit quality and tolerances to diseases and pests. In this study, the effective population size meaning the number of pea lines to use for breeding was determined. This information can now be used by existing and new pea breeding programs for the expanding plant-based protein market for new product development.

Technical Abstract: Effective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making long-term selection ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders to monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first effective population size estimates based on linkage disequilibrium (LD) in the pea genome. We calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the pea genome. Overall, NDSU had a higher and longer-range LD than USDA that could extend up to 500Kb, with genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea. Our results provided insights into genetic diversity of the germplasm studied, which can guide pulse crop breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.