Effective population size in field pea

Effective population size (N_e) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller N_e can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of N_e has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first N_e estimates based on linkage disequilibrium (LD) in the pea genome.

We calculated and compared N_e 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 genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r² of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated N_e for the USDA was nearly three-fold higher (N_e = 174) than NDSU (N_e = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea.

Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor N_e in successive cycles of breeding to sustain viability of the breeding efforts in the long term.