Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, 99164, USA.
BMC Genomics. 2024 Jul 16;25(1):695. doi: 10.1186/s12864-024-10587-6.
Effective population size (N) 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 can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of N 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 estimates based on linkage disequilibrium (LD) in the pea genome.
We calculated and compared N 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 r of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated N for the USDA was nearly three-fold higher (N = 174) than NDSU (N = 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 in successive cycles of breeding to sustain viability of the breeding efforts in the long term.
有效种群大小 (N) 是种群遗传学中的一个关键参数，因为它可以提供关于近交率和育种群遗传多样性的当代状况的信息。N 较小的种群会导致更快的近交，遗传增益的潜力很小，使选择无效。N 的重要性在植物育种中越来越受到重视，这可以帮助育种者监测和增强遗传变异性，或重新设计他们的选择方案。在这里，我们根据豌豆基因组中的连锁不平衡 (LD) 首次估算了 N。
我们使用来自北达科他州立大学 (NDSU) 现代育种系和美国农业部 (USDA) 多样性面板的 SNP 标记计算并比较了 N。LD 的程度不仅在种群之间，而且在基因组的不同区域和染色体之间都高度可变。总体而言，NDSU 的 LD 比 USDA 的 LD 更高且范围更长，可达 500 Kb，全基因组平均 r 值为 0.57（vs 0.34），这可能是由于其较低的重组率和选择背景。USDA 的估计 N 几乎是 NDSU 的三倍（N=174），NDSU 的估计 N 为 64），这可能是由于豌豆的自交性质导致种群结构高度复杂所致。
我们的结果提供了对所研究种质遗传多样性的深入了解，这可以指导植物育种者在连续的育种循环中积极监测 N，以长期维持育种工作的活力。
