Single nucleotide polymorphism profile for quantitative trait nucleotide in populations with small effective size and its impact on mapping and genomic predictions.

ABSTRACT: Increasing SNP density by incorporating sequence information only marginally increases prediction accuracies of breeding values in livestock. To find out why, we used statistical models and simulations to investigate the shape of distribution of estimated SNP effects (a profile) around quantitative trait nucleotides (QTNs) in populations with a small effective population size (Ne). A QTN profile created by averaging SNP effects around each QTN was similar to the shape of expected pairwise linkage disequilibrium (PLD) based on Ne and genetic distance between SNP, with a distinct peak for the QTN. Populations with smaller Ne showed lower but wider QTN profiles. However, adding more genotyped individuals with phenotypes dragged the profile closer to the QTN. The QTN profile was higher and nar

SUBMITTER: Pocrnic I 

PROVIDER: S-EPMC11304960 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature