The Changes in Genetic Parameters and Genomic Selection of Lambing Rate in Hu Sheep Following Marker-Assisted Selection

Abstract

The identification of quantitative trait locus (QTL) or genes responsible for key agronomic traits has significantly enhanced genetic improvement through marker-assisted selection (MAS). However, the impacts of MAS on genetic parameters and subsequent selection processes have not been thoroughly characterised. Here, through genome-wide selective sweep analysis, we identified a diverse set of genes involved in oocyte meiosis, including PPP3CA, AR, PPP1CB, SPDYA, MAD1L1, and BMPR1B. The genome-wide association study (GWAS) further identified three genes UNC5C, BMPR1B, and PDLIM5 as being associated with lambing rate in Hu sheep. From these analyses, the FecB loci emerged as a potential molecular marker for lambing rate. with an increase of 0.5 lambs per G allele. The heritability of the lambing rate was estimated to be 0.19 (±0.02). Moreover, based on 10-fold cross-validation, the accuracy of genomic selection (GS) was found to be 0.30. Simulated MAS resulted in a reduction of the additive genetic variance components, with estimated heritability dropping to 0.14 (±0.02) and GS accuracy decreasing to 0.18—representing a decline of 26.42% and 34.81%, respectively. To address the reduced GS accuracy, we performed GWAS on the reference set to identify weighted single nucleotide polymorphisms (SNPs). This method has the potential to increase accuracy by 13.8%. Our study found that MAS has a negative impact on GS. To address this issue, we integrated prior information on SNPs from GWAS, which exhibit pleiotropic genetic architecture. This integration enables us to utilise genetic markers for complex traits more effectively, thereby improving the accuracy and efficiency of GS.