Genomic Selection for Live Weight in the 14th Month in Alpine Merino Sheep Combining GWAS Information

Simple Summary The weight features of Alpine Merino Sheep, particularly their live weight in the 14th month (WT), are crucial in production and breeding, as they live at high altitudes and in highland areas where oxygen is scarce. Genome selection (GS) offers the advantages of minimizing breeding costs and generational intervals, and the main objective of genome selection breeding is the accuracy of GS. Genome-wide association studies (GWASs) were used in this study to extract the variation information related to the 14-month-old body weight trait of Alpine Merino Sheep, identify candidate genes associated with this trait, and employ GWAS results as prior information to conduct GS research on the trait to determine the most suitable GS breeding model for the target trait. Abstract Alpine Merino Sheep is a novel breed reared from Australian Merino Sheep as the father and Gansu Alpine Fine-Wool Sheep as the mother, living all year in cold and arid alpine areas with exceptional wool quality and meat performance. Body weight is an important economic trait of the Alpine Merino Sheep, but there is limited research on identifying the genes associated with live weight in the 14th month for improving the accuracy of the genomic prediction of this trait. Therefore, this study’s sample comprised 1310 Alpine Merino Sheep ewes, and the Fine Wool Sheep 50K Panel was used for genome-wide association study (GWAS) analysis to identify candidate genes. Moreover, the trial population (1310 ewes) in this study was randomly divided into two groups. One group was used as the population for GWAS analysis and screened for the most significant top 5%, top 10%, top 15%, and top 20% SNPs to obtain prior marker information. The other group was used to estimate the genetic parameters based on the weight assigned by heritability combined with different prior marker information. The aim of this study was to compare the accuracy of genomic breeding value estimation when combined with prior marker information from GWAS analysis with the optimal linear unbiased prediction method for genome selection (GBLUP) for the breeding value of target traits. Finally, the accuracy was evaluated using the five-fold cross-validation method. This research provides theoretical and technical support to improve the accuracy of sheep genome selection and better guide breeding. The results demonstrated that eight candidate genes were associated with GWAS analysis, and the gene function query and literature search results suggested that FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, and SYN3 were candidate genes affecting live weight in the 14th month (WT), which regulated the growth of muscle and bone in sheep. In genome selection analysis, the heritability of GBLUP to calculate the WT was 0.335–0.374, the accuracy after five-fold cross-verification was 0.154–0.190, and after assigning different weights to the top 5%, top 10%, top 15%, and top 20% of the GWAS results in accordance with previous information to construct the G matrix, the accuracy of the WT in the GBLUP model was improved by 2.59–7.79%.