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%.

This study aims to compare the accuracy of genomic estimated breeding values (GEBV) estimated using a genomic best linear unbiased prediction (GBLUP) method and GEBV estimates incorporating prior marker information from a genome-wide association study (GWAS) for the weaning weight trait in highland Merino sheep. The objective is to provide theoretical and technical support for improving the accuracy of genomic selection. The study used a population of 1007 highland Merino ewes, with the weaning weight at 3 months as the target trait. The population was randomly divided into two groups. The first group was used for GWAS analysis to identify significant markers, and the top 5%, top 10%, top 15%, and top 20% markers were selected as prior marker information. The second group was used to estimate genetic parameters and compare the accuracy of GEBV predictions using different prior marker information. The accuracy was obtained using a five-fold cross-validation. Finally, both groups were subjected to cross-validation. The study’s findings revealed that the heritability of the weaning weight trait, as calculated using the GBLUP model, ranged from 0.122 to 0.394, with corresponding prediction accuracies falling between 0.075 and 0.228. By incorporating prior marker information from GWAS, the heritability was enhanced to a range of 0.125 to 0.407. The inclusion of the top 5% to top 20% significant SNPs from GWAS results as prior information into GS showed potential for improving the accuracy of predicting genomic breeding value.

Objective: Although Hu sheep are renowned for their high fecundity, the multi-tissue regulatory networks governing spermatogenesis, particularly within the hypothalamic–pituitary–testicular (HPT) axis, remain poorly understood. This study aimed to elucidate these mechanisms by performing a comparative proteomic analysis of the HPT axis in Hu sheep and three other breeds. Methods: We utilized data-independent acquisition (DIA) proteomics to analyze hypothalamic, pituitary, and testis tissues from 36 samples across four breeds. The experimental workflow included protein extraction, enzymatic digestion, LC-MS/MS, and subsequent bioinformatic analyses, complemented by histological examination. Results: Hu sheep exhibited accelerated testicular development and an earlier onset of spermatogenesis. Comprehensive proteomic profiling identified a total of 10,528 proteins, with 771 differentially expressed proteins (DEPs) detected in the testis. These testicular DEPs were significantly enriched in pathways related to spermatogenesis, the blood–testis barrier, and steroid hormone biosynthesis. Notably, the cAMP signaling pathway was consistently enriched across all three tissues, underscoring its pivotal role in regulating spermatogenesis. Protein–protein interaction (PPI) network analysis further highlighted hub proteins, such as MET, suggesting their potential involvement in somatic cell functions and the spermatogenic microenvironment. Key findings were validated by Western blot analysis. Conclusion: This study is the first multi-tissue proteomic investigation proposing a model in which the high reproductive performance of Hu sheep is potentially linked to the efficient, coordinated regulation of spermatogenesis-related proteins and signaling pathways—particularly in the testis. These findings offer novel insights into the molecular mechanisms of male reproduction in sheep and identify potential targets for future research and breeding applications.