Shudong Liu

Growth and body conformation traits are key determinants of meat production efficiency and economic performance in sheep. However, the genetic architecture underlying these complex traits remains incompletely understood, particularly across multi-breed populations. In this study, we performed a genome-wide association study (GWAS) for seven growth and developmental traits in a combined population of 401 sheep, including Qira Black, Kyrgyz, Dorset × Hu crossbred, and Suffolk × Karakul crossbred sheep. After genotype harmonization and quality control, 47,674 autosomal SNPs were retained for analysis. Population structure was assessed using principal component analysis, and association testing was conducted using a mixed linear model incorporating breed, principal components, and a kinship matrix. A total of 44 independent loci were detected at a nominal significance threshold, encompassing 112 candidate genes. The strongest association was identified for cannon bone circumference near RPS6KA5 (Chr7; p = 1.40 × 10⁻⁷). Several biologically relevant genes involved in osteogenesis, cartilage development, and metabolic regulation were detected, including STEAP3, SLC26A2, PPARGC1B, COL11A1, CALN1, and CITED2. Two genomic regions exhibited pleiotropic effects, which were identified as being associated with multiple traits, suggesting shared genetic regulation of correlated skeletal characteristics. These findings are consistent with a polygenic architecture underlying growth trait in sheep and highlight candidate genomic regions potentially involved in skeletal development and body conformation. Although further validation is required, the identified loci provide preliminary evidence for regions that may influence growth-related phenotypes and offer a reference for future molecular breeding efforts in indigenous and crossbred sheep populations.

Myostatin (MSTN) is a key negative regulator of skeletal muscle development, and its deficiency can markedly enhance muscle growth. However, the application of CRISPR/Cas12Mix in large livestock remains limited. In this study, 11 Xinjiang Brown calves were generated via embryo-stage CRISPR/Cas12Mix editing, among which five were confirmed as MSTN-knockout. These five edited calves were compared with five unedited controls to evaluate early growth traits and serum untargeted metabolomics at one month of age. MSTN-knockout calves exhibited significantly higher body weight, hip width, chest girth, and abdominal girth than controls (p < 0.05). Untargeted metabolomics identified 225 and 129 differential metabolites in positive and negative ion modes, mainly enriched in lipid, organic acid, and amino acid metabolism. KEGG pathway analysis revealed significant alterations in arginine and proline, tryptophan, and carbohydrate metabolism. These results demonstrate that CRISPR/Cas12Mix efficiently mediates MSTN knockout in cattle, conferring early growth advantages, accompanied by systemic metabolic reprogramming.

This experiment aimed to investigate the effects of replacing alfalfa hay with Glycyrrhiza stem and leaf silage (moisture content: 45%) on rumen in vitro fermentation parameters, nutrient digestibility, and dynamic changes of microbial community composition. In vitro fermentation was conducted with 0% (control group G0A100), 50% (G50A50), and 100% (G100A0) alfalfa hay replaced by semi-dry silage of Glycyrrhiza stems and leaves with 45% moisture content for 72 h. Cumulative gas production (GP), fermentation parameters, microbial community composition at different time points, and post-fermentation nutrient digestibility were determined, with comprehensive evaluation by principal component analysis (PCA) and gray relational analysis (GRA). Results showed that GP of G50A50 and G100A0 was significantly higher than G0A100 at 3 h (p < 0.05), and that of G50A50 was significantly higher than the other two groups at 24 h (p < 0.05). pH of G50A50 was significantly lower than the other two groups at 3 h (p < 0.05). In vitro dry matter digestibility (IVDMD) at 24 h and 72 h, in vitro neutral detergent fiber digestibility (IVNDFD) at 12 h, and in vitro acid detergent fiber digestibility (IVADFD) at 12, 24 and 72 h of G0A100 and G50A50 were significantly higher than G100A0 (p < 0.05). PCA comprehensive scores ranked as G0A100 (0.170) > G50A50 (0.141) > G100A0 (−0.311). GRA comprehensive scores ranked as G50A50 (0.792) > G0A100 (0.756) > G100A0 (0.681). LEfSe analysis indicated distinct microbial biomarkers at 72 h, and KEGG functional profiles were highly consistent among groups. Under the experimental conditions, 50% Glycyrrhiza stem and leaf silage is recommended to replace alfalfa hay in dairy cow diets.

Hornless trait in sheep is one of the important traits affecting their economic production efficiency. In order to screen the molecular markers related to hornless trait in Qira black sheep, we used Illumina Ovine 50 K SNP chip data of 189 Qira black sheep, which were divided into two groups based on their horned and hornless traits. GWAS analysis of individuals of interest. Used the horned trait group as the reference group, and performed xp-EHH analysis with the hornless group. The hornless group was subjected to iHS and Pi analyses. After annotating the relevant candidate regions based on the sheep 4.0 genome microarray data. 681 candidate genes were obtained from the xp-EHH analysis, 87 candidate genes from the iHS analysis, and 2,171 candidate genes from the Pi analysis. A total of 19 candidate genes were obtained from further analysis of the candidate regions. Candidate genes were analyzed by GO and KEGG, and RXFP2, TNS3, EYA2 and OCSTAMP genes were found to be associated with horned traits in Qira black sheep. Further PCR validation of RXFP2 revealed that loci 10: 29,501,280 (P = 0.002), 10: 29,501,431 (P = 0.003) and 10: 29,051,333 (P = 0.0001) were significantly associated with hornless trait in Qira black sheep.

Runs of Homozygosity (ROH) are homozygous genomic fragments inherited from parents to offspring. ROH can be used to indicate the level of inbreeding, as well as to identify possible signatures of artificial or natural selection. Indigenous sheep populations on the southern edge of the Taklimakan Desert have evolved unique genetic traits adapted to extreme desert environments. In an attempt to better understand the adaptive mechanisms of these populations under harsh conditions, we used Illumina® Ovine SNP50K BeadChip to perform a genomic characterization of three recognized breeds (Duolang: n = 36, Hetian: n = 84, Qira black: n = 189) and one ecotypic breed (Kunlun: n = 27) in the region. Additionally, we assessed genomic inbreeding coefficients through ROH analysis, revealing insights into the inbreeding history of these populations. Subsequently, we retrieved candidate genes associated with economic traits in sheep from ROH islands in each breed. To better understand the autozygosity and distribution of ROH islands in these indigenous sheep breeds relative to international breeds, we also included three commercial mutton breeds (Poll Dorset: n = 108, Suffolk: n = 163, Texel: n = 150). The study revealed that among seven sheep breeds, Hetian exhibited the shortest linkage disequilibrium (LD) decay distance, while Kunlun demonstrated the highest LD levels. A total of 10,916 ROHs were obtained. The number of ROHs per breed ranged from 34 (Kunlun) to 2,826 (Texel). The length of ROH was mainly 1–5 Mb (63.54%). Furthermore, 991 candidate genes specific to indigenous sheep breeds were identified, including those associated with heat tolerance, adaptability, energy metabolism, reproduction, and immune response. These findings elucidate the genetic adaptation of indigenous sheep in the Taklimakan Desert, uncovering distinctive characteristics of indigenous sheep formation, and advocating for the conservation and genetic enhancement of local sheep populations.

Black wool can effectively prevent sheep from DNA damage as well as fungal infection, and can improve reproductive performance. In order to explore the candidate genes related to black wool formation in Qira sheep. We selected 123 adult healthy ewes with different coat colors in Qira sheep groups (black (B), brown (Y) and grey (G)) and extracted DNA from their venous blood to obtain Illumina Ovine SNP 50K chip data. Subsequently, our PCA, NJ-tree, and Admixture population structure analyses of the 3 wool color Qira sheep populations showed that the 3 middle wool color populations exhibited the same genetic traits. Fst, xp-EHH, iHS, and π were detected for selection signals, and the 5% SNPs loci positively selected from the analyses were annotated based on SheepOar_v4.0. The region of exon 1 of the TYRP1 gene was further screened, amplified and sequenced through the DNA of the Qira sheep and associated with goodness-of-fit using the chi-square test. The results showed that 71 SNPs associated with black wool traits, among which TYRP1, PARD3 and CDH2 genes were strongly associated with black wool production. Three mutations were detected in the exon 1 region of the TYRP1 gene that were significantly associated with coat color variation inQira sheep (2:81,183,168, 2:81,183,281 and 2:81,183,284). In this paper, Qira sheep could not differentiate the genetic structure of this population by wool color, and obtained 71 SNPs related to black wool. Detection of mutation sites on the TYRP1 gene affecting hair color change provides a basis for black sheep line selection as well as breed conservation.

The frigid and droughty climate of Xinjiang in China has given rise to unique indigenous sheep breeds with robust adaptability and resistance. To investigate the genetic mechanism of adaptability of Xinjiang sheep to the local extreme environment, we conducted population genetic structure analyses for three native Xinjiang sheep breeds: Altay sheep (ALT), Bashbay Sheep (BSBC), and Duolang sheep (DLC), as well as two foreign sheep breeds: Suffolk and Dorset, using the Ovine Infinium HD SNP BeadChip(680 K). Our findings revealed distinct genetic and evolutionary histories between Xinjiang and foreign sheep breeds. Principal Component Analysis (PCA) and phylogenetic tree effectively differentiate these five sheep breeds based on their geographical origins, and the domestication level of Xinjiang sheep is comparatively lower than that of foreign sheep breeds. Furthermore, by utilizing three selective signature methods, namely Fixation Index (Fst), Cross Population Extended Haplotype Homozygosity Test (XP-EHH), and Nucleotide Diversity (π), we have successfully identified 22 potential candidate genes. Among these genes, there are TBXT, PDGFD, and VEGFA, which are closely related to tail type and lipid metabolism; VIL1, SLC11A1, and ZBTB46, which are associated with immune function; and candidate genes such as BNC1, HDAC1, and BMP5, which impact sheep reproductive traits. This study establishes a foundation for conserving and utilizing local sheep germplasm resources in Xinjiang and provides molecular insights into the genetic mechanisms governing sheep adaptation to extreme cold and arid environments.