In this study, genome-wide association analysis was performed on the growth traits (body height, body length, chest circumference, chest depth, chest width, tube circumference, and body weight) of Inner Mongolian cashmere goats (Erlangshan type) based on resequencing data. The population genetic parameters were estimated, haplotypes were constructed for the significant sites, and association analysis was conducted between the haplotypes and phenotypes. A total of two hundred and eighty-four SNPs and eight candidate genes were identified by genome-wide association analysis, gene annotation, and enrichment analysis. The phenotypes of 16 haplotype combinations were significantly different by haplotype analysis. Combined with the above results, the TGFB2, BAG3, ZEB2, KCNJ12, MIF, MAP2K3, HACD3, and MEGF11 functional candidate genes and the haplotype combinations A2A2, C2C2, E2E2, F2F2, I2I2, J2J2, K2K2, N2N2, O2O2, P2P2, R1R1, T1T1, W1W1, X1X1, Y1Y1, and Z1Z1 affected the growth traits of the cashmere goats and could be used as molecular markers to improve the accuracy of early selection and the economic benefits of breeding.

The Inner Mongolia cashmere goat is a local breed valued for both its cashmere and meat production. Early growth traits include birth weight and weaning weight. Generally, cashmere goats with higher birth and weaning weights tend to exhibit a higher carcass weight at slaughter. Consequently, exploring the genetic variation associated with these early growth traits is crucial in enhancing the meat production performance of Inner Mongolia cashmere goats. For this study, we performed genome-wide association analysis and haplotype analysis on the early growth traits of 212 Inner Mongolia cashmere goats (72 rams, 140 ewes) to identify molecular markers and haplotypes significantly associated with birth and weaning weights. Through genome-wide association analysis and gene annotation, we identified 21 SNPs and 117 candidate genes linked to early growth traits. Notably, genes such as RUNX1T1, ERBIN, MYO15B, NT5C, GRB2, ITGB4, and GALK emerged as significant factors influencing the early growth of Inner Mongolia cashmere goats. Additionally, nine haplotype blocks related to early growth traits were constructed, resulting in eight haplotype combinations. In conclusion, the haplotype combinations A1A1, C1C1, and D1D1 were found to be beneficial for the genetic improvement of early growth traits in Inner Mongolia cashmere goats.

Sheep and goats, among the earliest domesticated animals, hold significant historical importance in Chinese animal husbandry. The rapid advancement of modern biotechnology has rendered genome wide association studies (GWAS) and selection signature analyses have become indispensable tools in livestock genetic research. This review summarizes recent progress in the application of these methods to sheep and goat breeding in China, analyzes existing challenges in the research, and suggests potential research strategies. GWAS and selection signature analyses have identified key genomic regions associated with agronomically important traits. Genes such as LHX2, FGF12 and Notch3 are associated with hair follicle growth and development, while RBM11, SMARCA5 and GAB1 are linked to body size in sheep. Additionally, BMPRIB has been identified as a determinant of reproductive performance and growth rate in both sheep and goats. Despite progress, several challenges remain, including incomplete reference genomes, insufficient phenotypic data, inadequate algorithms, and a lack of functional validation and practical application of findings. Future work must prioritize genomic refinement, the integration of multi-omics, and the development of algorithm. Enhanced international collaboration is crucial to deciphering the genetic basis of key traits, thereby advancing global industry. These initiatives will enable highly precise breeding strategies. Through precise identification and selection of individuals with desirable genetic traits, breeders can significantly enhance the efficiency of genetic improvement. Using Hua sheep 50k chip as an example, it effectively identifies individuals with superior reproductive genes (such as BMPRIB) at an early stage, increases the lambing rate by 27.7%, accelerates the propagation of high-quality breeding groups, provides a large number of breeding sheep with excellent genetic traits for the global sheep industry, and improve the overall quality of germplasm. This will ultimately enhance the sustainable development of global sheep and goat production.

Objective: Inner Mongolia cashmere goats are superior indigenous breeds developed through long-term natural selection and systematic artificial selection, which have experienced a certain intensity of selection pressure during the breeding process, leading to bipolar differentiation trends in cashmere traits. Therefore, identifying genomic selection signatures associated with cashmere traits in Inner Mongolia cashmere goats is crucial for breeding high-quality cashmere-producing goats.Methods: To unravel the genetic basis of cashmere traits, this study stratified 375 Inner Mongolia cashmere goats into eight subgroups based on breeding values for cashmere traits: high-yield vs low-yield cashmere types (HYCG vs LYCG), fine vs coarse cashmere types (FCG vs CCG), long vs short cashmere types (LCG vs SCG), and long vs short fleece types (LFCG vs SFCG). Whole-genome resequencing was performed for genotyping, followed by detection of selection signatures.Results: Results revealed 144, 158, 147, and 147 high-frequency run of homozygosity (ROH) regions in HYCG, FCG, LCG, and LFCG subgroups, respectively, annotating to 515, 565, 510, and 521 genes. Additionally, genomic regions under positive selection were identified using Fst, θπ ratios, and XP-EHH methods, with overlapping regions detected by ≥2 methods defined as candidate regions. Gene annotation identified 777, 660, 712, and 726 candidate genes in HYCG vs LYCG, FCG vs CCG, LCG vs SCG, and LFCG vs SFCG comparisons, respectively. These genes were enriched in 3,051 GO terms and 318 KEGG pathways, including Hippo, MAPK, Wnt, PI3K-Akt, and mTOR signaling pathways associated with cashmere growth and development, involving genes such as LGR6, RUNX2, IGF1R, FGF9, and TCF7L1.Conclusion: In this study, we employed four complementary approaches, including ROHs, Fst, θπ ratios, and XP-EHH, to identify genomic signatures of selection for cashmere traits in Inner Mongolia cashmere goats. These findings provide valuable insights for improving cashmere production performance and developing novel strains with highquality cashmere in Inner Mongolia cashmere goats.