Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

The Inner Mongolia cashmere goat is an excellent local breed in China. According to the characteristics of wool quilts, the Inner Mongolia cashmere goat can be divided into three types: a long-hair type (hair length of >22 cm), a short-hair type (hair length of ≤13 cm), and an intermediate type (hair length of >13 cm and ≤22 cm). It is found that hair length has a certain reference value for the indirect selection of other important economic traits of cashmere. In order to explore the molecular mechanisms and related regulatory genes of the different hair types, a weighted gene coexpression network analysis (WGCNA) was carried out on the gene expression data and phenotypic data of 12-month-old Inner Mongolia cashmere goats with a long-hair type (LHG) and a short-hair type (SHG) to explore the coexpression modules related to different coat types and nine candidate genes, and detect the relative expression of key candidate genes. The results showed that the WGCNA divided these genes into 19 coexpression modules and found that there was a strong correlation between one module and different hair types. The expression trends of this module’s genes were different in the two hair types, with high expression in the LHG and low expression in the SHG. GO functions are mainly concentrated in cellular components, including intermediate filaments (GO:0005882), intermediate filament cytoskeletons (GO:0045111), and cytoskeletal parts (GO:0044430). The KEGG pathway is mainly enriched in arginine as well as proline metabolism (chx00330) and the MAPK signaling pathway (chx04010). The candidate genes of the different hair types, including the KRT39, KRT74, LOC100861184, LOC102177231, LOC102178767, LOC102179881, LOC106503203, LOC108638293, and LOC108638298 genes, were screened. Through qRT-PCR, it was found that there were significant differences in these candidate genes between the two hair types, and most of them had a significant positive correlation with hair length. It was preliminarily inferred that these candidate genes could regulate the different hair types of cashmere goats and provide molecular markers for hair growth.

Background: The cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct haplotypes that significantly affect cashmere traits. Results: We estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109–1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed. Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield, haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness, haplotypes H2H2 was associated with increased cashmere thickness, haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05). Conclusions: In conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat.

Identifying markers or genes crucial for growth traits in Zhongwei goats is pivotal for breeding. Pinpointing genetic factors linked to body size gain enhances breeding efficiency and economic value. In this study, we used the MGISEQ-T7 platform to re-sequence 240 Zhongwei goats (133 male; 107 female) belonging to 5 metrics of growth traits at different growth stages (40 days and 6 months, here in after referred to as 40d and 6 m), namely, Body Weight (BW), Body Height (BH), Body Length (BL), Chest Circumference (CC), Tube Circumference (TC) were examined. A Genome-wide association study (GWAS) was conducted to identify candidate genes associated with the five indicators of body conformation traits, thereby establishing a foundation for subsequent investigations into the biological functions of these genes. A total of 19.89 Tb of raw data was generated with an average sequencing depth of about 20×. After quality control, 15,958,716 SNPs were available for the analysis. A total of 342 genome-wide significant SNPs were obtained. Among them, in the two physiological stages of 40d and 6 m, 147 and 32 SNPs were significantly associated with BW; 1 and 4 SNPs were significantly associated with BH; 19 and 6 SNPs were significantly associated with BL; 33 and 64 SNPs were significantly associated with CC, 34 and 2 SNPs were significantly associated with TC. These SNPs were annotated to 425 candidate genes. Finally, A total of 39 candidate genes are closely related to biological processes such as skeletal muscle development, skeletal formation, carcass quality, and embryonic development, where ADIPOQ, CCDD39, PTPRT, ZNF215, VRTN, ABCD4, DLST, ADAMTS2, ROBO1, AKAP13, AQPI, SOX2, and AHSG were identified as an important component of the genetic framework that may control somatic conformational traits in Zhongwei goats. which warrants further investigation and review. We verified the polymorphism of 11 SNPs by KASP, and found that Chr13_g.11,700,438 A > G, Chr15_g.37,120,328 A > G, Chr6_g.7,209,383 C > T, Chr20_g.51277932T > A, Chr19_g.17,078,199 A > G, and Chr1_g.79,943,276 C > T were significantly genotyped in verified populations (P < 0.001). It is the first GWAS study to analyze genomic data from 40d and 6 m of Zhongwei goats to understand the molecular genetic mechanisms of growth. Our research identified a series of SNPs and candidate genes associated with growth traits, which could assist us in developing the meat production trait in Zhongwei goats.

Background: The cashmere goat is a biological resource that mainly produces cashmere. Cashmere has a soft hand feel and good luster, with high economic value. The quality and yield of cashmere are determined by the process of hair follicle development during the embryonic period. Methods: In this study, the skin of the Inner Mongolia cashmere goat at different embryonic stages (45, 55, 65, and 75d) was collected, and the differentially expressed lncRNA MSTRG.20890.1 at 75d was obtained by screening. Dual luciferase reporter gene system, qRT-PCR, and EDU experiments were used to verify further the regulatory role and molecular mechanism of the lncRNA in dermal fibroblasts. Results: Based on the transcriptome database of Inner Mongolia cashmere goat skin at different embryonic stages, which was previously constructed by our group, according to the characteristics of hair follicle development in the embryonic stage, we screened out the lncRNA MSTRG.20890.1 that was down-expressed on the 75-SHFINI day of the embryonic stage. We found that lncRNA MSTRG.20890.1 was mainly located in the cytoplasm of cells, and it could inhibit the proliferation and directional migration of dermal fibroblasts through the chi-miR-24-3p/ADAMTS3 signaling axis, thereby inhibiting the formation of dermal papilla structure at embryonic stage. Conclusions: This study revealed that lncRNA MSTRG.20890.1 regulated secondary hair follicle morphogenesis and development in cashmere goats through the chi-miR-24-3p/ADAMTS3 signaling axis.