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.

Background: Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. Results: In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals’ genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. Conclusions: The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs’ germplasm resources.

The leptin receptor (LEPR) gene is a member of the class I cytokine receptor family, which plays an important role in weight regulation, fat accumulation and neuroendocrine function in animals. This study aimed to explore the association of single nucleotide polymorphisms (SNPs) of the LEPR gene with growth and carcass traits in meat-type quail by PCR amplification and DNA direct sequencing. In this study, genomic DNA was extracted from blood samples of 36 female Savimalt (SV) quails and 49 female French Giant (FG) quails. Growth traits (measured at 3 or 5 wk) and carcass traits (measured at 5 wk) were used for LEPR gene association analysis. The results showed the existence of 9 SNPs (T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A, and G373A) of the LEPR gene in the 2 quail strains. The statistical analyses indicated that these SNPs of LEPR gene was significantly associated with shank circumference (SC), shank length (SL), breastbone length (BBL), heart rate (HR), and whole net carcass rate (WNCR) of FG (P < 0.05); chest width (CW), body length (BL), leg muscle rate (LMR), whole net carcass rate (WNCR), and heart rate (HR) of SV (P < 0.05). While haplotypes showed significant effect on SL, BBL, heart weight (HW), WNCR, and HR of FG (P < 0.05). Therefore, the LEPR gene may serve as a molecular genetic marker for improving growth and carcass traits in quails.

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.

This study aimed to estimate the genetic and non-genetic factors that affect the nine early growth traits of Dumeng sheep, as well as to estimate the variance components and genetic parameters associated with these traits. A dataset containing detailed information on 17,896 preweaning trait records of 4474 lambs was collected. In addition, 5015 postweaning trait records of 1003 lambs were documented. The effects of recipient dam age, sex, year, season, and herd on the early growth traits were assessed using the general linear model procedure of the statistical analysis system, revealing different levels of significance across different traits. To determine the most suitable model for estimating the genetic parameters, the likelihood ratio (LR) test was employed, fitting six animal models that either excluded or included maternal genetic and maternal permanent environmental effects within the average information restricted maximum likelihood (AIREML) framework using WOMBAT software (Version: 23/11/23). The model incorporating direct additive genetic effects, maternal genetic effects, and maternal permanent environment effects as random effects (model 6) provided the best fit for birth weight (BW) estimation. In contrast, the model combining direct additive genetic effects and maternal permanent environment effects as random effects (model 2) demonstrated a superior fit for estimating the genetic parameters of weaning weight (WW), average daily gain weight from birth to weaning (ADG1), and Kleiber ratio from birth to weaning (KR1). With regard to the genetic parameters of body weight at 6 months of age (6MW), average daily gain weight from weaning to 6 months (ADG2), average daily gain weight from birth to 6 months (ADG3), Kleiber ratio from weaning to 6 months (KR2), and Kleiber ratio from birth to 6 months (KR3), model 1, which incorporates only direct additive genetic effects, was identified as the optimal choice. With the optimal model, the heritability estimates ranged from 0.010 ± 0.033 for 6MW to 0.1837 ± 0.096 for KR3. The bivariate analysis method was employed to estimate the correlation between various traits using the most suitable model. The absolute values of genetic correlation coefficients among the traits spanned a range from 0.1460 to 0.9998, highlighting both weak and strong relationships among the studied traits. Specifically, the estimated genetic correlations between WW and ADG1, ADG3, KR1, and KR3 were 0.9859, 0.9953, 0.9911, and 0.9951, respectively, while the corresponding phenotypic correlations were 0.9752, 0.7836, 0.8262, and 0.5767. These findings identified that WW could serve as an effective selection criterion for enhancing early growth traits.

Insulin-like growth factor 1 receptor (IGF-1R) gene is the main effector of insulin-like growth factor (IGF), which plays an important role in growth, development and reproduction of the animal organism. This study aimed to investigate the association of IGF-1R gene single nucleotide polymorphisms (SNPs) with egg quality and carcass traits of quail by direct sequencing. In this study, genomic DNA was extracted from quail blood samples of 46 Chinese yellow (CY) quail, 49 Beijing white (BW) quail and 48 Korean (KO) quail strains. Egg quality and carcass traits were measured and used for IGF-1R gene analysis in 3 quail strains. The results showed that 2 SNPs (A57G and A72T) of the IGF-1R gene were detected in 3 quail strains. The A57G was significantly associated with yolk width (YWI) in BW strain (P < 0.05). Whereas A72T was significantly associated with egg shell thickness (EST) in BW strain (P < 0.05), and significantly associated with egg weight (EW), egg long (EL), and egg short (ES) in KO strain (P < 0.05). Haplotypes based on 2 SNPs showed significant effect on EST in 3 quail strains (P < 0.05), it also has a significant effect on EW in KO strain (P < 0.05). Meanwhile, A72T was significantly associated with liver weight (LW) and dressing percentage (DP) in 3 strains (P < 0.05). Haplotypes showed significant effect on LW (P < 0.05). Therefore, the IGF-1R gene may be a molecular genetic marker to improve egg quality and carcass traits in quails.