Genome-wide association study for cashmere traits in Inner Mongolia cashmere goat population reveals new candidate genes and haplotypes.

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.

Role of Csdc2 in Regulating Secondary Hair Follicle Growth in Cashmere Goats.

Cashmere goats possess two types of hair follicles, with the secondary hair follicles producing valuable cashmere fiber used for textiles. The growth of cashmere exhibits a seasonal pattern arising from photoperiod change. Transcription factors play crucial roles during this process. The transcription factor, cold-shock domain, containing C2 (Csdc2) plays a crucial role in modulating cell proliferation and differentiation. Our preceding research indicated that the expression of Csdc2 changes periodically during anagen to telogen. However, the mechanisms of Csdc2 in regulating SHF growth remain unclear. Here, we found that the knockdown of Csdc2 inhibits the proliferation of dermal papilla cells. ChIP-Seq analysis showed that Csdc2 had a unique DNA binding motif in SHFs. Through conjoint analysis of ChIP-Seq and RNA-Seq, we revealed a total of 25 candidate target genes of Csdc2. Notably, we discovered a putative Csdc2 binding site within roundabout guidance receptor 2 (Robo2) on chromosome 1 of the goat genome. Furthermore, qRT-PCR and dual-luciferase reporter assay confirmed Csdc2's positive regulatory influence on Robo2. These findings expand the research field of hair follicle transcriptional regulatory networks, offering insights into molecular breeding strategies to enhance cashmere production in goats.

Metabolomic and Transcriptomic Analyses Reveal the Potential Mechanisms of Dynamic Ovarian Development in Goats during Sexual Maturation.

The ovary is a crucial reproductive organ in mammals, and its development directly influences an individual's sexual maturity and reproductive capacity. To comprehensively describe ovarian sexual maturation in goats, we integrated phenotypic, hormonal, metabolomic, and transcriptomic data from four specific time points: after birth (D1), at 2 months old (M2), at 4 months old (M4), and at 6 month old (M6). The study showed that during the early stage (D1-M2), ovarian growth was the most rapid, with weight and morphology increasing by 284% and 65%, respectively, and hormone levels rose significantly, with estradiol increasing by 57%. Metabolomic analysis identified 1231 metabolites, primarily lipids, lipid molecules, and organic acids, which can support hormone balance and follicle development by providing energy and participating in signaling transduction. Transcriptomic analysis identified 543 stage-specific differentially expressed genes, mainly enriched in steroid biosynthesis, amino acid metabolism, and the PI3K/AKT pathway, which are key factors influencing ovarian cell proliferation, apoptosis, hormone secretion, and metabolism. The integrated analysis revealed the key processes in the ovarian steroid hormone biosynthesis pathway and gene/metabolite networks associated with ovarian phenotypes and hormone levels, ultimately highlighting scavenger receptor class B type 1 (SCARB1), Cytochrome P450 Family 1 Subfamily A Member 1 (CYP11A1), 3beta-hydroxysteroid dehydrogenase (3BHSD), progesterone, estradiol, and L-phenylalanine as key regulators of ovarian morphological and functional changes at different developmental stages. This study is the first to reveal the metabolic changes and molecular regulatory mechanisms during ovarian sexual maturation in goats, providing valuable insights for understanding reproductive system development and optimizing reproductive performance and breeding efficiency.

The Transcriptome Characterization of the Hypothalamus and the Identification of Key Genes during Sexual Maturation in Goats.

Sexual maturation in goats is a dynamic process regulated precisely by the hypothalamic-pituitary-gonadal axis and is essential for reproduction. The hypothalamus plays a crucial role in this process and is the control center of the reproductive activity. It is significant to study the molecular mechanisms in the hypothalamus regulating sexual maturation in goats. We analyzed the serum hormone profiles and hypothalamic mRNA expression profiles of female goats during sexual development (1 day old (neonatal, D1, n = 5), 2 months old (prepuberty, M2, n = 5), 4 months old (sexual maturity, M4, n = 5), and 6 months old (breeding period, M6, n = 5)). The results indicated that from D1 to M6, serum hormone levels, including FSH, LH, progesterone, estradiol, IGF1, and leptin, exhibited an initial increase followed by a decline, peaking at M4. Furthermore, we identified a total of 508 differentially expressed genes in the hypothalamus, with a total of four distinct expression patterns. Nuclear receptor subfamily 1, group D, member 1 (NR1D1), glucagon-like peptide 1 receptor (GLP1R), and gonadotropin-releasing hormone 1 (GnRH-1) may contribute to hormone secretion, energy metabolism, and signal transduction during goat sexual maturation via circadian rhythm regulation, ECM receptor interactions, neuroactive ligand-receptor interactions, and Wnt signaling pathways. This investigation offers novel insights into the molecular mechanisms governing the hypothalamic regulation of goat sexual maturation.

Application of growth models to South African Boer goat castrates and does under feedlot conditions.

Mathematical models may aid researchers in describing biological processes, like growth, in animals. This study aimed to collect the body weight data of 18 Boer goat castrates and 20 Boer goat does, from birth until maturity, to model growth and determine growth trends. This is a novel investigation as sufficient information on an age-weight database for these two Boer goat sexes from birth to maturity, is lacking. Using age-weight data, four nonlinear models, namely the Brody, Gompertz, Logistic and Von Bertalanffy growth models, were plotted and evaluated. The model parameters of each growth model were compared for differences between the two sexes. The statistical effectiveness of fit was determined for each model using AIC and RMSE, with R2 also being considered. All models except the Brody model, predicted significantly heavier mature weights for castrates. The Brody model was deemed unfit to describe Boer goat growth as the function severely over-predict weights from birth until maturity for both sexes. The Von Bertalanffy (R2 = 91.3) and Gompertz functions (R2 = 91.3) showed the best fit for Boer goat castrates, while the Gompertz model (R2 = 95.1) showed the best fit for Boer goat does. The Gompertz function is the preferred model to depict Boer goat growth overall, as it accurately characterized growth of both sexes. According to the Gompertz model the age at which the inflection point of the growth curve was reached, did not differ significantly between castrates and does (141.80 days versus 136.31 days). There was also no significant difference in maturation rate between the two sexes.

Preliminary outcomes on phenotypic and genetic parameter estimates for body weight of indigenous Tswana goats in Botswana.

The aims of this study were to estimate the genetic and phenotypic parameters for growth traits and evaluate genetic trends on 585 indigenous Tswana goats. The population was maintained under low input production system at the Department of Agricultural Research in Lesego ranch, Botswana, from 2005 to 2008. Data included birth weight (BW), weaning weight (WW), weight at 8 months (PW), yearling weight (YW), pre-weaning average daily gain (ADG) and two post weaning average daily gains (ADG2 and ADGYW). Data was analysed using general linear model of SAS to determine non-genetic effects. Estimation of genetic and phenotypic parameters were estimated using ASREML fitting an animal model that accounted for fixed effect of parity, sex, type of birth and year of birth. Least squares means for BW, WW, PW and YW were 2.88 ± 0.03, 12.15 ± 0.17, 16.52 ± 0.28 and 21.04 ± 0.32Kg, respectively, while those for ADG, ADG2 and ADGYW were 74.52 ± 1.41, 28.78 ± 1.55 and 33.66 ± 2.28 g/day, respectively. Estimates of heritability for BW, WW, PW and YW were 0.79 ± 0.11, 0.63 ± 0.14, 0.32 ± 0.13 and 0.48 ± 0.16, respectively. The genetic correlations for all the traits studied were positive and moderate to high (0.48 to 0.82) whilst phenotypic correlations ranged from 0.21 to 0.72. Positive average genetic trends of 12.32% (WW), 13.39% (PW) and 7.38% (YW) were attained. The results have demonstrated the potential of this breed to be improved through selection.

Machine learning-based early prediction of growth and morphological traits at yearling age in pure and hybrid goat offspring.

The purpose of this study was to evaluate the performance of various prediction models in estimating the growth and morphological traits of pure Hair, Alpine × Hair F1 (AHF1), and Saanen × Hair F1 (SHF1) hybrid offspring at yearling age by employing early body measurement records from birth till 9th month combined with meteorological data, in an extensive natural pasture-based system. The study also included other factors such as sex, farm, doe and buck IDs, birth type, gestation length, age of the doe at birth etc. For this purpose, seven different machine learning algorithms-linear regression, artificial neural network (ANN), support vector machines (SVM), decision tree, random forest, extra gradient boosting (XGB) and ExtraTree - were applied to the data coming from 1530 goat offspring in Türkiye. Early predictions of growth and morphological traits at yearling age; such as live weight (LW), body length (BL), wither height (WH), rump height (RH), rump width (RW), leg circumference (LC), shinbone girth (SG), chest width (CW), chest girth (CG) and chest depth (CD) were performed by using birth date measurements only, up to month-3, month-6 and month-9 records. Satisfactory predictive performances were achieved once the records after 6th month were used. In extensive natural pasture-based systems, this approach may serve as an effective indirect selection method for breeders. Using month-9 records, the predictions were improved, where LW and BL were found with the highest performance in terms of coefficient of determination (R2 score of 0.81 ± 0.00) by ExtraTree. As one of the rarely applied machine learning models in animal studies, we have shown the capacity of this algorithm. Overall, the current study offers utilization of the meteorological data combined with animal records by machine learning models as an alternative decision-making tool for goat farming.

Effects of drinking saline water on carcass traits and meat quality of growing and mature Blackhead Ogaden sheep and Somali goats.

Water salinity has a significant impact on water quality, posing challenges for livestock production and productivity, particularly in arid regions where climate change affects freshwater availability. This study aimed to determine the effect of drinking saline water on the carcass and meat quality traits of sheep and goats in Ethiopia. A total of 100 males with an average initial body weight of growing (18.17 ± 0.51) and mature (22.22 ± 0.52 kg) Blackhead Ogaden sheep and growing (17.99 ± 0.50) and mature (21.99 ± 0.54) kg) Somali goats were used. The design of the experiment was a three-way factorial RCBD with three-factor combinations (5 treatment levels, 2 species, and 2 age groups).Water treatments were natural water (Lake Basaka water (control), low saline water (L-SW), moderate saline water (M-SW), high saline water (H-SW), and very high saline water (VH-SW); that is, NaCl was added to natural water at concentrations of 7.95, 11.93, 15.90, and 19.88 g TDS/L, respectively. The finding showed that increasing salinity levels in drinking water reduced slaughter body weight (SBW), carcass weight (CW), dressing percentage (DP), rib eye area (RAE), total edible components (TEC), and increased total non-edible components (TNEC) (P < 0.05). Similarly, sheep and mature animals had higher (P < 0.001) SBW, CW, DP, RAE, and TEC than goats and growing animals. Sensory evaluation, shear force, and proximate analysis were affected by water salinity, species, and age groups (P < 0.05). Overall, the study revealed that consuming saline water above 11 g TDS/L affected carcass traits and meat quality in Somali goats and Blackhead Ogaden sheep.

Comparison of genomic prediction methods for early growth traits of Inner Mongolia cashmere goats based on multi trait models.

Inner Mongolia cashmere goat is an excellent livestock breed formed through long-term natural selection and artificial breeding, and is currently a world-class dual-purpose breed producing cashmere and meat. Multi trait animal model is considered to significantly improve the accuracy of genetic evaluation in livestock and poultry, enabling indirect selection between traits. In this study, the pedigree, genotype, environment, and phenotypic records of early growth traits of Inner Mongolia cashmere goats were used to build multi trait animal model., Then three methods including ABLUP, GBLUP, and ssGBLUP wereused to estimate the genetic parameters and genomic breeding values of early growth traits (birth weight, weaning weight, average daily weight gain before weaning, and yearling weight). The accuracy and reliability of genomic estimated breeding value are further evaluated using the five fold cross validation method. The results showed that the heritability of birth weight estimated by three methods was 0.13-0.15, the heritability of weaning weight was 0.13-0.20, heritability of daily weight gain before weaning was 0.11-0.14, and the heritability of yearling weight was 0.09-0.14, all of which belonged to moderate to low heritability. There is a strong positive genetic correlation between weaning weight and daily weight gain before weaning, daily weight gain before weaning and yearling weight, with correlation coefficients of 0.77-0.79 and 0.56-0.67, respectively. The same pattern was found in phenotype correlation among traits. The accuracy of the estimated breeding values by ABLUP, GBLUP, and ssGBLUP methods for birth weight is 0.5047, 0.6694, and 0.7156, respectively; the weaning weight is 0.6207, 0.6456, and 0.7254, respectively; the daily weight gain before weaning was 0.6110, 0.6855, and 0.7357 respectively; and the yearling weight was 0.6209, 0.7155, and 0.7756, respectively. In summary, the early growth traits of Inner Mongolia cashmere goats belong to moderate to low heritability, and the speed of genetic improvement is relatively slow. The genetic improvement of other growth traits can be achieved through the selection of weaning weight. The ssGBLUP method has the highest accuracy and reliability in estimating genomic breeding value of early growth traits in Inner Mongolia cashmere goats, and is significantly higher than that from ABLUP method, indicating that it is the best method for genomic breeding of early growth weight in Inner Mongolia cashmere goats.

Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes.

Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (AWt), Swiss markings (Asm), badgerface (Ab), and the newly proposed peacock (Apc) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.

PAX7 promotes CD49f-positive dairy goat spermatogonial stem cells' self-renewal.

Spermatogenesis is a complex process that originates from and depends on the spermatogonial stem cells (SSCs). The number of SSCs is rare, which makes the separation and enrichment of SSCs difficult and inefficient. The transcription factor PAX7 maintains fertility in normal spermatogenesis in mice. However, for large animals, much less is known about the SSCs' self-renewal regulation, especially in dairy goats. We isolated and enriched the CD49f-positive and negative dairy goat testicular cells by magnetic-activated cell sorting strategies. The RNA- sequencing and experimental data revealed that cells with a high CD49f and PAX7 expression are undifferentiated spermatogonia in goat testis. Our findings indicated that ZBTB16 (PLZF), PAX7, LIN28A, BMPR1B, FGFR1, and FOXO1 were expressed higher in CD49f-positive cells as compared to negative cells and goat fibroblasts cells. The expression and distribution of PAX7 in dairy goat also have been detected, which gradually decreased in testis tissue along with the increasing age. When the PAX7 gene was overexpressed in dairy goat immortal mGSCs-I-SB germ cell lines, the expression of PLZF, GFRα1, ID4, and OCT4 was upregulated. Together, our data demonstrated that there is a subset of spermatogonial stem cells with a high expression of PAX7 among the CD49f+ spermatogonia, and PAX7 can maintain the self-renewal of CD49f-positive SSCs.

Spatial and temporal organization of jejunal microbiota in goats during animal development process.

AIMS: This research aimed to investigate the temporal bacterial colonization relating to non-rumination, transition and rumination phases, together with the spatial organization of microbial community in the jejunal mucosa and digesta of goats. METHODS AND RESULTS: This study explored the colonization programme of the jejunal microbiota by employing 16S rRNA amplicon sequencing. The colonization pattern of jejunal bacterial community exhibited an age- and gut region-dependent progression during animal development process. Approximately 268 bacterial signatures contributed to the discrimination between gut regions, with Lactobacillus, Ruminococcus, Eubacterium and Clostridium_sensu_stricto were enriched in the jejunal digesta, and Bacteroides and unclassified bacteria were enriched in the jejunal mucosa. Intriguingly, a shift from Lactobacillus to Butyrivibrio, Eubacterium and Ruminococcus after d 20 was observed for jejunal digesta. In mucosa, Bifidobacterium, Corynebacterium, Faecalibacterium and Roseburia increased with age (P < 0·05) while Arcobacter, Bacteroides and Porphyromonas peaked at d 10. CONCLUSIONS: The jejunal bacterial community was settled after solid starter provision, which may mark the potential boundary of a timeframe for intervention in goats. The spatial heterogeneity highlighted the complicacy of ecological niches during manipulation of gut microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY: The present study extended the understanding of microbial programming and niche specific in the jejunum among different life stages and the basal cognition of persistent enhancement of nutrient utilization and decline of enteric diseases in ruminants.

Genome-wide selection signal analysis of Australian Boer goat reveals artificial selection imprinting on candidate genes related to muscle development.

As one of the best-known commercial goat breeds in the world, Boer goat has undergone long-term artificial selection for nearly 100 years, and its excellent growth rate and meat production performance have attracted considerable worldwide attention. Herein, we used single nucleotide polymorphisms (SNPs) called from the whole-genome sequencing data of 46 Australian Boer goats to detect polymorphisms and identify genomic regions related to muscle development in comparison with those of 81 non-specialized meat goat individuals from Europe, Africa, and Asia. A total of 13 795 202 SNPs were identified, and the whole-genome selective signal screen with a π ratio of nucleotide diversity (πcase /πcontrol ) and pairwise fixation index (FST ) was analyzed. Finally, we identified 1741 candidate selective windows based on the top 5% threshold of both parameters; here, 449 candidate genes were only found in 727 of these regions. A total of 433 genes out of the 449 genes obtained were annotated to 2729 gene ontology terms, of which 51 were directly linked to muscle development (e.g., muscle organ development, muscle cell differentiation) by 30 candidate genes (e.g., JAK2, KCNQ1, PDE5A, PDLIM5, TBX5). In addition, 246 signaling pathways were annotated by 178 genes, and two pathways related to muscle contraction, including vascular smooth muscle contraction (ADCY7, PRKCB, PLA2G4E, ROCK2) and cardiac muscle contraction (CACNA2D3, CASQ2, COX6B1), were identified. The results could improve the current understanding of the genetic effects of artificial selection on the muscle development of goat. More importantly, this study provides valuable candidate genes for future breeding of goats.

SNP screening of the MSTN gene and correlation analysis between genetic polymorphisms and growth traits in Dazu black goat.

The aim of this study was to detect SNPs in myostatin (MSTN) gene of four goat breeds, and analyze the correlation of these markers on body measurement traits in the Dazu black goat breed. In total, twenty polymorphic sites were found in one hundred forty-eight individuals, and all SNPs were distributed in introns 1 and 2, except g. 425 C > T, which was found in the regulatory region. Three SNPs (g. 2732 C > T, g. 2752 G > A and g. 4552 A > C) were polymorphic in all four breeds. None of the tag SNPs (g. 425 C > T, g. 1583 A > G, 2732 C > T, g. 4552 A > C and g. 5167 C > T) were significantly correlated with body measurement traits (p > 0.05) in the Dazu black goat. However, individuals with genotype combination 3 (GtC 3) of tag SNPs had higher birth weight and weaning weight than individuals with the other genotype combinations (p < 0.05). Moreover, the genotype combination 4 (GtC 4) was significantly associated with body length and height at the age of 2 months (p < 0.05), and genotype combination 13 (GtC 13) was significantly correlated with body height at 6 months (p < 0.05). Briefly, the combined tag SNP markers might be useful for goat marker-associated selective breeding.

A novel duplicated insertion/deletion (InDel) of the CPT1a gene and its effects on growth traits in goat.

Carnitine palmitoyltransferase 1a (CPT1a) is a rate-limited enzyme in the mitochondrial fatty acid ß-oxidation pathway. It acts as a bridge between PPARα and the fatty acid oxidation pathways and is closely related to ruminant growth and development. In this study, one 12 bp InDel polymorphism of the CPT1a gene was identified in 700 goats, and we designated these three genotypes II, ID, and DD. Association analysis showed that the InDel polymorphism was closely associated with trunk index (p = 0.008) and body length index (p = 0.034) in Hainan black goats, and body length (p = 0.010), chest circumference (p = 0.004), chest depth (p = 0.029), and huckle bone width (p = 0.002) in Nubian goats, as well as the chest circumference (p = 0.016) in the Fuqing goat breed. In both kids and adult goats, qRT-PCR results showed that the CPT1a gene was expressed in all tissues, showing the highest mRNA levels in the liver, lung, spleen, and kidney, followed by the adipose tissue and brain. This indicates an association between the InDel of the CPT1a gene and growth traits in selected goat breeds, which may facilitate marker-assisted selection in goat genetics and breeding.

Detection of insertions/deletions (InDels) within the goat Runx2 gene and their association with litter size and growth traits.

Runt-related transcription factor 2 (Runx2) is characterized by its critical functions in osteoblastic and ovulatory processes. The goal of this study was to explore the insertion/deletion (indel) variants of this gene and to evaluate their association with productive traits. Herein, a 12 bp and 6 bp insertion within the Runx2 gene was uncovered in Shaanbei white cashmere goats (SBWC; n = 1200). Chi-square analysis revealed that the 12 bp insertion was related to litter size (p < 0.01). Further association analysis also found this insertion was significantly associated with litter size (p = 1.1E-5). Interestingly, this insertion was also significantly associated with chest circumference (p = 0.018). Additionally, the 6 bp insertion was associated with body length (p = 0.003), chest width (p = 0.011), and chest circumference (p = 0.005). Furthermore, diplotype associations also uncovered that the combined genotypes of these two indels also significantly affected litter size and growth traits (p < 0.05). These findings suggested that these two insertions within the Runx2 gene were significantly associated with reproduction and growth traits, which would make them beneficial functional DNA markers that can be used in goat breeding.

Influence of maternal and additive genetic effects on offspring growth traits in Beetal goat.

The purpose of the present study was to obtain estimates of variance components and genetic parameters for direct and maternal effects on various growth traits in Beetal goat by fitting four animal models, attempting to separate direct genetic, maternal genetic and maternal permanent environmental effects under restricted maximum likelihood procedure. The data of 3,308 growth trait records of Beetal kids born during the period from 2004 to 2019 were used in the present study. Based on best fitted models, the direct additive h2 estimates were 0.06, 0.27, 0.37, 0.17 and 0.10 for birth weight (BWT), weight at 3 (WT3), 6 (WT6), 9 (WT9) and 12 (WT12) months of age, respectively. Maternal permanent environmental effects significantly contributed for 10% and 7% of total variance for BWT and WWT, respectively, which reduced direct heritability by 40 and 10% for respective traits from the models without these effects. For average daily gain (ADG1) and Kleiber ratios (KR1) up to weaning period (3 months) traits, maternal permanent environmental effects accounted for 7% and 8% of phenotypic variance, respectively, and resulted in a reduction of 6.6% and 5.4% in direct h2 of respective traits. For post-weaning traits, the maternal effects were non-significant (p > .05) which indicates diminishing influence of mothering ability for these traits. High and positive genetic correlations were obtained among WT3-WT6, WT6-WT9 and WT9-WT12 with correlations of 0.96 ± 0.25, 0.84 ± 0.23 and 0.90 ± 0.13, respectively. Thus, early selection at weaning age can be practised taking into consideration maternal variation for effective response to selection in Beetal goat.

Genome-wide CNV analysis revealed variants associated with growth traits in African indigenous goats.

Using the CaprineSNP50 data generated by the AGIN consortium, we detected common CNVs in 126 samples from four African indigenous goat breeds. A total of 30 CNVs ranging from 30,237 bp to 4,910,757 bp were identified. These CNVs were then associated with six growth traits by a linear regression analysis. Three significant associations were identified between two CNVs and two body traits after false discovery rate (FDR) correction (P < .05). One of them (CNV27) was significantly associated with both chest width and width of pin bones. It overlaps the SNX29 gene, the Gene Ontology (GO) annotations of which indicate CNV27 could be a potential functional candidate for meat production, health and reproduction traits. To our knowledge, this study is the first CNV-based association test of growth traits using SNP chip data in African meat goats.

Evaluation of non-linear models for growth curve in Brazilian tropical goats.

In the present study, 1060 body weight-age records were measured on 300 Canindé goats. The records were collected from Rio Grande do Norte state, North-eastern part of Brazil, and used for evaluation of non-linear models (Brody, Von Bertalanffy, Logistic, and Gompertz) describing growth curve in goats. The non-linear models were compared applying mean squared error of prediction (MSEP), mean squared residue (MSR), mean absolute deviation (MAD), adjusted coefficient of determination (R2aj), and convergence percentage (%C) for determining the most appropriate model describing the growth curve in Canindé goats. The absolute growth rate (AGR) was estimated based on the adjusted model as a function of time to describe the growth rate of the animals, and the effect of sex on the curve parameters was assessed. The Brody model was the most indicated to represent the average growth curve of Canindé goats. Furthermore, the growth curves estimated by the models under study show that the Brody model displayed the best fit, indicating a greater association between observed and estimated weights, suggesting that it can be used to describe the growth behavior and development of the animals analyzed of both sexes.

Genetic analysis of sexual size dimorphism in Markhoz goat.

Genetic bases of sexual size dimorphism (SSD) in Markhoz goat (5268 kids descended from 242 sires and 1499 dams) were unraveled as it was thought that sex-specific genetic mechanism is in the place governing SSD of birth weight (BW), weaning weight at 90 days of age (WW_90d), and post-weaning weights at 6 (W6), 9 (W9), and 12 (W12) months of age. Male kids excelled for BW, WW_90d, W6, W9, and W12 than their female counterparts in the tune of 10, 17, 14, 17, and 23%, respectively. Estimates of sexual dimorphism levels (expressed as M/F) were 1.09, 1.17, 1.14, 1.17, and 1.23 for BW, WW_90d, W6, W9, and W12, respectively, which indicated relatively low levels of sexual size dimorphism in the studied traits. Though the additive genetic, residual and phenotypic variances were higher in males than females, for mostly all studied traits, but the heritability estimates for all traits except birth weight were higher in females. Differences in direct and maternal effects between male and female kids indicated that body weights traits could be treated as separate trait for male and female kids. Cross-sex genetic correlations revealed that almost all ages, genetic correlations between the two sexes, were high, and the lowest estimate (0.88) was for W6, which highlighted this trait as the most dimorphic trait in this breed. High and positive genetic correlations between the sexes indicated that selection for body weight in males would result in a correlated response in females and vice versa and, consequently, would prevent phenotypic divergence.