Illuminating Genetic Diversity and Selection Signatures in Matou Goats through Whole-Genome Sequencing Analysis.

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed.

Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat.

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat.

Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic differentiation but exhibit relatively greater divergence from Jining goats. An examination of genetic diversity within Xiangdong black goats revealed a moderate level of diversity, minimal inbreeding, and a substantial effective population size, which are more reflective of random mating patterns than other Chinese goat breeds. Additionally, we applied four distinct selective sweep methods, namely, the composite likelihood ratio (CLR), fixation index (F ST), θ π ratio and cross-population extended haplotype homozygosity (XP-EHH), to identify genomic regions under positive selection and genes associated with fundamental biological processes. The most prominent candidate genes identified in this study are involved in crucial aspects of goat life, including reproduction (CCSER1, PDGFRB, IFT88, LRP1B, STAG1, and SDCCAG8), immunity (DOCK8, IL1R1, and IL7), lactation and milk production (SPP1, TLL1, and ERBB4), hair growth (CHRM2, SDC1, ITCH, and FGF12), and thermoregulation (PDE10A). In summary, our research contributes valuable insights into the genomic characteristics of the Xiangdong black goat, underscoring its importance and utility in future breeding programs and conservation initiatives within the field of animal breeding and genetics.

Feasibility of feeding cadmium accumulator maize (Zea mays L.) to beef cattle: Discovering a strategy for eliminating phytoremediation residues.

Eco-friendly and efficient strategies for eliminating cadmium (Cd) phytoremediation plant residues are needed. The present study investigated the feasibility of feeding Cd accumulator maize to beef cattle. In total, 20 cattle at 6 months of age were selected and randomly allocated into two groups fed with 85.82% (fresh basis) Cd accumulator maize (CAM) or normal maize (control [Con]) silage diets for 107 d. Feeding CAM did not affect the body weight (P = 0.24), while it decreased feed intake and increased feed efficiency of beef cattle (P < 0.01). Feeding CAM increased serum concentrations of immunoglobulin A and G, complement 3 and 4, blood urea nitrogen, and low-density lipoprotein cholesterol, decreased serum concentrations of interleukin-6 and lipopolysaccharide (P < 0.05), and caused wider lumens in the renal tubules. The Cd residue in meat was 7 µg/kg beyond the restriction for human food. In the muscle, the unsaturated fatty acids (t11C18:1 and C20:4), Lys, Arg, Pro, and Cys were decreased, while the saturated fatty acids (C10:0, C12:0, and C17:0) and Leu were increased (P < 0.05). Therefore, at the current feeding level, phytoremediation maize increased the feed efficiency of beef cattle, but did present risks to cattle health and production safety, and decreased the meat nutrition and flavor. Further research must be performed to determine whether a lower proper dose of phytoremediation maize and an appropriate feeding period may be possible to ensure no risk to cattle health and the supply of safe meat for humans.

Identification and Regulatory Network Analysis of Genes Related to Reproductive Performance in the Hypothalamus and Pituitary of Angus Cattle.

In this study, we explored the gene expression patterns of the pituitary gland and hypothalamus of Angus cows at different growth and developmental stages by deep sequencing and we identified genes that affect bovine reproductive performance to provide new ideas for improving bovine fertility in production practice. We selected three 6-month-old (weaning period), three 18-month-old (first mating period), and three 30-month-old (early postpartum) Angus cattle. The physiological status of the cows in each group was the same, and their body conformations were similar. After quality control of the sequencing, the transcriptome analyses of 18 samples yielded 129.18 GB of clean data. We detected 13,280 and 13,318 expressed genes in the pituitary gland and hypothalamus, respectively, and screened 35 and 50 differentially expressed genes (DEGs) for each, respectively. The differentially expressed genes in both tissues were mainly engaged in metabolism, lipid synthesis, and immune-related pathways in the 18-month-old cows as compared with the 6-month-old cows. The 30-month-old cows presented more regulated reproductive behavior, and pituitary CAMK4 was the main factor regulating the reproductive behavior during this period via the pathways for calcium signaling, longevity, oxytocin, and aldosterone synthesis and secretion. A variant calling analysis also was performed. The SNP inversions and conversions in each sample were counted according to the different base substitution methods. In all samples, most base substitutions were represented by substitutions between bases A and G, and the probability of base conversion exceeded 70%, far exceeding the transversion. Heterozygous SNP sites exceeded 37.68%.

Calcium Homeostasis and Bone Metabolism in Goats Fed a Low Protein Diet.

The objective of this study was to investigate the effects of low-protein diets on blood calcium (Ca) level, bone metabolism, and the correlation between bone metabolism and blood calcium in goats. Twenty-four female Xiangdong black goats with similar body weight (19.55 ± 3.55 kg) and age (8.0 ± 0.3 months) were selected and allocated into two groups: control group (CON, 10.77% protein content) and low-protein group (LP, 5.52% protein content). Blood samples were collected on days 1, 4, 7, 16 and 36 before morning feeding to determine the concentration of calcium (Ca), parathyroid hormone (PTH), bone gla protein (BGP), C-terminal telopeptide of type 1 collagen (CTX-1), bone alkaline phosphatase (BALP), and 1, 25-dihydroxyvitamin D3 [1,25(OH)2D3]. Liver samples were collected to determine the expression of bone metabolism-related genes. There was no difference observed between LP and CON in concentration of plasma Ca or any of bone metabolism markers (P > 0.05). In the liver, the mRNA expression of bone gamma carboxyglutamate protein (BGLAP), alkaline phosphatase (ALPL), and mothers against decapentaplegic homolog-1 (SMAD1) were increased (P < 0.05) in LP as compared with CON. The correlation analysis of Ca and bone metabolism markers showed no significant correlation between Ca and bone metabolism. These results suggest that the blood Ca concentration in mature goats may keep at a stable level through nitrogen cycling when the providing protein is not enough.

Effects of enzyme supplementation on the nutrient, amino acid, and energy utilization efficiency of citrus pulp and hawthorn pulp in Linwu ducks.

The objective of this study was to evaluate the effects of enzyme supplementation on the nutrient, amino acid, and energy utilization efficiency of citrus pulp and hawthorn pulp as unusual feedstuffs in Linwu ducks. Forty ducks were assigned to each treatment group and fed diets with or without complex enzyme supplementation. All birds received the same quantity of raw material (60 g) via the force-feeding procedure. With the exception of leucine and phenylalanine, amino acid concentrations in hawthorn pulp were twice those in citrus pulp. Enzyme supplementation significantly increased apparent dry matter digestibility (ADM) of citrus pulp (P < 0.05), but had no significant effects (P > 0.05) on the apparent and true utilization rates of other nutrients, apparent metabolizable energy (AME), or true metabolizable energy (TME), from citrus pulp and hawthorn pulp by Linwu ducks. However, enzyme supplementation significantly increased (P < 0.05) apparent gross energy, true gross energy, AME, and TME of hawthorn pulp for Linwu ducks. There were no differences in the apparent and true utilization rates of amino acids from citrus pulp (P > 0.56) between the groups, with the exception of arginine (P < 0.05). There was an increasing trend in the apparent and true utilization rates of alanine (P = 0.06) and tyrosine (P = 0.074) from citrus pulp with enzyme supplementation. The apparent and true utilization rates of threonine in hawthorn pulp were increased significantly (P < 0.05) following enzyme supplementation. The addition of exogenous enzymes improved the forage quality of citrus pulp and hawthorn pulp, which represent potential feed resources for husbandry production.