Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat.

Northwest Xizang White Cashmere Goat (NXWCG) is the first new breed of cashmere goat in the Xizang Autonomous Region. It has significant characteristics of extremely high fineness, gloss, and softness. Genome-wide association analysis is an effective biological method used to measure the consistency and correlation of genotype changes between two molecular markers in the genome. In addition, it can screen out the key genes affecting the complex traits of biological individuals. The aim of this study was to analyze the genetic mechanism of cashmere trait variation in NXWCG and to discover SNP locus and key genes closely related to traits such as superfine cashmere. Additionally, the key genes near the obtained significant SNPs were analyzed by gene function annotation and biological function mining. In this study, the phenotype data of the four traits (cashmere length, fiber length, cashmere diameter, and cashmere production) were collected. GGP_Goat_70K SNP chip was used for genotyping the ear tissue DNA of the experimental group. Subsequently, the association of phenotype data and genotype data was performed using Gemma-0.98.1 software. A linear mixed model was used for the association study. The results showed that four fleece traits were associated with 18 significant SNPs at the genome level and 232 SNPs at the chromosome level, through gene annotated from Capra hircus genome using assembly ARS1. A total of 107 candidate genes related to fleece traits were obtained. Combined with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, we can find that CLNS1A, CCSER1, RPS6KC1, PRLR, KCNRG, KCNK9, and CLYBL can be used as important candidate genes for fleece traits of NXWCG. We used Sanger sequencing and suitability chi-square test to further verify the significant loci and candidate genes screened by GWAS, and the results show that the base mutations loci on the five candidate genes, CCSER1 (snp12579, 34,449,796, A → G), RPS6KC1 (snp41503, 69,173,527, A → G), KCNRG (snp41082, 67,134,820, G → A), KCNK9 (14:78472665, 78,472,665, G → A), and CLYBL (12: 9705753, 9,705,753, C → T), significantly affect the fleece traits of NXWCG. The results provide a valuable basis for future research and contribute to a better understanding of the genetic structure variation of the goat.

16S rRNA Gene Sequencing Revealed Changes in Gut Microbiota Composition during Pregnancy and Lactation in Mice Model.

The gut microbiota play a vital role in regulating endocrine-mediated metabolism, immunity, and energy metabolism. However, little is known about the gut microbiota and metabolite composition and development throughout pregnancy and lactation. Here, we used amplicon sequencing to analyze the gut microbiota composition of 35 female mice in five stages of pregnancy and lactation, namely, non-receptive (NR) stages, sexually-receptive (SR) stages, at day 15 of pregnancy (Pre_D15), at the day of birth (Del), and at day 10 of lactation (Lac_D10). The results revealed that the α diversity of gut microbiota was significantly increased during pregnancy and lactation. In addition, the principal coordinate analysis (PCoA) conducted on the amplicon sequence variants' (ASVs') distribution of the 16S rRNA amplicons indicated that the microbiota composition was significantly different among the five groups. Based on a random forest analysis, Oscillospira, Dehalobacterium, and Alistipes were the most important microbiota. The abundance of Allobaculum, Oscillospira, and Ruminococcus were negatively correlated with the serum progesterone concentration, while the abundance of Oscillospira was positively correlated with the propionate and valerate concentration in the caecal contents. Moreover, the concentration of acetate and propionate in the Del and Lac_D10 stages was significantly lower than in the SR and Pre_D15 stages. Our findings indicate that some gut microbes and metabolites vary considerably at the different stages of pregnancy and during lactation stages, which can potentially be used as microbial biomarkers. These results provide information on the potential use of the identified microbes as probiotics to maintain a healthy pregnancy and lactation.

Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture.

Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.