Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers.

As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.

Whole genome resequencing reveals the genetic contribution of Kazakh and Swiss Brown cattle to a population of Xinjiang Brown cattle.

Xinjiang Brown cattle is characterized by wide environmental adaptation from its female parent (Kazakh cattle) and good production performance from its male parent (Swiss Brown cattle). However, the genetic basis underlying these characteristics hasnotbeenexplored. Here we compared 50 genomes of Xinjiang Brown cattle to the genomes of other eight breeds worldwide to analyze patterns of genetic variation in the Xinjiang Brown cattle. We found canonical genomic characteristics of cross breed with the lowest linkage disequilibrium and the highest effective population size. At the global level, Xinjiang Brown cattle had 9.88% Kazakh cattle and 90.12% Swiss Brown cattle inheritance. Our local ancestry inference revealed the segments with the excess of Kazakh cattle blood enriched in genes or pathways involved in digestion,absorption,metabolism and disease. More importantly, we also observed the completely fixed haplotypes inherited from Swiss Brown cattle harboring genes (LCORL, GHR, MEF2D, PCSK1 and MSRB3), KEGG pathways, cattle QTLs or human NHGRIGWAS catalog related to body measurement and growth traits. Our findings will not only help understand the process of cross breeding but can provide basic materials for further QTL mapping and improvement of important traits in Xinjiang Brown cattle.

Polymorphisms and association of GRM1, GNAQ and HCRTR1 genes with seasonal reproduction and litter size in three sheep breeds.

Litter size is one of the important economic traits of livestock. Seasonal oestrus, ovulation and lambing of sheep have severely restricted the development of sheep farming in Xinjiang, China. The purpose of this study was to investigate the polymorphisms and genetic correlation between GRM1, GNAQ and HCRTR1 genes and the seasonal reproduction and litter size in three sheep breeds. The DNA mixed pool sequencing and PCR-SSCP methods were used to detect single nucleotide polymorphisms (SNPs) of GRM1, GNAQ and HCRTR1 genes in seasonal oestrous (Kazakh and Chinese Merino [Xinjiang Junken type]) and perennial oestrous (Hu) sheep breeds. The association between genetic polymorphism and litter size was also analysed. The results showed that T945C in exon 2 of GRM1 gene, C589T in exon 2 of HCRTR1 gene and A191G in exon 2 of GNAQ gene were identified by Sanger sequencing, and three genotypes were existed in each SNP site, which all belonged to the synonymous mutation. GRM1 (CC), GNAQ (GA) and HCRTR1 (TC) were the dominant genotypes of seasonal reproduction and litter size in Kazakh sheep and Chinese Merino sheep, respectively, while, in perennial oestrous Hu sheep populations, the dominant genotypes were GRM1 (TC), GNAQ (GA) and HCRTR1 (TC), respectively, and association analysis also confirmed the results. The above results implied that GRM1, GNAQ and HCRTR1 genes are significantly associated with lambing traits in Kazakh, Chinese Merino and Hu sheep. Among them, the locus of GRM1 (T945C), GNAQ (A191G) and HCRTR1 (C589T) might be considered as a potential molecular marker, which controls seasonal reproduction and litter size in sheep.

Protective Effect of Resveratrol Improves Systemic Inflammation Responses in LPS-Injected Lambs.

Highly intensive livestock production often causes immune stress to animals, which makes them more susceptible to infections. The aim of this study was to examine whether resveratrol (Res) alleviates inflammation in lambs. In Experiment 1, 16 male lambs were injected with lipopolysaccharides (LPS) at an initial dose of 0.25, 1.25, and 2.5 µg/kg body weight (BW) for 9 days. Average daily gain and blood parameters were measured and clinical symptoms were recorded. In Experiment 2, 20 male lambs were injected intravenously with LPS (0 mg/kg) + Res (0 mg), LPS (2.5 µg /kg) + Res (0 mg, 82.5 mg, 165 mg, 330 mg), 4 h after LPS injection. Jugular blood was collected from each lamb to determine white blood cell (WBC) counts and the expression of inflammatory genes. In Experiment 1, all LPS-treated lambs showed clinical signs of sickness including rhinorrhea, lethargy, and shivering, and systemic inflammatory responses of increased inflammatory genes levels and cortisol concentration. The lambs had increased respiratory and heart rates and rectal temperature and decreased average daily gain and feed intake. In Experiment 2, resveratrol significantly reduced WBCs and the expression levels of several genes associated with inflammation response (TLR4, NF-κB, c-jun) and inhibited the signaling cascades of NF-κB and MAPKs by down-regulating the expression levels of inflammatory cytokines (IL-1ß, IL-4, IL-6, TNF-α, IFN-γ) induced by LPS. Resveratrol attenuated the LPS-evoked inflammatory responses in lambs by suppressing expression levels of inflammatory cytokines, and blocking NF-κB and MAPK signaling pathways.

The effect of GNAQ methylation on GnRH secretion in sheep hypothalamic neurons.

Kazakh sheep are seasonal estrous animals, and gonadotropin-releasing hormone (GnRH) is the key to fertility regulation. The nutritional level has a certain regulatory effect on estrous, and vitamin B folate plays a role in DNA methylation, directly participating in the process. The goal of this study was to determine whether folate is involved in GnAQ methylation and its effect on GnRH secretion. The hypothalamic neurons of Kazakh fetal sheep were treated with folate at concentrations of 0 mg/mL, 4 mg/mL, 40 mg/mL, and 80 mg/mL. GnAQ promoter methylation, DNMT1, GnAQ expression, and GnRH secretion following treatment with different concentrations of folate were analyzed. One CpG site was methylated in the GNAQ promoter with 40 mg/mL folic acid, and no CpG methylation was found in the other groups. GnAQ expression was related to folate concentration and showed a trend of increasing first and then decreasing. The GnRH expression level in the 40 mg/mL folate group was significantly higher than in the other three groups ( P < .05). These results demonstrate that the appropriate folate concentration promoted GANQ promoter methylation, which in turn affected GnRH secretion.

Comparative profiling of differentially expressed microRNAs in estrous ovaries of Kazakh sheep in different seasons.

Seasonal estrus is a critical limiting factor for animal fecundity. However, estrus occurs in some seasonally estrous sheep in the non-breeding season, and this phenomenon involves changes in ovarian biology. Previous studies indicated that small RNAs, such as microRNAs (miRNAs), play important regulatory roles in ovarian biology. Differentially expressed miRNAs in the ovaries of estrous sheep were identified using Solexa sequencing technology. A total of 423 known miRNAs were identified in ovaries of estrous sheep in the breeding season and non-breeding season. In the comparison of these two groups, 48 miRNAs were identified that were differentially expressed between the two groups (including 5 up-regulated and 43 down-regulated miRNAs). KEGG pathway analysis revealed that the target genes of some differentially expressed miRNAs were involved in pathways related to reproductive hormone signaling and follicular development. Furthermore, the levels of estradiol (E2), progesterone (P4), luteinizing hormone (LH) and follicle-stimulating hormone (FSH) were lower in anestrus sheep than in sheep during the breeding season. Upon combining the pathway enrichment analysis, target gene expression and hormone measurement results, we suggest that these differentially expressed miRNAs might influence ovarian activity in the non-breeding season by regulating the above pathways. The identification of miRNAs that are differentially expressed between ovines in the breeding season and non-breeding season will contribute to our understanding of the role of miRNAs in estrus regulation, and these data may provide a basis for regulating estrus in sheep during the non-breeding season.