Dataset Information

Population genetic variations of the MMP3 gene revealed hypoxia adaptation in domesticated yaks (Bos grunniens).

ABSTRACT: Objective:As an iconic symbol of Qinghai-Tibetan Plateau and of high altitude, yak is subjected to hypoxic conditions that challenge aerobic metabolism. Matrix metalloproteinases-3 (MMP3) is assumed to be a key target gene of hypoxia-inducible factor-1? (HIF-1?) that function as a master regulator of the cellular response to hypoxia. Therefore, the aim of this investigation was to identify the DNA polymorphism of MMP3 gene in domestic yak and to explore its possible association with high-altitude adaptation. Methods:The single-nucleotide polymorphisms (SNPs) genotyping and mutations scanning at the MMP3 locus were conducted in total of 344 individuals from four domestic Chinese yak breeds resident at different altitudes on the Qinghai-Tibetan Plateau, using high-resolution melting analysis?HRM?and DNA sequencing techniques. Results:The novel of SNPs rs2381 A?G and rs4331 C?G were identified in intron ? and intron ? of MMP3, respectively. Frequencies of the GG genotype and the G allele of SNP rs2381 A?G observed in high-altitude Pali yak were significantly higher than that of the other yak breeds resident at middle or low altitude (p < 0.01). No significant difference was mapped for SNP rs4331 C?G in the yak population (p > 0.05). Haplotype GC was the dominant among the 4 yak breeds, and Pearson correlation analysis showed that the frequencies of GC was significantly lower in GN (Ganan), DT (Datong) and WY (Tianzhu white) yaks compared with Pali yak (PL). The two SNPs were in moderate linkage disequilibrium in high-altitude yaks (PL) but not in middle-altitude (GN, DT) and low-altitude (WY) yaks. Conclusion:These results indicate that MMP3 may have been subjected to positive selection in yak, especially that the SNP rs2381 A?G mutation and GC haplotypes might contribute to adaptation for yak in high-altitude environments.

SUBMITTER: Ding X

PROVIDER: S-EPMC6819682 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Population genetic variations of the MMP3 gene revealed hypoxia adaptation in domesticated yaks (Bos grunniens).

Ding Xuezhi X Yang Chao C Bao Pengjia P Wu Xiaoyun X Pei Jie J Yan Ping P Guo Xian X

Asian-Australasian journal of animal sciences 20181029 12

<h4>Objective</h4>As an iconic symbol of Qinghai-Tibetan Plateau and of high altitude, yak is subjected to hypoxic conditions that challenge aerobic metabolism. Matrix metalloproteinases-3 (MMP3) is assumed to be a key target gene of hypoxia-inducible factor-1α (HIF-1α) that function as a master regulator of the cellular response to hypoxia. Therefore, the aim of this investigation was to identify the DNA polymorphism of MMP3 gene in domestic yak and to explore its possible association with high ...[more]

PMID: 30381735

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Project description:Purpose: The goal of this study was to reveal epigenetic differences in the microRNA transcriptomes of two organs (heart and lung) between yak and cattle. Methods: Three unrelated 2-year old adult females for both of yaks and cattle (Luxi Huang cattle) were used in this study. Two of significant hypoxia-responsive tissues (heart and lung) were rapidly collected from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen. All frozen samples were stored at –80 °C until RNA extraction.The total RNA were extracted with Trizol (Ambion, USA). NanoDrop ND-2000 spectrophotometer (Nano Drop, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) were used to monitor the concentration and integrity of RNA, respectively. In brief, several successive steps consist the Illumina sequencing. The small RNA with length of 14-40 nt were first purified by polyacrylamide gel electrophoresis (PAGE), and then specific adapters were ligated to the purified small RNA. The ligated RNA were reverse transcribed to cDNA libraries. Finally, each library were sequenced on Genome Analyzer. Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: In this study, we illustrated the differences in the microRNA transcriptomes level for heart and lung between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation. The work performed here will provide a typical demonstration for future deciphering the mechanism of high altitude adaptation

Project description:Proliferation of shrubs at the expense of native forage in pastures has been associated with large changes in dry-matter intake and dietary components for grazing ruminants. These changes can also affect the animals' physiology and metabolism. However, little information is available concerning the effect of pastoral-shrub grazing on the rumen bacterial community. To explore rumen bacteria composition in grazing yaks and the response of rumen bacteria to increasing shrub coverage in alpine meadows, 48 yak steers were randomly assigned to four pastures with shrub coverage of 0%, 5.4%, 11.3%, and 20.1% (referred as control, low, middle, and high, respectively), and ruminal fluid was collected from four yaks from each pasture group after 85 days. Rumen fermentation products were measured and microbiota composition determined using Ion S5TM XL sequencing of the 16S rRNA gene. Principal coordinates analysis (PCoA) and similarity analysis indicated that the degree of shrub coverage correlated with altered rumen bacterial composition of yaks grazing in alpine shrub meadows. At the phyla level, the relative abundance of Firmicutes in rumen increased with increasing shrub coverage, whereas the proportions of Bacteroidetes, Cyanobacteria and Verrucomicrobia decreased. Yaks grazing in the high shrub-coverage pasture had decreased species of the genus Prevotellaceae UCG-001, Lachnospiraceae XPB1014 group, Lachnospiraceae AC2044 group, Lachnospiraceae FCS020 group and Fretibacterium, but increased species of Christensenellaceae R-7 group, Ruminococcaceae NK4A214 group, Ruminococcus 1, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005 and Lachnospiraceae UCG-008. These variations can enhance the animals' utilization efficiencies of cellulose and hemicellulose from native forage. Meanwhile, yaks grazed in the high shrub-coverage pasture had increased concentrations of ammonia nitrogen (NH3-N) and branched-chain volatile fatty acids (isobutyrate and isovalerate) in rumen compared with yaks grazing in the pasture without shrubs. These results indicate that yaks grazing in a high shrub-coverage pasture may have improved dietary energy utilization and enhanced resistance to cold stress during the winter. Our findings provide evidence for the influence of shrub coverage on the rumen bacterial community of yaks grazing in alpine meadows as well as insights into the sustainable production of grazing yaks on lands with increasing shrub coverage on the Qinghai-Tibet Plateau.

Dataset Information

Population genetic variations of the MMP3 gene revealed hypoxia adaptation in domesticated yaks (Bos grunniens).

Publications

Population genetic variations of the MMP3 gene revealed hypoxia adaptation in domesticated yaks (Bos grunniens).

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