Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5′UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying “C-INDEL” of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying “CA-INDEL” of HAG1. We concluded that “C-INDEL” variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.
Due to the harsh environment in the Tibetan Plateau, traditional grazing greatly limits the growth potential of local animals and causes severe ecosystem degradation. This is an urgent issue to be solved, which requires alternative strategies for grazing animals in the Tibetan alpine pastoral livestock systems. This study aimed to investigate the effects of different feeding strategies on growth performance and ruminal microbiota-host interactions in the local breed of sheep (Gangba sheep). Thirty 9-month old Gangba sheep (n = 10 per group) were assigned to natural grazing (G), semi-grazing with supplementation (T), and barn feeding (F) groups (supplementation of concentrate and oat hay) based on body weight. At the end of the experiment (75 d), all sheep were weighed, rumen fluid was obtained from six sheep per group, and ruminal epithelium was obtained from 3 sheep per group. The results showed that: (1) Compared with the G and T groups, the F group significantly increased dry matter intake, average daily gain, and feed conversion ratio of animals. Additionally, Gangba sheep in the F group had higher concentrations of ruminal short-chain volatile fatty acids (VFAs), especially propionate and butyrate (P <0.05) than sheep in the G and T groups. (2) The principal coordinates analysis indicated a significant difference in bacterial composition among different feed strategies. More specifically, the relative abundance of propionate (unidentified F082 and Succiniclasticum) and butyrate-producing (Eubacterium_coprostanoligenes_group) genera were also observed to be increased in the F group, in which unidentified F082 was identified as a differential biomarker among the three groups according to linear discriminant analysis effect size analysis. (3) The dynamics of the rumen epithelial transcriptome revealed that ECM-receptor interactions, focal adhesion, and PI3K-Akt signaling pathways, which are critical in mediating many aspects of cellular functions such as cell proliferation and motility, were upregulated in the F group. In conclusion, under harsh conditions in the Tibetan alpine meadow, barn feeding increased ruminal VFAs concentrations (especially propionate and butyrate), which stimulated gene expression related to cell proliferation in rumen epithelium, appearing to be superior to natural grazing and semi-grazing in gaining body weight of the local Gangba sheep.
Tibetan sheep have lived on the Qinghai-Tibetan Plateau for thousands of years and have good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism by which Tibetan sheep adapt to this extreme environment, especially the role of genetic regulation, is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in the adaptation to high-altitude hypoxia of Tibetan sheep, we analysed the expression profile of lncRNAs and mRNAs in the liver and lung tissues of sheep using comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and one Hu sheep population (low altitude). The results showed a total of 7848 differentially expressed (DE) lncRNA transcripts, and 22,971 DE mRNA transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR, and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA–mRNA and lncRNA–mRNA interaction networks further revealed transcripts potentially involved in adaptation to high-altitude hypoxia, and the hub genes DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, and TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1, were also identified as candidate genes associated with high-altitude hypoxia adaptation. In conclusion, a collection of novel expressed lncRNAs, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results are the first to identify the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provide insights into the genetic regulation mechanisms by which Tibetan sheep adapt to high-altitude hypoxic environments.
Leptomias sp. belongs to Coleoptera, Curculionidae, Leptomias Faust. It is mainly distributed in the Himalayas and Yarlung Zangbo River valleys in Tibet. It is the first time to report the complete mitochondrial genome of Leptomias sp., which featured a typical circular molecule of 16,801 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs, and one control region. The overall nucleotide composition was 38.7% of A, 10.0% of G, 34.3% of T, and 17.0% of C. The content of A þ T was higher than G þ C. In this study, we also determined that Leptomias sp. was the sister to the Sympiezomias velatus based the phylogenetic analysis of nucleotide sequence datasets. This study provides a useful resource for further studies on conservation and population genetics of Leptomias species.
Background: Tibetan sheep have lived on the Tibetan Plateau for thousands of years and they have a good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism of the Tibetan sheep adapting to this extreme environment, especially the role of genetic regulation is still unknown. Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in Tibetan sheep adapting to high altitude hypoxia environment, we analyzed the expression profile of lncRNAs and mRNAs in liver and lung tissue of sheep based on the comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and Hu sheep (low altitude). Results: A total of 7848 differentially expressed (DE) lncRNAs transcripts and 22971 DE mRNAs transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, heme binding, immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA-mRNA and lncRNA-mRNA interaction networks further revealed transcripts potentially involved in adaptation to high altitude hypoxia, the hub genes that DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1 were also identified as candidate genes associated with high altitude hypoxia adaptation. Conclusions: A collection of aberrantly expressed lncRNA, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results first identified the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provides insights into the genetic regulation mechanisms for Tibetan sheep adaptation to high altitude hypoxia environments.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.