Comprehensive Analysis of Long Non-coding RNA and mRNA Transcriptomes Related to Hypoxia Adaptation in Tibetan Sheep

Coping with extremes: the rumen transcriptome and microbiome co-regulate plateau adaptability of Xizang goat

The interactions between the rumen microbiota and the host are crucial for the digestive and absorptive processes of ruminants, and they are heavily influenced by the climatic conditions of their habitat. Owing to the harsh conditions of the high-altitude habitat, little is known about how ruminants regulate the host transcriptome and the composition of their rumen microbiota. Using the model species of goats, we examined the variations in the rumen microbiota, transcriptome regulation, and climate of the environment between high altitude (Lhasa, Xizang; 3650 m) and low altitude (Chengdu, Sichuan, China; 500 m) goats. The results of 16 S rRNA sequencing revealed variations in the abundance, diversity, and composition of rumen microbiota. Papillibacter, Quinella, and Saccharofermentans were chosen as potential microbes for the adaptation of Xizang goats to the harsh climate of the plateau by the Spearman correlation study of climate and microbiota. Based on rumen transcriptome sequencing analysis, 244 genes were found to be differentially expressed between Xizang goats and low-altitude goats, with 127 genes showing up-regulation and 117 genes showing down-regulation. SLC26A9, GPX3, ARRDC4, and COX1 were identified as potential candidates for plateau adaptation in Xizang goats. Moreover, the metabolism of fatty acids, arachidonic acids, pathway involving cytokines and their receptors could be essential for adaptation to plateau hypoxia and cold endurance. The expression of GPX3, a gene linked to plateau acclimatization in Xizang goats, was linked to the abundance of Anaerovibrio, and the expression of SLC26A9 was linked to the quantity of Selenomonas, according to ruminal microbiota and host Spearman correlation analysis. Our findings imply that in order to adapt harsh plateau conditions, Xizang goats have evolved to maximize digestion and absorption as well as to have a rumen microbiota suitable for the composition of their diet.

Expression of MSTN/Smad signaling pathway genes and its association with meat quality in Tibetan sheep (Ovis aries)

Tibetan sheep is a unique breed living in Qinghai-Tibet Plateau. Since MSTN/Smad signaling pathway plays a critical role in the regulation of muscle development, we aimed to study the mutton quality, mRNA expression of main transduction genes in the MSTN/Smad signaling pathway, and the effects of those genes on the mutton quality of Tibetan sheep in this study. Six-month-old Qinghai-Tibetan sheep were selected, slaughtered, and their Longissimus lumborum, semitendinosus muscle, arm triceps, and quadriceps femoris muscle were collected. The mutton quality was evaluated, and gene expression and their association with the mutton quality were analyzed using RT-qPCR. The results showed that the indexes of mutton quality were not significantly different between ewes and rams (p > .05) except for Warner-Bratzler shear force (WBSF) (p < .05). A total of 21 different fatty acids were detected in the muscles of Tibetan sheep, including nine types of SFA, four types of MUFA, and eight types of PUFA. The main transduction genes of the MSTN/Smad signaling pathway were found to be widely expressed in muscle tissues, but no significant differences were observed (p > .05). The correlation analysis of the main genes and mutton quality showed that MSTN was significantly correlated with redness and cooking time; Smad2, Smad3, Smad4, and TGFβRI had significant positive correlations with marbling in arm triceps; Smad3 and TGFβRII had strong negative correlations with pH24 h in Longissimus lumborum; Smad2 was negatively correlated with drip loss in Longissimus lumborum. In short, the expression level of MSTN in muscles was positively correlated with Smad2, Smad3, and Smad4 genes and negatively correlated with TGFβRII genes. Thus, the results of this study provide a theoretical basis for the regulation mechanism of the MSTN/Smad pathway on mutton quality.

Whole transcriptome sequencing reveals core genes related to spermatogenesis in Bactrian camels

Bactrian camels survive and reproduce better in extreme climatic conditions than other domestic animals can. However, the reproductive efficiency of camels under their natural pastoral conditions is low. Several factors affect mammalian reproductive performance, including testicular development, semen quality, libido, and mating ability. Testis is a main reproductive organ of the male and is responsible for producing spermatozoa and hormones. However, our understanding of the expression patterns of the genes in camel testis is minimal. Thus, we performed total RNA-sequencing to investigate the gene expression pattern. As a result, 1,538 differential expressed mRNAs (DEmRNAs), 702 differential expressed long non-coding RNAs (DElncRNAs), and 61 differential expressed microRNAs (DEmiRNAs) were identified between pubertal and adult Bactrian camel testes. Then the genomic features, length distribution, and other characteristics of the lncRNAs and mRNAs in the Bactrian camel testis were investigated. Target genes of the DEmiRNAs and DEmRNAs were further subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Genes, such as AMHR2, FGF1, ACTL7A, GATA4, WNT4, ID2, LAMA1, IGF1, INHBB, and TLR2, were mainly involved in the TGF-β, PI3K-AKT, Wnt, GnRH, and Hippo signaling pathways which relate to spermatogenesis. Some of the DEmiRNAs were predicted to be associated with numerous DElncRNAs and DEmRNAs through competing endogenous RNA (ceRNA) regulatory network. At last, the candidate genes were validated by RT-qPCR, dual fluorescent reporter gene, and a fluorescence in situ hybridization (FISH) assay. This research provides high-throughput RNA sequencing data of the testes of Bactrian camels across different developmental stages. It lays the foundation for further investigations on lncRNAs, miRNAs, and mRNAs that involved in Bactrian camel spermatogenesis.

Molecular Characterization, Expression Profiles of SMAD4, SMAD5 and SMAD7 Genes and Lack of Association with Litter Size in Tibetan Sheep

SMAD4, SMAD5 and SMAD7 belonging to the transforming growth factor β (TGF-β) superfamily are indispensable for oocyte formation and development, ovarian organogenesis and folliculogenesis. However, only a few studies have investigated the characteristics of SMAD4, SMAD5 and SMAD7 in Tibetan sheep and the effect of their polymorphism on litter size. In this study, we examined the expression of SMAD4, SMAD5 and SMAD7 in 13 tissues of Tibetan sheep by reverse transcription-quantitative polymerase chain reaction. Further, cDNA of these genes was cloned, sequenced and subjected to bioinformatics analysis. DNA sequencing was also used to detect single nucleotide polymorphisms (SNPs). However, iM-LDRTM technology was used for SNP genotyping. Associations between polymorphisms and litter size were analyzed using data from genotyping of 433 Tibetan sheep. The results showed that the expression of SMAD4, SMAD5 and SMAD7 genes was ubiquitous in the tissues of Tibetan sheep, such as the ovary, uterus and oviduct, hypothalamus, hypophysis, heart, liver, spleen, lung, kidney, rumen, duodenum and longissimus dorsi. However, the expression was unbalanced and upregulated in the spleen, lung, ovary and uterus and downregulated in the longissimus dorsi. The bioinformatics analysis showed that SMAD4, SMAD5 and SMAD7 in Tibetan sheep encoded proteins of 533, 465 and 427 amino acids, respectively. Sequence homology analysis of the three proteins among other animals showed that the sequences of SMAD4, SMAD5 and SMAD7 of Tibetan sheep were similar to those in sheep, yak, cattle, dog, human, pig, chimpanzee, rhesus monkey and house mouse. Two synonymous mutations, g.51537A>G and g.319C>T, were detected in SMAD5 and SMAD7, respectively. The associations of these SNPs and litter size were determined, and it was found that both g.51537A>G and g.319C>T have no significant effect on the litter size of Tibetan sheep. The results provided novel insights into the molecular characterization, expression profiles and polymorphisms of SMAD4, SMAD5 and SMAD7 in Tibetan sheep, but our results do not support associations between these genes and the litter size of Tibetan sheep.