Comparative proteomic analysis of spleen reveals key immune-related proteins in the yak (Bos grunniens) at different growth stages

Transcriptome profiling of triploid Crassostrea gigas gills indicates the host immune mechanism against bacterial infection

As an important member of global aquaculture, oysters (Crassostrea gigas) have significant economic value. With the development of commercial aquaculture, the frequent occurrence of diseases caused by Vibrio alginolyticus has become a hindrance to high-density aquaculture. Gill tissue, as an important component of immune system of the oysters, plays the key point in the face of invasion by foreign substances. Compared to the diploid oyster, the triploid oyster presents a higher growth rate and lower growth investment, making it a more ideal model for studying oyster immune defense. In this study, triploid oysters were as the research subject, and gill tissues attacked by V. alginolyticus were sequenced. By analyzing samples from different time points, 1746 DEGs were obtained. The KEGG and GO functional enrichment analysis showed that gill tissues mainly participate in immune function through the PIK3-Akt signaling pathway and the MAPK signaling pathway. The protein interaction network revealed three genes (CASP8, CASP9 and PIK3CA) that play core roles in immune defense by analyzing the interaction relationship between genes. Finally, qRT-PCR verified the expression of key genes. This study provides a more effective scientific basis for disease prevention and control of oysters and other bivalve shellfish, and helps to promote the sustainable development of aquaculture.

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

BACKGROUND

The yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding.

MATERIAL AND METHOD

Here, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation.

RESULTS

By comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1).

CONCLUSIONS

We provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.

Transcriptomic analysis reveals differentially expressed genes and key immune pathways in the spleen of the yak (Bos grunniens) at different growth stage

Yak is one of the rare and unique cattle species on the Qinghai-Tibetan Plateau, which has strong adaptability to the extreme environment of the plateau. The spleens are important functional organs that enable animals to adapt to their external environment and are vital in the growth and development process. To further investigate changes in immune function during yak development, we compared the transcriptome profiles of spleen tissues among juvenile (1-day old), youth (15-months old), and prime (5-years old) yaks. Immunology of spleen development was evaluated based on histological analyses and global gene expression was examined by using RNA-sequencing (RNA-seq) technology. In this work, we found 6378 genes with significant differences between the spleen of juvenile yak and youth yak, with the largest difference between groups. There were 3144 genes with significant differences between the spleen of young yak and prime yak, with the smallest differences between groups. Further, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for the functional annotation of these genes. GO and KEGG analysis showed that some of them were related to growth, disease, immune, and metabolism. However, the genetic mechanism underlying the adaptability of yak spleens at different ages to harsh plateau environments remains unknown. These findings are important for studying the mechanisms of spleen development in yaks of different age groups.

Antioxidant and Immune Stimulating Effects of Allium hookeri Extracts in the RAW 264.7 Cells and Immune-Depressed C57BL/6 Mice

We investigated the antioxidant and immune-enhancing effects of the extracts from Allium hookeri leaves and roots (AHL and AHR) in in vitro and in vivo models. Their antioxidant effects were determined by total phenolic content (TPC), DPPH and ABTS radical scavenging activities, and superoxide dismutase and catalase activities. The immunomodulatory effects were evaluated by nitric oxide (NO) production and cytokine concentrations produced from RAW 264.7, and by serum IgA and IgG levels, cytokine levels, and NK cell activities in the immunosuppressed C57BL/6 mice. AHL and AHR extracts improved antioxidant activities and productions of NO and cytokines without cytotoxicity in the RAW 264.7 cells. AHL and AHR groups showed significantly higher serum IgA and IgG levels, Th1 cytokine concentrations, splenocyte proliferations, and NK cell activities than the NC group which was not treated with AHL or AHR extract. AHR extract showed higher values than AHL extract in the factors evaluated in this study. The results show that they have high antioxidant and immunomodulatory effects and can be used as novel potential therapeutic candidates to treat related diseases and to improve public health.

Genome-Wide Association Study of Body Weight Trait in Yaks

The yak is the largest meat-producing mammal around the Tibetan Plateau, and it plays an important role in the economic development and maintenance of the ecological environment throughout much of the Asian highlands. Understanding the genetic components of body weight is key for future improvement in yak breeding; therefore, genome-wide association studies (GWAS) were performed, and the results were used to mine plant and animal genetic resources. We conducted whole genome sequencing on 406 Maiwa yaks at 10 × coverage. Using a multiple loci mixed linear model (MLMM), fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK), we found that a total of 25,000 single-nucleotide polymorphisms (SNPs) were distributed across chromosomes, and seven markers were identified as significantly (p-values < 3.91 × 10−7) associated with the body weight trait,. Several candidate genes, including MFSD4, LRRC37B, and NCAM2, were identified. This research will help us achieve a better understanding of the genotype−phenotype relationship for body weight.