Genetic diversity of MYH3 gene associated with growth and carcass traits in Chinese Qinchuan cattle

ADAR1 Promotes Myogenic Proliferation and Differentiation of Goat Skeletal Muscle Satellite Cells

As one of the most important economic traits for domestic animal husbandry, skeletal muscle is regulated by an intricate molecular network. Adenosine deaminase acting on RNA (ADAR1) involves various physiological processes and diseases, such as innate immunity and the development of lung adenocarcinoma, breast cancer, gastric cancer, etc. However, its role in skeletal muscle growth requires further clarification. Here, we explored the functions of ADAR1 in the myogenic process of goat skeletal muscle satellite cells (MuSCs). The ADAR1 transcripts were noticeably enriched in goat visceral tissues compared to skeletal muscle. Additionally, its levels in slow oxidative muscles like the psoas major and minor muscles were higher than in the fast oxidative glycolytic and fast glycolytic muscles. Among the two common isoforms from ADAR1, p110 is more abundant than p150. Moreover, overexpressing ADAR1 enhanced the proliferation and myogenic differentiation of MuSCs. The mRNA-seq performed on MuSCs' knockdown of ADAR1 obtained 146 differentially expressed genes (DEGs), 87 upregulated and 59 downregulated. These DEGs were concentrated in muscle development and process pathways, such as the MAPK and cAMP signaling pathways. Furthermore, many DEGs as the key nodes defined by protein-protein interaction networks (PPI), including STAT3, MYH3/8, TGFβ2, and ACTN4, were closely related to the myogenic process. Finally, RNA immunoprecipitation combined with qPCR (RIP-qPCR) showed that ADAR1 binds to PAX7 and MyoD mRNA. This study indicates that ADAR1 promotes the myogenic development of goat MuSCs, which provides a useful scientific reference for further exploring the ADAR1-related regulatory networks underlying mammal skeletal muscle growth.

RNA-Seq Reveals miRNA and mRNA Co-regulate Muscle Differentiation in Fetal Leizhou Goats

Muscle differentiation is an essential link in animal growth and development, and microRNA and mRNA are indispensable in skeletal muscle differentiation. To improve the meat quality and production of the Leizhou goat, it is vital to understand the molecular mechanism by which its skeletal muscle differentiates. By RNA sequencing (RNA-SEQ), we established miRNA-mRNA profiles of Leizhou goats at three stages: fetal day 70, 90, and 120. There were 991 differently expressed mRNAs and 39 differentially expressed miRNAs found, with the differentially expressed mRNAs mainly enriched in calcium ion binding, ECM-receptor interaction, and Focal adhesion. CKM and MYH3, two muscle differentiation markers, were significantly differentially expressed during this period. In addition, we found that chi-miR-129-5p, chi-miR-433, and chi-miR-24-3p co-regulate muscle differentiation with their target genes. Finally, we can confirm that muscle differentiation occurred in Leizhou goat between 90 and 120 days of the fetus. This study is helpful to better explore the molecular mechanism of goat muscle differentiation.

Uncovering the mechanism whereby dietary nicotinic acid increases the intramuscular fat content in finishing steers by RNA sequencing analysis

In our previous study, we found that a higher dosage of nicotinic acid (NA) in the diet dramatically increases intramuscular fat (IMF) content and improves meat quality in finishing steers. We hypothesised that increased IMF results from the regulation of genes associated with adipogenesis. To address this hypothesis, RNA-seq was used to investigate gene-expression profiles of longissimus muscles from the same 16 cattle that were also used in our previous study and treated with or without dietary NA. Four cDNA libraries were constructed and sequenced. The repeatability and reproducibility of RNA-seq data were confirmed by quantitative reverse-transcription polymerase-chain reaction. In total, 123 differentially expressed genes (DEGs) were identified between longissimus muscles treated and those not treated with dietary NA. Of the 123 DEGs, 117 genes were upregulated by the NA treatment. These DEGs were enriched in 21 pathways, including the extracellular matrix (ECM) –receptor interaction, PPAR signalling pathway, adipocytokine signalling pathway and transforming growth factor-β signalling pathway, all of which are associated with lipid metabolism. Furthermore, candidate genes related to adipocyte differentiation and adipogenesis (PLIN1, PLIN2, ADPN, LEP, LCN2 and SOCS3), lipid metabolism (FABP4, RBP4, GAL, ANXA1, ANXA2 and PTX3) and fatty acid synthesis and esterification (ELOVL6, ACSM1, SOT1 and PTGIS) were upregulated in the NA group. Three genes involved in glucose metabolism (PGAM1, UGDH and GLUT3) were also transcriptionally upregulated. However, MYH4 that encodes glycolytic Type IIb muscle fibres was downregulated by dietary NA. These gene expression results indicated a confirmation of our hypothesis that dietary NA increases the IMF content of longissimus muscle through upregulating the expression of the genes related to adipocyte differentiation, adipogenesis and lipid and glucose metabolism.

bta-miR-378 promote the differentiation of bovine skeletal muscle-derived satellite cells

The mechanism by which bta-miR-378 regulates bovine skeletal muscle-derived satellite cell (bMDSC) myogenesis remains unknown. In this study, stem-loop RT-PCR was used to assess bta-miR-378 expression during the proliferation and differentiation of bMDSCs. The results showed that bta-miR-378 expression did not obviously change during bMDSC proliferation but increased significantly when bMDSCs began to differentiate. Then, a bta-miR-378 mimic (bta-miR-378-M) and bta-miR-378 inhibitor (bta-miR-378-I) were transfected into bMDSCs to explore the effect of bta-miR-378 on bMDSC differentiation. Cell differentiation was detected using myosin heavy chain 3 immunofluorescence, myotube formation, and desmin and myogenin western blotting analyses. As expected, bta-miR-378-M enhanced bMDSC differentiation, whereas bta-miR-378-I had the opposite effect. Moreover, luciferase reporter and western blotting assays showed that bta-miR-378 directly targeted the 3'-untranslated regions of DNA polymerase alpha subunit B (POLA2) to regulate its protein expression. In summary, these data indicate that bta-miR-378 targets POLA2 to promote the differentiation of bMDSCs, which provides further insight into the biological functions of bta-miR-378 in bovines.

Detection of genomic signatures of recent selection in commercial broiler chickens

Background

Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines.

Results

A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts.

Conclusions

Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.

Detection of copy number variations and their effects in Chinese bulls

Background

Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.

Results

We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits.

Conclusions

The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users.