Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array

Of all the mammals of the world, the yak lives at the highest altitude area of more than 3000 m. Comparison between yak and cattle of the low-altitude areas will be informative in studying animal adaptation to higher altitudes. To investigate the molecular mechanism involved in meat quality differences between the two Chinese special varieties Qinghai yak and Qinchuan cattle, 12 chemical–physical characteristics of the longissimus dorsi muscle related to meat quality were compared at the age of 36 months, and the gene expression profiles were constructed by utilizing the bovine genome array. Significant analysis of microarrays was used to identify the differentially expressed genes. Gene ontology and pathway analysis were performed by a free Web-based Molecular Annotation System 2.0. The results reveal ~11 000 probes representing about 10 000 genes that were detected in both the Qinghai yak and Qinchuan cattle. A total of 1922 genes were shown to be differentially expressed, 633 probes were upregulated and 1259 probes were downregulated in the muscle tissue of Qinghai yak that were mainly involved in ubiquitin-mediated proteolysis, muscle growth regulation, glucose metabolism, immune response and so on. Quantitative real-time PCR (qRT-PCR) was performed to validate some differentially expressed genes identified by microarray. Further analysis implied that animals living at a high altitude may supply energy by more active protein catabolism and glycolysis compared with those living in the plain areas. Our results establish the groundwork for further studies on yaks’ meat quality and will be beneficial in improving the yaks’ breeding by molecular biotechnology.     

利用基因芯片技术筛选秦川牛公牛与阉牛肌肉组织差异表达基因

为了筛选秦川牛公牛和阉牛肌肉组织差异表达的基因,探讨二者肉质差异的分子生物学机理,文章利用Affymetrix公司生产的牛基因组芯片技术,分别检测了3头36月龄秦川牛公牛与阉牛背最长肌肌肉组织的mRNA表达水平变化;运用Significance Analysis of Microarrays(SAM)法对秦川牛公牛和阉牛基因表达谱进行了差异分析;并通过分子注释系统平台(MAS2.0)对差异表达基因进行了功能富集类分析和调控通路分析;最后应用实时定量PCR技术对部分差异表达基因进行了验证。基因表达谱分析结果显示,在36月龄秦川牛的肌肉组织中,共检测到约11000个探针,代表大约10000个基因。共筛选出差异表达基因143条,主要涉及胶原纤维的组织和合成、细胞粘附、细胞生长调控、泛素介导的蛋白分解代谢和横纹肌收缩等生物学过程;在分子注释系统数据库中注释到的显著调控通路为细胞外基质受体反应、细胞通讯、焦点粘连和紧密连接等;所验证的差异表达基因的荧光定量PCR结果与芯片结果基本一致。结合已有的文献报道,文章初步认为ECM受体反应、细胞通讯、焦点粘连、紧密接头等调控通路及COL3A1、COL1A1、COL1A2、SPP1、FBN1、MMP2、ECM1、MYH3、MYH8、S100A4、ASPN、CFD等基因可能是参与调控秦川牛阉割前后肉质性状差异的重要调控通路和基因。此外,还筛选出一些尚未在GenBank上登陆的序列,推测可能是未知的新基因,它们在牛肉质代谢过程中的作用还需进一步的研究证明。     

Skeletal muscle transcriptional profiles in two Italian beef breeds, <Emphasis Type="Italic">Chianina</Emphasis> and <Emphasis Type="Italic">Maremmana</Emphasis>, reveal breed specific variation

Chianina and Maremmana breeds play an important role in the Italian cattle meat market. The Chianina breed is an ancient breed principally raised for draught. Now this breed is the worldwide recognized producer of top quality beef, tasteful and tender, specifically the famous “Florentine steak”. The Maremmana characterized by a massive skeletal structure, is a rustic cattle breed selected for adaptability to the marshy land of the Maremma region. We used a high throughput mRNA sequencing to analyze gene expression in muscle tissues of two Italian cattle breeds, Maremmana (MM) and Chianina (CN) with different selection history. We aim to examine the specific genetic contribution of each breed to meat production and quality, comparing the skeletal muscle tissue from Maremmana and Chianina. Most of the differentially expressed genes were grouped in the Glycolysis/Gluconeogenesis pathways. The rate and the extent of post-mortem energy metabolism have a critical effect on the conversion of muscle to meat. Furthermore, we aim at discovering the differences in nucleotide variation between the two breeds which might be attributable to the different history of selection/divergence. In this work we could emphasize the involvement of pathways of post-mortem energy metabolism. Moreover, we detected a collection of coding SNPs which could offer new genomic resources to improve phenotypic selection in livestock breeding program.     

中国肉牛分子与基因修饰育种研究进展

随着世界肉牛产业科技的快速发展,我国肉牛产业的整体水平得到明显提高并取得丰硕成果。肉牛育种技术实现了由常规杂交育种向分子标记辅助育种、全基因组选择育种和基因组修饰育种的技术跨越,揭示出大量与生长发育、肉质品质、繁殖与疾病等相关的候选基因与分子标记,并逐步应用于肉牛育种实践。与生长发育性状相关的基因或分子标记主要集中在生长激素基因、生肌调节因子家族、肌肉生长抑制因子和胰岛素样生长因子等;参与肉质形成的基因主要集中在脂肪酸运输与沉积相关信号通路、钙蛋白酶信号通路、生肌调节因子家族与肌肉生长抑制因子等;繁殖性状相关基因或分子标记主要集中在GnRH-FSHR-LH、生长分化因子9、催乳素受体和FoxO1等;抗病相关基因主要有MHC基因家族、TOLL样受体4基因等。目前,利用精准基因编辑技术已培育出促生长发育与提高肉品质的肉牛育种新材料。本文总结了近年来我国在肉牛分子与基因组修饰育种领域取得的研究进展,以期为我国肉牛遗传育种技术研究提供参考和借鉴。     

Muscle transcriptomic analyses in Angus cattle with divergent tenderness

Beef tenderness contributes significantly to variation of beef palatability, and is largely influenced by various genetic and environmental factors. To identify candidate genes and pathways related to beef tenderness, we analyzed the longissimus dorsi (LD) muscle of Angus cattle that had different degrees of tenderness, measured by Warner-Bratzler shear force (WBSF). Microarray and RT-PCR analyses identified 53 genes that were differentially expressed in LD samples categorized as either tough or tender, including myosin, heavy chain 3 skeletal muscle embryonic (MYH3), myosin heavy chain 8 skeletal muscle perinatal (MYH8), guanylate binding protein 5 (GBP5), fatty acid binding protein 4 (FABP4), Stearoyl-coenzyme A desaturase (SCD), Fatty acid synthase (FASN), ubiquitin-like with PHD and ring finger domains 1 (UHRF1). Most of these genes are involved in lipid metabolism and skeletal muscle contraction. Employing Gene ontology (GO) and Ingenuity Pathway Analysis (IPA), several GO terms and pathways were found to be related to hydrolase, peptidase and GTPase activity, lipid metabolism, small molecule biochemistry, molecular transport, and tissue development. Overall, this analysis provides insight into the metabolic relationships between muscle biology and beef quality.     

Characterization of cadmium-responsive MicroRNAs and their target genes in maize (Zea mays) roots

MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain–calpastatin system. The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.     

Growth performance,carcass trait,meat quality and oxidative stability of beef cattle offered alternative silages in a finishing ration

As lack of forage resource, alternative roughage sources have been developed for ruminant production and their inclusion would exert a great effect on the dietary nutrition, consequently affecting animal performance. Four silages (corn silage (CS), corn stalk silage (SS), inoculated CS and inoculated SS) were separately offered to 60 Bohai Black cattle (15 cattle/group) during a 24-week finishing period, in which the growth performance, carcass trait, beef quality and oxidative stability of steers were determined. Neither silage material nor silage inoculant exerted a significant effect on the growth performance, carcass trait and oxidative stability of beef cattle (P>0.05). As to beef quality, cattle offered CS had higher (P<0.05) contents of intramuscular fat than those offered SS along with a lower moisture content (P<0.05). The contents (mg/g muscle) of C10 : 0, C12 : 0, C14 : 1, C16 : 0, C16 : 1, C18 : 1n9c, C18 : 2n6c, C18 : 3n3, C20 : 1n9, C20 : 2, C20 : 3n6, saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids and n-6 fatty acids were higher (P<0.05) in the beef muscle of animals offered CS than those offered SS, whereas inoculated treatment made no difference (P>0.05) on the proximate components and fatty acids profile of beef muscle. There was neither an interaction (P>0.05) between inoculated treatment and silage material. There were no differences (P>0.05) in cholesterol content and meat quality traits in animals fed alternative silages. The collective findings suggest that it is not economical to substitute high-quality forage for relative low-quality forage in a high-concentrate finishing ration of beef cattle and silage inoculant inclusion would not exert a direct effect on animal performance.     

Genome-wide association study identifies loci and candidate genes for meat quality traits in Simmental beef cattle

Improving meat quality is the best way to enhance profitability and strengthen competitiveness in beef industry. Identification of genetic variants that control beef quality traits can help breeders design optimal breeding programs to achieve this goal. We carried out a genome-wide association study for meat quality traits in 1141 Simmental cattle using the Illumina Bovine HD 770K SNP array to identify the candidate genes and genomic regions associated with meat quality traits for beef cattle, including fat color, meat color, marbling score, longissimus muscle area, and shear force. In our study, we identified twenty significant single-nucleotide polymorphisms (SNPs) (p < 1.47 × 10^?6) associated with these five meat quality traits. Notably, we observed several SNPs were in or near eleven genes which have been reported previously, including TMEM236, SORL1, TRDN, S100A10, AP2S1, KCTD16, LOC506594, DHX15, LAMA4, PREX1, and BRINP3. We identified a haplotype block on BTA13 containing five significant SNPs associated with fat color trait. We also found one of 19 SNPs was associated with multiple traits (shear force and longissimus muscle area) on BTA7. Our results offer valuable insights to further explore the potential mechanism of meat quality traits in Simmental beef cattle.     

Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs

Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc‐miR‐129‐5p, ssc‐miR‐30 and ssc‐miR‐150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA–target gene and miRNA–phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.     

Transcriptomic investigation of meat tenderness in two Italian cattle breeds

Our objectives for this study were to understand the biological basis of meat tenderness and to provide an overview of the gene expression profiles related to meat quality as a tool for selection. Through deep mRNA sequencing, we analyzed gene expression in muscle tissues of two Italian cattle breeds: Maremmana and Chianina. We uncovered several differentially expressed genes that encode for proteins belonging to a family of tripartite motif proteins, which are involved in growth, cell differentiation and apoptosis, such as TRIM45, or play an essential role in regulating skeletal muscle differentiation and the regeneration of adult skeletal muscle, such as TRIM32. Other differentially expressed genes (SCN2B, SLC9A7 and KCNK3) emphasize the involvement of potassium–sodium pumps in tender meat. By mapping splice junctions in RNA‐Seq reads, we found significant differences in gene isoform expression levels. The PRKAG3 gene, which is involved in the regulation of energy metabolism, showed four isoforms that were differentially expressed. This distinct pattern of PRKAG3 gene expression could indicate impaired glycogen storage in skeletal muscle, and consequently, this gene very likely has a role in the tenderization process. Furthermore, with this deep RNA‐sequencing, we captured a high number of expressed SNPs, for example, we found 1462 homozygous SNPs showing the alternative allele with a 100% frequency when comparing tender and tough meat. SNPs were then classified into categories by their position and also by their effect on gene coding (174 non‐synonymous polymorphisms) based on the available UMD_3.1 annotations.     

NCAPG is differentially expressed during longissimus muscle development and is associated with growth traits in Chinese Qinchuan beef cattle

Based on RNA-seq analysis, we recently found that the bovine NCAPG (non-SMC condensin I complex, subunit G) gene is differentially expressed during development of the longissimus muscle. In the present study, we validated this result and, using quantitative real-time PCR analysis, identified two adjacent genes, LCORL and DCAF16, that are more abundant in fetal muscle tissue; further analysis of tissue-specific expression patterns indicated high abundance of NCAPG in muscle. Since no polymorphisms were detected in a previous study of Qinchuan cattle, we extended our investigation to examine the occurrence of single-nucleotide polymorphisms (SNPs) in the NCAPG gene. Three SNPs, i.e., one located in the intron region (g47747: T > G), a synonymous mutation (g52535: A > G) and a missense mutation (g53208: T > G) that leads to a change in the amino acid of interest (pIle442Met), were detected in a population of Qinchuan beef cattle (n = 300). Association analysis showed that these SNPs were significantly associated with the growth traits of Qinchuan beef cattle. Our results indicate that the bovine NCAPG gene may be involved in the development of the longissimus muscle. These polymorphisms in the NCAPG gene may be useful for marker-assisted selection of optimal body size in Qinchuan beef cattle.