Mining the key regulatory genes of chicken inosine 5′-monophosphate metabolism based on time series microarray data

IMP (inosine 5′-monophosphate) is a compound that enhances the flavor of poultry meat. IMP has become a new breeding trait to improve poultry meat quality. We tried to identify several potential regulatory genes, and construct their predicted regulatory relationships. Time series gene expression profiles of thigh muscle tissues of Rugao chicken, a famous indigenous breed in China, were performed for analysis of genes that are co-expressed or correlated with the concentration of IMP. We found 15 crucial co-expression genes, which are Hspa2, Pten, Gabpa, Bpi, Mkl1, Srf, Cd34, Hspa4, Etv6, Bmpr2, Gde1, Igfbp5, Cd28, Pecam1 and Gja1, that may directly or indirectly regulate IMP metabolism. Eventually, we computed the correlation coefficient between 19 IMP Genes and 15 CGs (15 co-expression genes), and we identified and constructed a predicted regulation network. In conclusion, variation of IMP concentration was primarily connected with the muscle development process. During this process, 15 CGs were identified that may have significant influence on IMP metabolism. In particular, Bmpr2, Pten and co-expression genes correlated with Entpd8 might play important roles in regulating IMP de novo synthesis, decomposition and salvage synthesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s40104-015-0022-3) contains supplementary material, which is available to authorized users.     

金茅黑鸡肉品质性状的关联转录组分析

为深入了解家禽肉品质性状形成的分子机制,本实验测定金茅黑鸡胸肌的肉品质,利用RNA-seq技术进行转录组测序,分析转录组基因表达量与肉品质性状间的关联性。结果显示:与金茅黑鸡14周龄肉色显著相关的基因5个,pH57个,剪切力33个,系水力17个;PLEKHS1、MUC等基因为影响肉色的候选基因,LHX9、SPDEF、GRXCR1等基因为系水力的候选基因,NPY、POMC、FGF20、MGAT4C和GUK1基因为影响肌肉pH的候选基因,EDAR基因和HS6ST3基因为肌肉剪切力的主要候选基因;功能分析发现这些基因在调节肌肉纤维、肌间脂肪沉积、脂类代谢、糖代谢过程和磷酸二酯酶水解等方面发挥重要作用,进而影响胸肌肌肉品质的形成。     

畜禽肌纤维发育规律及相关基因研究进展

肌肉组织分为骨骼肌、心肌和平滑肌3种类型。其中骨骼肌是畜禽最大的器官，约占畜禽身体质量的40%，它由大小、形状及肌肉收缩蛋白含量不同的肌纤维构成，对维持身体姿势、呼吸和体温调节是必不可少的。在肌纤维发育的各阶段，复杂的外在和内在机制共同调控着肌肉的发生，相关的信号机制在这当中起着决定性作用。畜禽的骨骼肌是主要的肉产品来源，而肉质性状的改善也是每个畜禽场的重要目标，因此对肌纤维的发生及相关机制的全面了解是很有必要的。本文通过整合1987—2022年国内外肌纤维研究相关文献，对肌纤维的发生、类型及调控机制进行了综述，重点介绍了与畜禽肌纤维发育规律相关的基因及信号通路，并对目前畜禽肌纤维调控机制研究存在的问题提出了建议和未来研究的方向进行了展望。     

鸡肉质风味性状相关候选基因的研究进展

家禽的肉质性状已经成为育种工作者一个重要的研究方向,而影响家禽肉质的因素有很多,如:遗传、营养、环境、疾病等。研究结果表明,肌内脂肪与肉的嫩度及肉质相关;另外,肌苷酸(IM P)是鸡肉质鲜味特性的主要物质基础,影响IM P生成的各种基因都是潜在的候选基因。作者综述了与肌内脂肪及肌苷酸合成代谢相关的脂蛋白脂酶(LPL)、细胞外脂肪酸结合蛋白(EX-FABP)、瘦蛋白受体(OBR)、解偶联蛋白(UCP)、腺苷琥珀酸裂解酶(ADSL)、腺苷一磷酸脱氨酶1(AM PD 1)等基因的研究进展。     

影响藏猪与大约克夏猪肌肉品质的lncRNA的筛选及功能分析

旨在分析藏猪和大约克夏猪(180日龄)背最长肌组织中与猪肉质性状相关的长链非编码RNA (lncRNAs)和基因,探讨lncRNAs在猪肉品质中的分子调控作用,为猪肉质性状的改良提供理论依据.本研究根据先前公布的数据,以饲养在相同条件下的180日龄健康藏公猪(n-3)和大约克夏公猪(n-3)为研究对象,收集背最长肌肉品...     

蛋白质组学技术解析急性免疫应激影响肉仔鸡肉品质的机理

旨在探讨免疫应激对肉仔鸡胸肌肉品质的影响机理。采用非标定量蛋白质组学技术研究免疫应激对AA肉仔鸡胸肌肉品质和蛋白质组学变化的影响。本试验选取120只1日龄健康AA肉仔公鸡，随机分为2个处理，分别为对照组和免疫应激处理组，每个处理6个重复，每个重复10只鸡。分别在36、38、40日龄时，于腹腔注射1 mL生理盐水（对照组）或5.0 mg·kg^-1体重的LPS溶液（免疫应激组）。42日龄时，每重复随机抽取2只鸡，采集胸肌肌肉组织测定滴水损失、蒸煮损失、肌苷酸含量和pH，及蛋白质组的定性、定量分析。结果显示：1）与对照组相比，免疫应激显著增加了肉鸡胸肌的滴水损失和蒸煮损失（P<0.05），显著降低了胸肌内肌苷酸（IMP）含量（P<0.05）；免疫应激对肉鸡胸肌宰后静置24和48 h的pH影响不显著（P>0.05）；免疫应激组肉鸡胸肌肌纤维的横截面周长和面积均极显著增加（P<0.01）。2）定性蛋白质组学分析结果显示，对照组特异表达蛋白质功能富集到了细胞呼吸、有氧呼吸、己糖代谢与生物合成过程、单糖生物合成过程、葡萄糖代谢过程和糖异生生物学过程；而免疫应激组特异表达蛋白质富集到了紧密连接代谢通路和大分子复合物分解、蛋白质分解与解聚、核酸合成和代谢、糖基化合物合成与代谢和含碱基小分子物质代谢生物学过程。3）定量蛋白质组学分析表明，免疫应激组和对照组有21个蛋白质发生差异化表达，其中15个蛋白质在免疫应激组上调表达，6个蛋白质在免疫应激组下调表达；免疫应激组上调表达的蛋白包括参与碳水化合物代谢和能量产生相关蛋白（AMPD1、GPD1L2、LDHA、UQCRC2）、肌肉收缩相关蛋白（MYH1C、MYH1A、CASQ2、TMEM38A）和参与免疫反应保护细胞免受损伤相关蛋白（HMGB1、PPP1R1A、LOC101747971、PRDX1、ABCF2）；免疫应激组下调表达的蛋白有HBBA、CS、ATP5A1WL、HSP90B1、ABCB6和SYNJ2。综上所述，LPS诱导的免疫应激通过改变肉鸡肌肉与能量代谢和肌肉收缩相关蛋白质的表达，从而增加了肌纤维的面积，并降低了肌细胞持水力，导致肉品质下降。     

牛肉质性状相关基因的研究进展

钙蛋白酶系统在动物屠宰后肌肉蛋白质水解和肌肉嫩化过程中发挥重要的作用;脂肪酸结合蛋白参与脂肪酸的转运代谢,影响肌肉的嫩度、风味和多汁性,与背膘厚、大理石花纹、嫩度和系水力等肉用性状有较高关联度;生肌调节因子在肌肉分化过程中可控制启动成肌细胞的融合和肌纤维的形成;肌肉生成抑制素是控制肌肉生长的负调控因子,影响畜禽瘦肉率、改善肉质性状的重要营养基因。作者综述了钙蛋白酶系统家族、脂肪酸结合蛋白基因、生肌调节因子和肌肉生长抑制素等影响肉牛肉品质性状的基因,以期在肉牛育种选择中找到使产肉量和肉质得到同步提高的途径,进一步通过标记辅助选择来改善肉牛的肉质性状。     

Correlation between polymorphisms in ADSL and GARS-AIRS-GART genes with inosine 5'-monophosphate (IMP) contents in Beijing-you chickens

1. The association of single nucleotide polymorphisms identified within the ADSL (adenylosuccinate lyase deficiency) gene and GARS-AIRS-GART (glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase) gene with the content of inosine 5'-monophosphate (IMP) was studied in a population of male Beijing-you (BJY) chickens slaughtered at 90 d of age. 2. A single nucleotide polymorphism in exon 2 of the ADSL gene had an effect on IMP content. Chickens inheriting the positive allele at ADSL, both homozygous and heterozygous genotypes, had a higher content of IMP in breast muscle than did individuals without it. 3. Similar results were obtained for the GARS-AIRS-GART gene. The marker at the 5' untranslated region (UTR) of the GARS-AIRS-GART gene was also significant for the IMP value. Chickens inheriting the genotypes with the positive allele at this locus had a much higher content of IMP than did those homozygous for the unfavourable one. 4. Interactions between ADSL and GARS-AIRS-GART were detected for such traits as body weight and muscle yields in the tested population. The two loci acted in an additive fashion. Because IMP is one of the most important flavour components in meat, markers developed at these two genes, as well as the combination genotypes, could be used as potential molecular markers for improving chicken quality.     

基于WGCNA技术研究驴肉嫩度基因及代谢物调控网络

旨在通过WGCNA技术解析转录组和代谢组数据,探究驴肉嫩度调控机制。试验动物采用24～36月龄的健康雌性广灵驴(平均体重236.10 kg),将驴肉剪切力和肌内脂肪含量作为表型数据,以每个样品3个重复进行表型数据测定。本试验基于前期研究的具有显著剪切力和肌内脂肪含量差异的14个广灵驴背最长肌样本的转录组和代谢组测序数据,运用WGCNA技术筛选与驴肉嫩度相关的基因及代谢物并进行转录组与代谢组联合分析,解析嫩度相关基因与代谢物。结果表明,利用WGCNA技术通过|r|≥0.5以及P≤0.05筛选标准得到3个与嫩度相关的关键基因模块Greenyellow、Darkgrey、Darkgreen以及2个关键代谢物模块Brown、Yellow。对关键基因模块进行GO富集分析发现,模块内基因主要在甘油磷脂的生物合成、脂质氧化、脂肪酸β-氧化、细胞大分子分解代谢过程、肌肉器官发育、钙离子结合等GO功能上富集。存在于关键模块内的基因及代谢物经KEGG功能富集分析发现,其大多集中在精氨酸和脯氨酸代谢、Wnt信号通路、蛋白质消化吸收、脂肪酸代谢、TCA循环、胰高血糖素信号通路、甘油磷脂代谢、嘌呤代谢、β-丙氨...     

驴肌内脂肪沉积关键调控因子研究

旨在基于转录组(RNA-Seq)和代谢组(UPLC-MS/MS)关联分析,筛选驴肌内脂肪沉积的关键调控因子.本研究选用饲养条件相同、平均体重为236.10 kg的雌性广灵驴30头,对其背最长肌进行肌内脂肪(IMF)含量的测定,选择年龄一致的驴,并根据其IMF含量的高低分为两组:低肌内脂肪组(L组,每组3头)与高肌内脂肪...     

Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

ABSTRACT

1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library.

2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes.

3. Certain DEMs (such as miR-204, miR-133b, and miR-12 229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.     

MyoD and Myf6 gene expression patterns in skeletal muscle during embryonic and posthatch development in the domestic duck (Anas platyrhynchos domestica)

The MyoD and Myf6 genes, which are muscle regulatory factors (MRFs), play major roles in muscle growth and development and initiate muscle fibre formation via the regulation of muscle‐specific gene translation. Therefore, MyoD and Myf6 are potential candidate genes for meat production traits in animals and poultry. The objective of this study was to evaluate MyoD and Myf6 gene expression patterns in the skeletal muscle during early developmental stage of ducks. Gene expression levels were detected using the quantitative RT‐PCR method in the breast muscle (BM) and leg muscle (LM) at embryonic days 13, 17, 21, 25, 27, as well as at 1 week posthatching in Gaoyou and Jinding ducks (Anas platyrhynchos domestica). The MyoD and Myf6 gene profiles in the two duck breeds were consistent during early development, and MyoD gene expression showed a ‘wave’ trend in BM and an approximate ‘anti‐√’ trend in LM. Myf6 gene expression in BM showed the highest level at embryonic day 21, which subsequently decreased, although remained relatively high, while levels at embryonic days 13, 17 and 21 were higher in LM. The results of correlation analysis showed that MyoD and Myf6 gene expression levels were more strongly correlated in LM than in BM in both duck breeds. These results indicated that different expression patterns of the MyoD and Myf6 genes in BM and LM may be related to muscle development and differentiation, suggesting that MyoD and Myf6 are integral to skeletal muscle development.     

中国美利奴羊胚胎骨骼肌发育的加权基因共表达网络分析

旨在对绵羊胚胎骨骼肌lncRNAs（long non-coding RNA）进行鉴定分析,以阐明其在肌纤维类型转换与肌纤维增粗过程中的调控机制。本研究选取体重相近的成年中国美利奴母羊进行同期发情和人工授精,通过全转录组测序技术对其妊娠第85（D85N）、105（D105N）和135天（D135N）的胎儿背最长肌组织进行测序,设置D85N vs D105N、D105N vs D135N和D85N vs D135N 3个比较组,通过比较筛选出显著差异表达的lncRNA与mRNA。利用加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）方法构建共表达模块,使用DAVID在线工具和R-package进行GO和KEGG富集分析以找到与肌肉发育相关的模块。最后从目标模块中筛选出高连通度的lncRNAs和mRNAs,通过它们与miRNAs间的靶向预测关系建立lncRNA-miRNA-mRNA共表达网络。根据WGCNA分析结果,共得到25个模块。功能富集显示,模块中的核心基因主要富集于细胞粘附、Wnt、紧密连接、mTOR、AMPK及ECM-受体相互作用等肌肉发育相关的信号通路,选出模块中连通度高的lncRNAs和mRNAs构建子网络,得到TNNI2、PIP5K1A、PDK4等关键相关基因,预测出MSTRG.3903、MSTRG.10154、MSTRG.1629、MSTRG.10496、MSTRG.9559、MSTRG.10178、MSTRG.10521、MSTRG.3911、MSTRG.4586、MSTRG.7232等10个与肌肉发育、肌肉疾病、细胞增殖相关的lncRNAs。本研究成功构建了肌纤维发育相关的lncRNA-miRNA-mRNA共表达网络,找到多个与妊娠后期胚胎骨骼肌发育相关的潜在候选基因,为深入研究lncRNA在中国美利奴羊胚胎发育过程中骨骼肌的发育调控机制奠定了基础,也为其他家畜骨骼肌发育机制的研究提供了参考和方向。     

利用加权基因共表达网络分析筛选天农麻鸡胴体性状候选基因

旨在通过转录组测序(RNA-Seq)与加权基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)筛选慢速型黄羽肉鸡天农麻鸡胴体性状相关候选基因。本研究以104只天农麻鸡为素材,在126日龄时进行屠宰,测定胸肌重等7个胴体性状,采集胸肌组织进行RNA-Seq。基于RNA-Seq数据获得基因表达矩阵后,结合表型进行WGCNA分析,确定目标模块,筛选目标模块的枢纽基因,并分别进行KEGG通路富集、蛋白质互作网络(protein-protein interaction network,PPI)构建和相关性分析。104份胸肌组织RNA-Seq质控后获得15 092个基因的表达量。与胴体表型进行WGCNA,共得到19个模块,其中4个模块与胴体性状极显著相关。功能富集结果表明,目标模块内基因主要富集在ECM-受体相互作用、黏着力等通路。以|Module membership|> 0.8、|Gene significance|> 0.2为标准筛选到58个枢纽基因,并通过PPI网络构建鉴定到5个网络节点基因,整合相关性分析确定COL1A2和SPARC为最重要候选基因。本研究通过大样本量转录组分析,发现ECM-受体相互作用等通路在天农麻鸡胴体性状调控中发挥主要作用,筛选到COL1A2和SPARC是影响全净膛率性状的重要候选基因,研究结果为鉴定选育分子标记,解析胴体性状分子机制奠定理论基础,为慢速型黄羽肉鸡育种提供重要参考。     

畜禽肉中代谢物质对肉品质的影响及相关基因研究进展

肉质风味是味觉和嗅觉感知的感官印象,其根本是由肉中的代谢物质的含量及复杂的化学过程所决定。随着代谢物质测定技术的不断进步,肉中代谢物质的含量对肉品质的影响也越来越受到关注,肉中代谢物质含量也逐渐成为研究及育种工作的热点,进而挖掘出了很多调控代谢物质的候选基因。本文综述了畜禽肉中代谢物质的种类、形成风味的代谢物质化学反应、代谢物质对肉品质的影响以及代谢物质遗传调控。旨在阐明肉中代谢物质对肉质风味形成的调控机制,为畜禽肉质风味的改良提供理论基础和研究思路。     

鸭胸肌肉色性状全基因组关联分析

试验旨在利用全基因组关联分析（GWAS）定位影响鸭胸肌肉色性状的候选基因及分子标记,探究肉色性状的遗传基础。本研究中,共测定了555只北京鸭×野鸭F2代资源群体的3种胸肌肉色性状（包括红度a^*、黄度b^*、亮度L^*）。利用北京鸭×野鸭F2代资源群体胸肌肉色性状数据并结合全基因组重测序数据进行全基因组关联分析,检测影响胸肌肉色性状的相关基因及可能的因果变异位点。结果显示,肌肉亮度L^*、红度a^*、黄度b^*均属于低遗传力性状,遗传力分别为0.23、0.12、0.13,且肌肉黄度b^*变异系数较大（26.18%）。通过相关性分析可知,肌肉黄度与红度存在较强正表型相关（r=0.52）,肌纤维直径与肌肉黄度存在弱负相关性（r=-0.16）。利用混合线性模型进行GWAS,发现了1个SNP与肌肉黄度b^*潜在显著关联（-log₁₀ P=8.28）。对最高效应SNP进行连锁不平衡检验,发现42个SNPs与最高点SNP存在高相关性（r²>0.4）,这些SNPs位于9号染色体0.37~0.43 Mb之间,区间中共包含7个基因。通过转录组测序数据分析,发现只有5个基因在胸肌组织中表达。对这5个基因进行功能注释,确定硒蛋白T（SELENOT）基因为影响肌肉黄度的候选基因。该结果为解析鸭胸肌肉色性状和提高鸭肉品质的遗传改良提供重要参考。     

绵羊骨骼肌生长发育调控基因研究进展

骨骼肌发育是一个复杂的过程,其中包括肌细胞的形成与增殖、肌管和肌纤维的形成及最后的成熟过程。骨骼肌生长发育直接影响到绵羊的生产性能。随着测序技术的发展,更多人尝试从基因层面来阐述骨骼肌发育过程中系统的调控网络,挖掘与肉品质、产肉性能等重要功能性状相关的分子标记。肌细胞增强因子2(MEF2)是控制肌肉基因表达的保守且功能显著的转录因子,在调节肌肉生成、神经发育与分化等方面起作用。成肌细胞决定因子(myogenic differentiation,MyoD)基因家族调控肌细胞分化和骨骼肌系统的发育成熟。为了更深入地认识与绵羊骨骼肌生长发育相关的调控基因的功能,作者从骨骼肌的结构特点入手,重点介绍MEF2与MyoD基因家族的结构与功能,以及非编码RNA对骨骼肌中基因表达的调控作用。