Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs
Identification of Candidate Genes and Regulatory Factors Underlying Intramuscular Fat Content Through Longissimus Dorsi Transcriptome Analyses in Heavy Iberian Pigs
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DOI：
10.3389/fgene.2018.00608
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发表时间：
2018-12-04
影响因子：
3.7
通讯作者：
Silio, Luis
中科院分区：
文献类型：
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作者：
Munoz, Maria;Maria Garcia-Casco, Juan;Silio, Luis
肌内脂肪（IMF）含量是决定肉质的最重要因素之一。RNA-seq等高通量技术的发展允许识别具有差异表达（DE）的基因通路和网络，这些基因通路和网络在特定性状的动物群体之间存在差异。伊比利亚猪的特点是具有优良的肉质和高含量的肌内脂肪。本研究的目的是分析纯种伊比利亚猪背最长肌转录组的差异表达基因和影响基因表达的调控因子。RNA-seq允许在分析的样品中识别出25，878个注释基因中的10，000个类似基因。除此之外，42.46%的转录本对应于新预测的亚型。差异表达分析显示，共221 DE注释的基因和116 DE新的异构体。功能分析发现，在IMF含量较高的动物中，参与脂质代谢的过表达基因（FXR、SCD、FXR VL 6、DGAT 2、PLIN 1、CIDEC和ADIPOQ）富集，而在IMF含量较低的动物中，与肌生成和脂肪生成相关的过表达基因（EGR 1、EGR 2、EGR 3、JUNB、FOSB和SEMA 4D）富集。除此之外，这些DE基因的潜在调控元件被确定。共表达网络分析揭示了六个长的非编码RNA（IncRNA）（ALDBSSCG 0000002079、ALDBSSCG 0000002093、ALDBSSCG 000003455、ALDBSSCG 0000004244、ALDBSSCG 0000005525和ALDBSSCG 0000006849）与SEMA 4D和FOSB基因共表达，（ALDBSSCG 0000004790），带有SCD、PLCVL 6、DGAT 2、PLIN 1和CIDEC。对调控影响因子（Regulatory Impact Factor，RIF）的分析表明，有301个转录调控因子参与了基因表达的差异，其中5个与脂肪形成有关（ARID 5 B、CREB 1、VDR、ATF 6和SP1），另外3个与骨骼肌的发生和发育有关（ATF 3、KLF 11和MYF 6）。所获得的结果提供了相关的见解IMF内容在纯种伊比利亚猪的遗传机制和一组候选基因和调控因素，为进一步确定的多态性被纳入一个选择程序。
One of the most important determinants of meat quality is the intramuscular fat (IMF) content. The development of high-throughput techniques as RNA-seq allows identifying gene pathways and networks with a differential expression (DE) between groups of animals divergent for a particular trait. The Iberian pig is characterized by having an excellent meat quality and a high content of intramuscular fat. The objectives of the present study were to analyze the longissimus dorsi transcriptome of purebred Iberian pigs divergent for their IMF breeding value to identify differential expressed genes and regulatory factors affecting gene expression. RNA-seq allowed identifying similar to 10,000 of the 25,878 annotated genes in the analyzed samples. In addition to this, 42.46% of the identified transcripts corresponded to newly predicted isoforms. Differential expression analyses revealed a total of 221 DE annotated genes and 116 DE new isoforms. Functional analyses identified an enrichment of overexpressed genes involved in lipid metabolism (FASN, SCD, ELOVL6, DGAT2, PLIN1, CIDEC, and ADIPOQ) in animals with a higher content of IMF and an enrichment of overexpressed genes related with myogenesis and adipogenesis (EGR1, EGR2, EGR3, JUNB, FOSB, and SEMA4D) in the animals with a lower content of IMF. In addition to this, potential regulatory elements of these DE genes were identified. Co-expression networks analyses revealed six long non-coding RNAs (IncRNAs) (ALDBSSCG0000002079, ALDBSSCG0000002093, ALDBSSCG0000003455, ALDBSSCG0000004244, ALDBSSCG0000005525, and ALDBSSCG0000006849) co-expressed with SEMA4D and FOSB genes and one (ALDBSSCG0000004790) with SCD, ELOVL6, DGAT2, PLIN1, and CIDEC. Analyses of the regulatory impact factors (RIFs) revealed 301 transcriptionally regulatory factors involved in expression differences, with five of them involved in adipogenesis (ARID5B, CREB1, VDR, ATF6, and SP1) and other three taking part of myogenesis and development of skeletal muscle (ATF3, KLF11, and MYF6). The results obtained provide relevant insights about the genetic mechanisms underlying IMF content in purebred Iberian pigs and a set of candidate genes and regulatory factors for further identification of polymorphisms susceptible of being incorporated in a selection program.