Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F, 70.040-020, Brazil.
BMC Genomics. 2018 Feb 14;19(1):145. doi: 10.1186/s12864-018-4515-2.
The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content).
Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 logfold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 logfold-change), being upregulated in HIGH pigs.
The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest.
鉴定在生长和脂肪分布特征不同的猪骨骼肌中差异表达的基因，可能有助于鉴定影响这些性状表型变异的遗传因素。到目前为止，大多数猪转录组研究都是在全基因组范围内研究基因表达的差异，而不是在 mRNA 亚型水平上。在本研究中，我们调查了 52 头杜洛克猪（背膘厚、肌内脂肪和饱和及单不饱和脂肪酸含量增加的 HIGH 猪和多不饱和脂肪酸含量增加的相反表型的 LOW 猪）臀中肌（GM）中 mRNA 亚型的差异表达。
我们的分析表明，在 GM 肌肉中表达的 10.9%的基因产生了替代的 mRNA 亚型，每个基因的平均转录本为 2.9 个。通过使用两种不同的分析方法，一种基于 CLC Genomics Workbench，另一种基于 STAR、RSEM 和 DESeq2 软件，我们鉴定出了 10 个在 HIGH 猪和 LOW 猪之间被两种分析方法都归类为差异表达的 mRNA 亚型（P 值 < 0.01 和 ±0.6 倍对数变化）。只有五个 mRNA 亚型，由 ITGA5、SEMA4D、LITAF、TIMP1 和 ANXA2 基因产生，在经过多重检验校正后仍然显著（q 值 < 0.05 和 ±0.6 倍对数变化），在 HIGH 猪中上调。
HIGH 猪中特定的 ITGA5、LITAF、TIMP1 和 ANXA2 mRNA 亚型的水平升高，与这些基因的过表达与人类肥胖和代谢紊乱相关的报道一致。更广泛地了解这些 mRNA 变体的功能属性，对于阐明转录多样性对猪经济性状决定因素的影响至关重要。
