Martínez-Montes A M, Fernández A, Pérez-Montarelo D, Alves E, Benítez R M, Nuñez Y, Óvilo C, Ibañez-Escriche N, Folch J M, Fernández A I
Mejora Genética Animal, Instituto Nacional de Tecnología Agraria y Alimentaria, Ctra. de la Coruña km. 7.5, 28040, Madrid, Spain.
Genètica i Millora Animal, Institut de Recerca i Tecnologies Agroalimentàries, 25198, Lleida, Spain.
Anim Genet. 2017 Apr;48(2):151-165. doi: 10.1111/age.12507. Epub 2016 Sep 18.
RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.
RNA测序技术广泛应用于基因表达定量研究以及未注释转录本的鉴定。然而，该技术还可用于转录区域的多态性检测和RNA编辑，且高效经济。本研究利用RNA测序分析得到的单核苷酸多态性（SNP）数据，在一个实验猪群体中鉴定影响生产性状变异的基因和突变。通过RNA测序方法分析了（伊比利亚猪×长白猪）×长白猪回交群体中9头生长和脂肪性状极端个体的下丘脑和肝脏转录组，并进行了SNP分型。每个组织中均鉴定出超过12.5万个单核苷酸变异（SNV），其中78%被认为是潜在的SNP，即在本研究背景下分离的SNV。通过考虑在一个极端组中呈现纯合或杂合基因型而在另一组中呈现另一种基因型的SNV来检测潜在的信息性SNP。通过这种方式，在下丘脑和肝脏中分别检测到4396个和1862个信息性SNP。在选择用于验证的32个SNP中，25个（80%）被确认为实际的SNP。对19个选定的SNP进行了生长、脂肪和优质肉产量的关联分析，鉴定出四个潜在的因果基因（RETSAT、COPA、RNMT和PALMD）。有趣的是，检测并验证了NR3C1基因g.102797（ss1985401074）位点、ACSM2B基因g.13374（ss1985401075）位点以及先前在脊椎动物中鉴定出的COG3基因g3.4525（ss1985401087）位点的新的RNA编辑修饰，这些修饰可能导致表型变异，应进一步研究。
