Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M
Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland.
Department of Cattle Breeding, National Research Institute of Animal Production, 32-083, Balice, Poland.
Anim Genet. 2018 Jun;49(3):215-225. doi: 10.1111/age.12654. Epub 2018 Apr 10.
Variant calling analysis based on RNA sequencing data provides information about gene variants. RNA-seq is cheaper and faster than is DNA sequencing. However, it requires individual hard filters during data processing due to post-transcriptional modifications such as splicing and RNA editing. In the present study, RNA-seq transcriptome data on two Polish pig breeds (Puławska, PUL, n = 8, and Polish Landrace, PL, n = 8) were included. The pig breeds are significantly different with regard to meat qualities such as texture, water exudation, growth traits and fat content in carcasses. A total of 2451 significant mutations were identified by a chi square tests, and functional analysis was carried out using Panther, KEGG and Kobas. Interesting missense gene variants and mutations located in regulatory regions were found in a few genes related to fatty acid metabolism and lipid storage such as ACSL5, ALDH3A2, FADS1, SCD, PLA2G12A and ATGL. A validation of mutational influences on pig traits was performed for ALDH3A2, ATGL, PLA2G12A and MYOM1 variants using association analysis including 215 pigs of the PL and PUL breeds. The ALDH3A2ENSSSCT00000019636.2:c.470T>C polymorphism was found to affect the weight of the ham and loin eye area. In turn, an ENSSSCT00000004091.2:c.2836G>A MYOM1 mutation, which could be implicated in myofibrillar network organisation, had an effect on meatiness and loin texture parameters. The study aimed to estimate the usefulness of RNA-seq results for a purpose other than differentially expressed gene analysis. The analysis performed indicated interesting gene variants that could be used in the future as markers during selection.
基于RNA测序数据的变异检测分析可提供有关基因变异的信息。RNA测序比DNA测序更便宜、速度更快。然而，由于转录后修饰（如剪接和RNA编辑），在数据处理过程中需要进行单独的严格筛选。在本研究中，纳入了两个波兰猪品种（普瓦夫斯卡猪，PUL，n = 8；波兰大白猪，PL，n = 8）的RNA测序转录组数据。这两个猪品种在肉质（如质地、水分渗出、生长性状和胴体脂肪含量）方面存在显著差异。通过卡方检验共鉴定出2451个显著突变，并使用Panther、KEGG和Kobas进行功能分析。在一些与脂肪酸代谢和脂质储存相关的基因（如ACSL5、ALDH3A2、FADS1、SCD、PLA2G12A和ATGL）中发现了有趣的错义基因变异和位于调控区域的突变。使用包括215头PL和PUL品种猪的关联分析，对ALDH3A2、ATGL、PLA2G12A和MYOM1变异对猪性状的突变影响进行了验证。发现ALDH3A2 ENSSSCT00000019636.2:c.470T>C多态性影响火腿重量和腰大肌面积。反过来，一个可能与肌原纤维网络组织有关的MYOM1突变ENSSSCT00000004091.2:c.2836G>A对肉质和腰部质地参数有影响。该研究旨在评估RNA测序结果在差异表达基因分析之外的其他用途的有效性。所进行的分析表明了一些有趣的基因变异，未来可作为选择过程中的标记。
