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Detection of genetic variants between different Polish Landrace and Puławska pigs by means of RNA ‐seq analysis
Author(s) -
Piórkowska K.,
Żukowski K.,
RopkaMolik K.,
Tyra M.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12654
Subject(s) - biology , gene , rna seq , transcriptome , kegg , genetics , rna , loin , missense mutation , intron , rna splicing , mutation , gene expression , food science
Summary 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 ACSL 5 , ALDH 3A2 , FADS 1 , SCD , PLA 2G12A and ATGL . A validation of mutational influences on pig traits was performed for ALDH 3A2 , ATGL , PLA 2G12A and MYOM 1 variants using association analysis including 215 pigs of the PL and PUL breeds. The ALDH 3A2 ENSSSCT 19636.2:c.470T>C polymorphism was found to affect the weight of the ham and loin eye area. In turn, an ENSSSCT 4091.2:c.2836G>A MYOM 1 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.