Detection of genetic variants between different Polish Landrace and Puławska pigs by means of RNA‐seq analysis

Abstract

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.

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

“…Repeat sequences were inferred to comprised 33.1% of the genome in L. guanicoe, 32.7% in V. vicugna, and 27.02% in L. glama, lower values than in most mammals [11], although such sequences were difficult to assemble most likely due to the limitations of short-read sequencing. Resequencing of seven individuals per species (Additional file 1: Figure S2; Table S8) yielded an average sequence depth of 16-fold after filtering (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45) Gb, Additional file 1: Table S9). Resequencing uncovered 21.3 million SNPs and a heterozygous SNP rate of 0.0030 for alpaca, 25.2 million and 0.0023 for vicuña, 16.7 million and 0.0018 for guanaco, and 16.1 million and 0.0020 for llama, indicating a higher overall SNP rate for the Vicugna lineage.…”

Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile

“…These results support that higher expression of CTSC is associated with a higher activation of the proteolysis process favoring the meat tenderization. Besides, in a variant calling analyses based on RNA-seq data of two Polish pig breeds divergent for meat tenderness, variants with different genotype distribution between breeds on CTSC gene were detected [ 38 ]; however, any association analyses between the genetic variants identified and tenderness have been carried out so far.…”

An analysis of <i>MYH7</i> single nucleotide polymorphism (g.7:75667956G>A) in relation to growth and carcass traits in pigs

“…In other study it was also shown that SNP in pituitaryspecific transcription factor 1 (PIT1) is associated with growth traits (feed:gain ratio, daily feed intake, number of days in experiment) and carcass traits (average backfat thickness, loin eye area, lean meat percentage) (Piórkowska et al, 2013). The newest report, based on RNA-Seq analysis, proved that polymorphism in aldehyde dehydrogenase 3 family member A2 (ALDH3A2) affects the weight of the ham and loin eye area, however in myomesin-1 (MYOM1) -meatiness and loin texture parameters in Polish Landrace and Puławska pigs (Piórkowska et al, 2018). Examples mentioned above prove the validity and reliability of studies that concern genetic markers in pigs.…”