Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data

Abstract

ObjectiveThe aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants’ effect on histological microstructure and production traits in a larger pig population.MethodsRNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits.ResultsMapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin ‘eye’ area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism.ConclusionThis study’s results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

“…However, when we were looking for the overlapping results between F ST and eROHi analysis, three significant SNPs (MARC0058238, MARC0003342, and ALGA0077279, all on SSC14) pointing to the adaptive selection signals, were observed in Black Slavonian breed while only one such significant SNP (ALGA0036219 on SSC6) was observed in Turopolje breed. The first SNP for Black Slavonian was previously described (MARC0058238, located in the MYO18B genomic region on SSC14, which is found to be associated with muscle fiber types in pigs- Ropka-Molik et al, 2018). Second (MARC0003342) and third (ALGA0077279) SNP identified in Black Slavonian pig are located in non-coding intergenic region present in various domestic animal species, together with the SNP (ALGA0036219 on SSC6) found in Turopolje pig.…”

“…Most likely polymorphisms in these genes are the consequence of breed adaptation to environmental and human demands. For Black Slavonian pig, we identified important genes associated with steroid receptor activity, such as CYP-40 on porcine chromosome SSC8 (Ratajczak et al, 2015); meat-to-fat ratio in pigs, DEAF1 on SSC2 (Falker-Gieske et al, 2019); growth traits in cattle, KSR2 on SSC14 (Puig-Oliveras et al, 2014); animal organ and system development in pigs, SEZ6L on SSC14 (Kwon et al, 2019); hematological parameters in pigs, RHOBTB1 on SSC 14 (Bovo et al, 2019); female reproduction in mice, CDK1 on SSC 14 (Adhikari et al, 2016); salivary secretion in pigs, KCNMA1 on SSC14 (Li et al, 2013); milk fat percentage in buffaloes, KCTD8 on SSC8 (de Camargo et al, 2015); back fat thickness in pigs, RIMS4 on SSC17 (Lee and Shin, 2018); carcass length in pigs, SPTLC2 on SSC7 (Falker-Gieske et al, 2019); muscle fiber types in pigs, MYO18B on SSC14 (Ropka-Molik et al, 2018); and fatty acid profiles in cattle, RAPGEF2 on SSC8 (Cesar et al, 2014).…”

Gene Polymorphisms in Boar Spermatozoa and Their Associations with Post-Thaw Semen Quality

“…Hence, transcriptome alterations in spermatozoa have been considered to be one of the main factors affecting the cryo-survival of boar semen [8][9][10]. It should be emphasized that variant calling procedure based on RNA-Seq data has been suggested to be an important screening tool to identify polymorphisms in differentially expressed genes [7] and potential genetic markers associated with production traits in the pig industry [11].…”

Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

“…As a muscle satellite cell marker, Sox8-deficient mice exhibited a significant reduction in body weight ( Sock et al, 2001 ). TNNT2 is related to the contraction of striated muscles, and variations on its expression were associated with loin eye area in pigs ( Ropka-Molik et al, 2018 ). In turn, SMPX is a regulator of murine skeletal muscle hypertrophy ( Kemp et al, 2001 ).…”