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Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs.

ABSTRACT: This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F2 intercross between Landrace and Korean native pigs.Eighteen FA composition traits were measured in more than 960 F2 progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes.We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10-39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance.Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.

SUBMITTER: Park HB

PROVIDER: S-EPMC5494477 | biostudies-other | 2017 Aug

REPOSITORIES: biostudies-other

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Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in <i>longissimus dorsi</i> muscle in an F<sub>2</sub> intercross between Landrace and Korean native pigs.

Park Hee-Bok HB Han Sang-Hyun SH Yoo Chae-Kyoung CK Lee Jae-Bong JB Kim Ji-Hyang JH Baek Kwang-Soo KS Son Jun-Kyu JK Shin Sang-Min SM Lim Hyun-Tae HT Cho In-Cheol IC

Asian-Australasian journal of animal sciences. 20170102 8

<h4>Objective</h4>This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F<sub>2</sub> intercross between Landrace and Korean native pigs.<h4>Methods</h4>Eighteen FA composition traits were measured in more than 960 F<sub>2</sub> progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes.<h4>Results</h4>We detected 112 QTLs for the FA composition; Forty seven QTLs reached the g ...[more]

PMID: 28111443

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Project description:BackgroundEconomically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, little is known about the genes and molecular mechanisms involved in this process. Evaluating transcriptomic profiles of skeletal muscle during the initial steps leading to the conversion of muscle to meat can identify key regulators of polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker genotypes allows identification of genomic regions that control gene expression, referred to as expression quantitative trait loci (eQTL). In this study, we perform eQTL analyses to identify potential candidate genes and molecular markers regulating growth and meat quality traits in pigs.ResultsMessenger RNA transcripts obtained with RNA-seq of longissimus dorsi muscle from 168 F2 animals from a Duroc x Pietrain pig resource population were used to estimate gene expression variation subject to genetic control by mapping eQTL. A total of 339 eQTL were mapped (FDR ≤ 0.01) with 191 exhibiting local-acting regulation. Joint analysis of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for meat quality, carcass composition and growth traits. Ten of these pQTL were for meat quality phenotypes that co-localized with one eQTL on SSC2 (8.8-Mb region) and 11 eQTL on SSC15 (121-Mb region). Biological processes identified for co-localized eQTL genes include calcium signaling (FERM, MRLN, PKP2 and CHRNA9), energy metabolism (SUCLG2 and PFKFB3) and redox hemostasis (NQO1 and CEP128), and results support an important role for activation of the PI3K-Akt-mTOR signaling pathway during the initial conversion of muscle to meat.ConclusionCo-localization of eQTL with pQTL identified molecular markers significantly associated with both economically important phenotypes and gene transcript abundance. This study reveals candidate genes contributing to variation in pig production traits, and provides new knowledge regarding the genetic architecture of meat quality phenotypes.

Dataset Information

Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F2 intercross between Landrace and Korean native pigs.

Publications

Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in <i>longissimus dorsi</i> muscle in an F<sub>2</sub> intercross between Landrace and Korean native pigs.

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