Dataset Information

Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population.

ABSTRACT: Meat quality is an important trait for pig-breeding programs aiming to meet consumers' demands. Geneticists must improve meat quality based on their understanding of the underlying genetic mechanisms. Previous studies showed that most meat-quality indicators were low-to-moderate heritability traits; therefore, improving meat quality using conventional techniques remains a challenge. Here, we performed a genome-wide association study of meat-quality traits using the GeneSeek Porcine SNP50K BeadChip in 582 crossbred Duroc × (Landrace × Yorkshire) commercial pigs (249 males and 333 females). Meat conductivity, marbling score, moisture, meat color, pH, and intramuscular fat (IMF) content were investigated. The genome-wide association study was performed using both fixed and random model Circulating Probability Unification (FarmCPU) and a mixed linear model (MLM) with the rMVP software. The genomic heritability of the studied traits ranged from 0.13 ± 0.07 to 0.55 ± 0.08 for conductivity and meat color, respectively. Thirty-two single-nucleotide polymorphisms (SNPs) were identified for meat quality in the crossbred pigs using both FarmCPU and MLM. Among the detected SNPs, five, nine, seven, four, six, and five were significantly associated with conductivity, IMF, marbling score, meat color, moisture, and pH, respectively. Several candidate genes for meat quality were identified in the detected genomic regions. These findings will contribute to the ongoing improvement of meat quality, meeting consumer demands and improving the economic outlook for the swine industry.

SUBMITTER: Gao G

PROVIDER: S-EPMC8010252 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population.

Gao Guangxiong G Gao Ning N Li Sicheng S Kuang Weijian W Zhu Lin L Jiang Wei W Yu Weiwei W Guo Jinbiao J Li Zhili Z Yang Chengzhong C Zhao Yunxiang Y

Frontiers in genetics 20210317

Meat quality is an important trait for pig-breeding programs aiming to meet consumers' demands. Geneticists must improve meat quality based on their understanding of the underlying genetic mechanisms. Previous studies showed that most meat-quality indicators were low-to-moderate heritability traits; therefore, improving meat quality using conventional techniques remains a challenge. Here, we performed a genome-wide association study of meat-quality traits using the GeneSeek Porcine SNP50K BeadCh ...[more]

PMID: 33815461

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Project description:BackgroundGenomic selection is widely applied for genetic improvement in livestock crossbreeding systems to select excellent nucleus purebred (PB) animals and to improve the performance of commercial crossbred (CB) animals. Most current predictions are based solely on PB performance. Our objective was to explore the potential application of genomic selection of PB animals using genotypes of CB animals with extreme phenotypes in a three-way crossbreeding system as the reference population. Using real genotyped PB as ancestors, we simulated the production of 100,000 pigs for a Duroc x (Landrace x Yorkshire) DLY crossbreeding system. The predictive performance of breeding values of PB animals for CB performance using genotypes and phenotypes of (1) PB animals, (2) DLY animals with extreme phenotypes, and (3) random DLY animals for traits of different heritabilities ([Formula: see text] = 0.1, 0.3, and 0.5) was compared across different reference population sizes (500 to 6500) and prediction models (genomic best linear unbiased prediction (GBLUP) and Bayesian sparse linear mixed model (BSLMM)).ResultsUsing a reference population consisting of CB animals with extreme phenotypes showed a definite predictive advantage for medium- and low-heritability traits and, in combination with the BSLMM model, significantly improved selection response for CB performance. For high-heritability traits, the predictive performance of a reference population of extreme CB phenotypes was comparable to that of PB phenotypes when the effect of the genetic correlation between PB and CB performance ([Formula: see text]) on the accuracy obtained with a PB reference population was considered, and the former could exceed the latter if the reference size was large enough. For the selection of the first and terminal sires in a three-way crossbreeding system, prediction using extreme CB phenotypes outperformed the use of PB phenotypes, while the optimal design of the reference group for the first dam depended on the percentage of individuals from the corresponding breed that the PB reference data comprised and on the heritability of the target trait.ConclusionsA commercial crossbred population is promising for the design of the reference population for genomic prediction, and selective genotyping of CB animals with extreme phenotypes has the potential for maximizing genetic improvement for CB performance in the pig industry.

Project description:BackgroundCurrently, meat cut traits are integrated in pig breeding objectives to gain extra profit. However, little is known about the heritability of meat cut proportions (MCP) and their correlations with other traits. The aims of this study were to assess the heritability and genetic correlation of MCP with carcass and meat quality traits using single nucleotide polymorphism chips and conduct a genome-wide association study (GWAS) to identify candidate genes for MCP.ResultsSeventeen MCP, 12 carcass, and seven meat quality traits were measured in 2012 pigs from four populations (Landrace; Yorkshire; Landrace and Yorkshire hybrid pigs; Duroc, and Landrace and Yorkshire hybrid pigs). Estimates of the heritability for MCP ranged from 0.10 to 0.55, with most estimates being moderate to high and highly consistent across populations. In the combined population, the heritability estimates for the proportions of scapula bone, loin, back fat, leg bones, and boneless picnic shoulder were 0.44 ± 0.04, 0.36 ± 0.04, 0.44 ± 0.04, 0.38 ± 0.04, and 0.39 ± 0.04, respectively. Proportion of middle cuts was genetically significantly positively correlated with intramuscular fat content and backfat depth. Proportion of ribs was genetically positively correlated with carcass oblique length and straight length (0.35 ± 0.08 to 0.45 ± 0.07) and negatively correlated with backfat depth (- 0.26 ± 0.10 to - 0.45 ± 0.10). However, weak or nonsignificant genetic correlations were observed between most MCP, indicating their independence. Twenty-eight quantitative trait loci (QTL) for MCP were detected by GWAS, and 24 new candidate genes related to MCP were identified, which are involved with growth, height, and skeletal development. Most importantly, we found that the development of the bones in different parts of the body may be regulated by different genes, among which HMGA1 may be the strongest candidate gene affecting forelimb bone development. Moreover, as previously shown, VRTN is a causal gene affecting vertebra number, and BMP2 may be the strongest candidate gene affecting hindlimb bone development.ConclusionsOur results indicate that breeding programs for MCP have the potential to enhance carcass composition by increasing the proportion of expensive cuts and decreasing the proportion of inexpensive cuts. Since MCP are post-slaughter traits, the QTL and candidate genes related to these traits can be used for marker-assisted and genomic selection.

Dataset Information

Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population.

Publications

Genome-Wide Association Study of Meat Quality Traits in a Three-Way Crossbred Commercial Pig Population.

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