Dataset Information

Single-Step Genomic Evaluation for Meat Quality Traits, Sensory Characteristics, and Fatty-Acid Composition in Duroc Pigs.

ABSTRACT: Meat quality and carcass characteristics have gained the attention of breeders due to their increasing economic value. Thus, this study investigated the genomic prediction efficiencies of genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) for traits associated with meat quality, sensory characteristics, and fatty-acid composition. A total of 1237 Duroc finishing pigs with 654 individuals genotyped using the Illumina Porcine SNP 60k marker panel were used in this study. Prediction accuracy and bias for GBLUP and ssGBLUP were evaluated using a five-replicates of five-fold cross-validation. Estimation of genetic parameters for traits associated with meat quality, including lightness, yellowness, redness, pH at 24 h post-mortem, moisture content, fat content, water-holding capacity, cooking loss except for shear force (0.19), as well as fatty-acid composition (palmitic, stearic, oleic, linoleic, and linolenic fatty acids), revealed moderate to high heritability estimates ranging from 0.25 to 0.72 and 0.27 to 0.50, respectively, whereas all traits related to sensory characteristics (color, flavor, tenderness, juiciness, and palatability) showed low heritability estimates ranging from 0.08 to 0.14. Meanwhile, assessment of genomic prediction accuracy revealed that ssGBLUP exhibited higher prediction accuracy than GBLUP for meat quality traits, fatty-acid composition, and sensory characteristics, with percentage improvements ranging from 1.90% to 56.07%, 0.73% to 23.21%, and 0.88% to 11.85%, respectively. In terms of prediction bias, ssGBLUP showed less bias estimates than GBLUP for the majority of traits related to meat quality traits, sensory characteristics, and fatty-acid composition of Duroc meat. In this study, ssGBLUP outperformed GBLUP in terms of prediction accuracy and bias for the majority of traits. Through selection and breeding, our findings could be used to promote meat production with improved nutritional value.

SUBMITTER: Lopez BI

PROVIDER: S-EPMC7563502 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Single-Step Genomic Evaluation for Meat Quality Traits, Sensory Characteristics, and Fatty-Acid Composition in Duroc Pigs.

Lopez Bryan Irvine BI Santiago Kier Gumangan KG Lee Donghui D Cho Younggyu Y Lim Dajeong D Seo Kangseok K

Genes 20200909 9

Meat quality and carcass characteristics have gained the attention of breeders due to their increasing economic value. Thus, this study investigated the genomic prediction efficiencies of genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) for traits associated with meat quality, sensory characteristics, and fatty-acid composition. A total of 1237 Duroc finishing pigs with 654 individuals genotyped using the Illumina Porcine SNP 60k marker panel were used in this stud ...[more]

PMID: 32916909

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Project description:Simple Summary Due to the complexity of sperm cell reproduction and maturation, the genetic structure of semen traits remains largely unknown. In our study, we used weighted single-step GWAS to detect genetic regions and further candidate genes related to semen traits in Duroc boars. This study provides in-depth understanding of the genetic structure of semen traits and the biological information provided by gene networks, and can be applied to speed up the genetic process of semen traits in boars. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. Abstract Semen traits play a key role in the pig industry because boar semen is widely used in purebred and crossbred pigs. The production of high-quality semen is crucial to ensuring a good result in artificial insemination. With the wide application of artificial insemination in the pig industry, more and more attention has been paid to the improvement of semen traits by genetic selection. The purpose of this study was to identify the genetic regions and candidate genes associated with semen traits of Duroc boars. We used weighted single-step GWAS to identify candidate genes associated with sperm motility, sperm progressive motility, sperm abnormality rate and total sperm count in Duroc pigs. In Duroc pigs, the three most important windows for sperm motility—sperm progressive motility, sperm abnormality rate, and total sperm count—explained 12.45%, 9.77%, 15.80%, and 12.15% of the genetic variance, respectively. Some genes that are reported to be associated with spermatogenesis, testicular function and male fertility in mammals have been detected previously. The candidate genes CATSPER1, STRA8, ZSWIM7, TEKT3, UBB, PTBP2, EIF2B2, MLH3, and CCDC70 were associated with semen traits in Duroc pigs. We found a common candidate gene, STRA8, in sperm motility and sperm progressive motility, and common candidate genes ZSWIM7, TEKT3 and UBB in sperm motility and sperm abnormality rate, which confirms the hypothesis of gene pleiotropy. Gene network enrichment analysis showed that STRA8, UBB and CATSPER1 were enriched in the common biological process and participated in male meiosis and spermatogenesis. The SNPs of candidate genes can be given more weight in genome selection to improve the ability of genome prediction. This study provides further insight into the understanding the genetic structure of semen traits in Duroc boars.

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Dataset Information

Single-Step Genomic Evaluation for Meat Quality Traits, Sensory Characteristics, and Fatty-Acid Composition in Duroc Pigs.

Publications

Single-Step Genomic Evaluation for Meat Quality Traits, Sensory Characteristics, and Fatty-Acid Composition in Duroc Pigs.

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