Genetic parameters and predictions for direct and maternal growth traits in a multibreed Angus–Brahman cattle population using genomic–polygenic and polygenic models

Elzo, Mauricio A.; Thomas, M. G.; Johnson, D. D.; Martínez, Carlos Alberto; Lamb, G. C.; Rae, D. O.; Wasdin, J. G.; Driver, Joseph

doi:10.1016/j.livsci.2015.06.015

Cited by 6 publications

(5 citation statements)

References 33 publications

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“…The research protocol was approved by the University of Florida Institutional Animal Care and Use Committee number 201003744. Animals used in the study belong to the multibreed Angus–Brahman herd from University of Florida ( Elzo et al, 2015a , b , 2016 ), born between 2007 and 2014. Cattle were classified into six different groups based on their expected Angus and Brahman breed composition.…”

Section: Methodsmentioning

confidence: 99%

Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman–Angus Population

et al. 2018

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Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein degradation. As a result, the μ-calpain gene and its specific inhibitor, calpastatin, have been repeatedly investigated for their association with meat quality traits in cattle; however, no functional mutation has been identified for these two genes. The objectives of this study were: (1) to assess breed composition effect on tenderness; (2) to perform a linkage disequilibrium (LD) analysis in μ-calpain and calpastatin genes as well as an association analyses with tenderness; and (3) to analyze putative functional SNPs inside the significant LD block for an effect on tenderness. Tenderness measurements and genotypes for 16 SNPs in μ-calpain gene and 28 SNPs in calpastatin gene from 673 steers were analyzed. A bioinformatic analysis identified “putative functional SNPs” inside the associated LD block – polymorphisms able to produce a physical and/or chemical change in the DNA, mRNA, or translated protein in silico. Breed composition had a significant (P < 0.0001) effect on tenderness where animals with more than 80% Angus composition had the most tender meat. One 11-kb LD-block and three LD-blocks of 37, 17, and 14 kb in length were identified in the μ-calpain and calpastatin genes, respectively. Out of these, the LD-block 3 in calpastatin, tagged by SNPs located at 7-98566391 and 7-98581038, had a significant effect on tenderness with the TG-CG diplotype being approximately 1 kg more tender than the toughest diplotype, TG-CG. A total of 768 SNPs in the LD-block 3 of calpastatin were included in the bioinformatic analysis, and 28 markers were selected as putative functional SNPs inside the LD-block 3 of calpastatin; however, none of them were polymorphic in this population. Out of 15 initial polymorphisms segregating inside the LD-block 3 of calpastatin in this population, markers ARSUSMARC116, Cast5, rs730723459, and rs210861835 were found to be significantly associated with tenderness.

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Section: Methodsmentioning

confidence: 99%

Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman–Angus Population

et al. 2018

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“…The research protocol was approved by the University of Florida Institutional Animal Care and Use Committee number 201003744. Records from 726 steers born between 1990 and 2015 that belong to the Angus-Brahman multibreed herd from University of Florida ( Elzo et al, 2015a , b , 2016 ; Leal-Gutiérrez et al, 2018 ), and a four-generation pedigree with 1,122 animals were used in this study. A total of 22 phenotypes were utilized to construct three latent variables: growth, carcass quality, and meat quality.…”

Section: Methodsmentioning

confidence: 99%

Structural Equation Modeling and Whole-Genome Scans Uncover Chromosome Regions and Enriched Pathways for Carcass and Meat Quality in Beef

et al. 2018

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Structural equation models involving latent variables are useful tools for formulating hypothesized models defined by theoretical variables and causal links between these variables. The objectives of this study were: (1) to identify latent variables underlying carcass and meat quality traits and (2) to perform whole-genome scans for these latent variables in order to identify genomic regions and individual genes with both direct and indirect effects. A total of 726 steers from an Angus-Brahman multibreed population with records for 22 phenotypes were used. A total of 480 animals were genotyped with the GGP Bovine F-250. The single-step genomic best linear unbiased prediction method was used to estimate the amount of genetic variance explained for each latent variable by chromosome regions of 20 adjacent SNP-windows across the genome. Three types of genetic effects were considered: (1) direct effects on a single latent phenotype; (2) direct effects on two latent phenotypes simultaneously; and (3) indirect effects. The final structural model included carcass quality as an independent latent variable and meat quality as a dependent latent variable. Carcass quality was defined by quality grade, fat over the ribeye and marbling, while the meat quality was described by juiciness, tenderness and connective tissue, all of them measured through a taste panel. From 571 associated genomic regions (643 genes), each one explaining at least 0.05% of the additive variance, 159 regions (179 genes) were associated with carcass quality, 106 regions (114 genes) were associated with both carcass and meat quality, 242 regions (266 genes) were associated with meat quality, and 64 regions (84 genes) were associated with carcass quality, having an indirect effect on meat quality. Three biological mechanisms emerged from these findings: postmortem proteolysis of structural proteins and cellular compartmentalization, cellular proliferation and differentiation of adipocytes, and fat deposition.

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“…A total of 120 steers born between 2013 and 2014 were included in the analysis. The animals belong to the multibreed Angus-Brahman herd from the University of Florida [83][84][85]. Cattle were classified into three different groups based on their expected Angus and Brahman breed composition.…”

Section: Cattle Population and Phenotypic Datamentioning

confidence: 99%

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

Gutierrez

Elzo

Mateescu

2019

Preprint

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Background RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through identification of differentially expressed (DE) genes and pathways. Results A total of 80 steers were selected from the multibreed Angus-Brahman herd of the University of Florida. Sensory panel tenderness, juiciness and connective tissue as well as marbling, WBSF and cooking loss were assessed in longissimus dorsi muscle. Nuclear RNA was extracted from muscle and an RNA-seq library for each sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq 3000 PE100 platform to generate 2 × 101 bp paired-end reads. On average, 34.9 million high-quality paired reads were uniquely mapped to the Btau_4.6.1 reference genome and a total of 8,799 genes were analyzed. Including all 80 animals, gene and exon expression analysis was carried out using a meat quality index as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). Out of the 80 samples sequenced, 40 animals with extreme low and high WBSF, tenderness and marbling values were selected for a differential expression (DE) analysis for gene and isoforms. A total of 676 (adjusted p-value ≤ 0.05), 70 (adjusted p-value ≤ 0.1) and 198 (adjusted p-value ≤ 0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR ≤ 0.1) were DE. Conclusion A number of cytoskeletal and transmembrane anchoring related genes and pathways were identified in the expression, DE and gene enrichment analyses, and these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal ﬁlament interaction with myocyte and organelle membranes, contributing to cytoskeletal structure, microtubule network stability, and cellular architecture maintenance during the postmortem.

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Genetic parameters and predictions for direct and maternal growth traits in a multibreed Angus–Brahman cattle population using genomic–polygenic and polygenic models

Cited by 6 publications

References 33 publications

Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman–Angus Population

Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman–Angus Population

Structural Equation Modeling and Whole-Genome Scans Uncover Chromosome Regions and Enriched Pathways for Carcass and Meat Quality in Beef

RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

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