Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef
Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear f...
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doaj-0c19d6f526e842a29f2aa9d558e834b92020-11-25T03:26:42ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-09-011110.3389/fgene.2020.538640538640Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in BeefJoel D. Leal-Gutiérrez0Fernanda M. Rezende1Fernanda M. Rezende2James M. Reecy3Luke M. Kramer4Francisco Peñagaricano5Francisco Peñagaricano6Raluca G. Mateescu7Department of Animal Sciences, University of Florida, Gainesville, FL, United StatesDepartment of Animal Sciences, University of Florida, Gainesville, FL, United StatesFaculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, BrazilDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Science, Iowa State University, Ames, IA, United StatesDepartment of Animal Sciences, University of Florida, Gainesville, FL, United StatesUniversity of Florida Genetics Institute, University of Florida, Gainesville, FL, United StatesDepartment of Animal Sciences, University of Florida, Gainesville, FL, United StatesTenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein–protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders’ visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p-value lower than 1 × 10–3 were included. The genes identified as associated were included in a protein–protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655–44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein–protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection.https://www.frontiersin.org/article/10.3389/fgene.2020.538640/fullcellular structureconnective tissueenergy metabolismmarblingtenderness and Warner-Bratzler shear force |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Joel D. Leal-Gutiérrez Fernanda M. Rezende Fernanda M. Rezende James M. Reecy Luke M. Kramer Francisco Peñagaricano Francisco Peñagaricano Raluca G. Mateescu |
spellingShingle |
Joel D. Leal-Gutiérrez Fernanda M. Rezende Fernanda M. Rezende James M. Reecy Luke M. Kramer Francisco Peñagaricano Francisco Peñagaricano Raluca G. Mateescu Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef Frontiers in Genetics cellular structure connective tissue energy metabolism marbling tenderness and Warner-Bratzler shear force |
author_facet |
Joel D. Leal-Gutiérrez Fernanda M. Rezende Fernanda M. Rezende James M. Reecy Luke M. Kramer Francisco Peñagaricano Francisco Peñagaricano Raluca G. Mateescu |
author_sort |
Joel D. Leal-Gutiérrez |
title |
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef |
title_short |
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef |
title_full |
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef |
title_fullStr |
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef |
title_full_unstemmed |
Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef |
title_sort |
whole genome sequence data provides novel insights into the genetic architecture of meat quality traits in beef |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2020-09-01 |
description |
Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein–protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders’ visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p-value lower than 1 × 10–3 were included. The genes identified as associated were included in a protein–protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655–44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein–protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection. |
topic |
cellular structure connective tissue energy metabolism marbling tenderness and Warner-Bratzler shear force |
url |
https://www.frontiersin.org/article/10.3389/fgene.2020.538640/full |
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