Cargando…
The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction
BACKGROUND: Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene fam...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438070/ https://www.ncbi.nlm.nih.gov/pubmed/22894653 http://dx.doi.org/10.1186/1746-6148-8-135 |
_version_ | 1782242860672745472 |
---|---|
author | Hocquette, Jean-Francois Bernard-Capel, Carine Vidal, Veronique Jesson, Beline Levéziel, Hubert Renand, Gilles Cassar-Malek, Isabelle |
author_facet | Hocquette, Jean-Francois Bernard-Capel, Carine Vidal, Veronique Jesson, Beline Levéziel, Hubert Renand, Gilles Cassar-Malek, Isabelle |
author_sort | Hocquette, Jean-Francois |
collection | PubMed |
description | BACKGROUND: Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality. RESULTS: We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits. CONCLUSION: This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified. |
format | Online Article Text |
id | pubmed-3438070 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-34380702012-09-11 The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction Hocquette, Jean-Francois Bernard-Capel, Carine Vidal, Veronique Jesson, Beline Levéziel, Hubert Renand, Gilles Cassar-Malek, Isabelle BMC Vet Res Research Article BACKGROUND: Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality. RESULTS: We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits. CONCLUSION: This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified. BioMed Central 2012-08-15 /pmc/articles/PMC3438070/ /pubmed/22894653 http://dx.doi.org/10.1186/1746-6148-8-135 Text en Copyright ©2012 Hocquette et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Hocquette, Jean-Francois Bernard-Capel, Carine Vidal, Veronique Jesson, Beline Levéziel, Hubert Renand, Gilles Cassar-Malek, Isabelle The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title | The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title_full | The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title_fullStr | The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title_full_unstemmed | The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title_short | The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
title_sort | genotend chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438070/ https://www.ncbi.nlm.nih.gov/pubmed/22894653 http://dx.doi.org/10.1186/1746-6148-8-135 |
work_keys_str_mv | AT hocquettejeanfrancois thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT bernardcapelcarine thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT vidalveronique thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT jessonbeline thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT levezielhubert thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT renandgilles thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT cassarmalekisabelle thegenotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT hocquettejeanfrancois genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT bernardcapelcarine genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT vidalveronique genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT jessonbeline genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT levezielhubert genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT renandgilles genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction AT cassarmalekisabelle genotendchipanewtooltoanalysegeneexpressioninmusclesofbeefcattleforbeefqualityprediction |