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Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle

BACKGROUND: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to...

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Autores principales: Mudadu, Maurício A., Porto-Neto, Laercio R., Mokry, Fabiana B., Tizioto, Polyana C., Oliveira, Priscila S. N., Tullio, Rymer R., Nassu, Renata T., Niciura, Simone C. M., Tholon, Patrícia, Alencar, Maurício M., Higa, Roberto H., Rosa, Antônio N., Feijó, Gélson L. D., Ferraz, André L. J., Silva, Luiz O. C., Medeiros, Sérgio R., Lanna, Dante P., Nascimento, Michele L., Chaves, Amália S., Souza, Andrea R. D. L., Packer, Irineu U., Torres, Roberto A. A., Siqueira, Fabiane, Mourão, Gerson B., Coutinho, Luiz L., Reverter, Antonio, Regitano, Luciana C. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791965/
https://www.ncbi.nlm.nih.gov/pubmed/26979536
http://dx.doi.org/10.1186/s12864-016-2535-3
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author Mudadu, Maurício A.
Porto-Neto, Laercio R.
Mokry, Fabiana B.
Tizioto, Polyana C.
Oliveira, Priscila S. N.
Tullio, Rymer R.
Nassu, Renata T.
Niciura, Simone C. M.
Tholon, Patrícia
Alencar, Maurício M.
Higa, Roberto H.
Rosa, Antônio N.
Feijó, Gélson L. D.
Ferraz, André L. J.
Silva, Luiz O. C.
Medeiros, Sérgio R.
Lanna, Dante P.
Nascimento, Michele L.
Chaves, Amália S.
Souza, Andrea R. D. L.
Packer, Irineu U.
Torres, Roberto A. A.
Siqueira, Fabiane
Mourão, Gerson B.
Coutinho, Luiz L.
Reverter, Antonio
Regitano, Luciana C. A.
author_facet Mudadu, Maurício A.
Porto-Neto, Laercio R.
Mokry, Fabiana B.
Tizioto, Polyana C.
Oliveira, Priscila S. N.
Tullio, Rymer R.
Nassu, Renata T.
Niciura, Simone C. M.
Tholon, Patrícia
Alencar, Maurício M.
Higa, Roberto H.
Rosa, Antônio N.
Feijó, Gélson L. D.
Ferraz, André L. J.
Silva, Luiz O. C.
Medeiros, Sérgio R.
Lanna, Dante P.
Nascimento, Michele L.
Chaves, Amália S.
Souza, Andrea R. D. L.
Packer, Irineu U.
Torres, Roberto A. A.
Siqueira, Fabiane
Mourão, Gerson B.
Coutinho, Luiz L.
Reverter, Antonio
Regitano, Luciana C. A.
author_sort Mudadu, Maurício A.
collection PubMed
description BACKGROUND: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. RESULTS: Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches. CONCLUSIONS: The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2535-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-47919652016-03-16 Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle Mudadu, Maurício A. Porto-Neto, Laercio R. Mokry, Fabiana B. Tizioto, Polyana C. Oliveira, Priscila S. N. Tullio, Rymer R. Nassu, Renata T. Niciura, Simone C. M. Tholon, Patrícia Alencar, Maurício M. Higa, Roberto H. Rosa, Antônio N. Feijó, Gélson L. D. Ferraz, André L. J. Silva, Luiz O. C. Medeiros, Sérgio R. Lanna, Dante P. Nascimento, Michele L. Chaves, Amália S. Souza, Andrea R. D. L. Packer, Irineu U. Torres, Roberto A. A. Siqueira, Fabiane Mourão, Gerson B. Coutinho, Luiz L. Reverter, Antonio Regitano, Luciana C. A. BMC Genomics Research Article BACKGROUND: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample. RESULTS: Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches. CONCLUSIONS: The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2535-3) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-15 /pmc/articles/PMC4791965/ /pubmed/26979536 http://dx.doi.org/10.1186/s12864-016-2535-3 Text en © Mudadu et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Mudadu, Maurício A.
Porto-Neto, Laercio R.
Mokry, Fabiana B.
Tizioto, Polyana C.
Oliveira, Priscila S. N.
Tullio, Rymer R.
Nassu, Renata T.
Niciura, Simone C. M.
Tholon, Patrícia
Alencar, Maurício M.
Higa, Roberto H.
Rosa, Antônio N.
Feijó, Gélson L. D.
Ferraz, André L. J.
Silva, Luiz O. C.
Medeiros, Sérgio R.
Lanna, Dante P.
Nascimento, Michele L.
Chaves, Amália S.
Souza, Andrea R. D. L.
Packer, Irineu U.
Torres, Roberto A. A.
Siqueira, Fabiane
Mourão, Gerson B.
Coutinho, Luiz L.
Reverter, Antonio
Regitano, Luciana C. A.
Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title_full Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title_fullStr Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title_full_unstemmed Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title_short Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle
title_sort genomic structure and marker-derived gene networks for growth and meat quality traits of brazilian nelore beef cattle
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791965/
https://www.ncbi.nlm.nih.gov/pubmed/26979536
http://dx.doi.org/10.1186/s12864-016-2535-3
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