Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Mudadu MA

PROVIDER: S-EPMC4791965 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Publications

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

Mudadu Maurício A MA Porto-Neto Laercio R LR Mokry Fabiana B FB Tizioto Polyana C PC Oliveira Priscila S N PS Tullio Rymer R RR Nassu Renata T RT Niciura Simone C M SC Tholon Patrícia P Alencar Maurício M MM Higa Roberto H RH Rosa Antônio N AN Feijó Gélson L D GL Ferraz André L J AL Silva Luiz O C LO Medeiros Sérgio R SR Lanna Dante P DP Nascimento Michele L ML Chaves Amália S AS Souza Andrea R D L AR Packer Irineu U IU Torres Roberto A A RA Siqueira Fabiane F Mourão Gerson B GB Coutinho Luiz L LL Reverter Antonio A Regitano Luciana C A LC

BMC genomics 20160315

<h4>Background</h4>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 Informa ...[more]

PMID: 26979536

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Dataset Information

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

Background

Results

Conclusions

Publications

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

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