title: 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.
authors.affiliation: Embrapa Agricultural Informatics, Av. André Tosello, 209, Campinas, SP, Brazil. mauricio.mudadu@embrapa.br.|Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil. mauricio.mudadu@embrapa.br.
authors.forename: Maurício A
authors.identifier: http://orcid.org/0000-0002-2767-2507
authors.initials: MA
authors.lastname: Mudadu
authors.affiliation: Commonwealth Scientific and Industrial Research Organization - Agriculture, 306 Carmody Road, Brisbane, QLD, Australia.
authors.forename: Laercio R
authors.initials: LR
authors.lastname: Porto-Neto
authors.affiliation: Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil.
authors.forename: Fabiana B
authors.initials: FB
authors.lastname: Mokry
authors.affiliation: Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil.
authors.forename: Polyana C
authors.initials: PC
authors.lastname: Tizioto
authors.affiliation: Department of Genetics and Evolution, Federal University of São Carlos, Rodovia Washington Luiz, Km 235, São Carlos, SP, Brazil.
authors.forename: Priscila S N
authors.initials: PS
authors.lastname: Oliveira
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Rymer R
authors.initials: RR
authors.lastname: Tullio
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Renata T
authors.initials: RT
authors.lastname: Nassu
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Simone C M
authors.initials: SC
authors.lastname: Niciura
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Tholon
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Maurício M
authors.initials: MM
authors.lastname: Alencar
authors.affiliation: Embrapa Agricultural Informatics, Av. André Tosello, 209, Campinas, SP, Brazil.
authors.forename: Roberto H
authors.initials: RH
authors.lastname: Higa
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Antônio N
authors.initials: AN
authors.lastname: Rosa
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Gélson L D
authors.initials: GL
authors.lastname: Feijó
authors.affiliation: State University of Mato Grosso do Sul, Rodovia Uems-Aquidauana km 12, Aquidauana, MS, Brazil.
authors.forename: André L J
authors.initials: AL
authors.lastname: Ferraz
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Luiz O C
authors.initials: LO
authors.lastname: Silva
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Sérgio R
authors.initials: SR
authors.lastname: Medeiros
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Dante P
authors.initials: DP
authors.lastname: Lanna
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Michele L
authors.initials: ML
authors.lastname: Nascimento
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Amália S
authors.initials: AS
authors.lastname: Chaves
authors.affiliation: Faculdade de Medicina Veterinaria e Zootecnia, Federal University of Mato Grosso do Sul, Av. Senador Filinto Müller, 2443, Campo Grande, MS, Brazil.
authors.forename: Andrea R D L
authors.initials: AR
authors.lastname: Souza
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Irineu U
authors.initials: IU
authors.lastname: Packer
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Roberto A A
authors.initials: RA
authors.lastname: Torres
authors.affiliation: Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, Brazil.
authors.forename: Fabiane
authors.initials: F
authors.lastname: Siqueira
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Gerson B
authors.initials: GB
authors.lastname: Mourão
authors.affiliation: Department of Animal Science, University of São Paulo, Av. Padua Dias, 11306, Piracicaba, SP, Brazil.
authors.forename: Luiz L
authors.initials: LL
authors.lastname: Coutinho
authors.affiliation: Commonwealth Scientific and Industrial Research Organization - Agriculture, 306 Carmody Road, Brisbane, QLD, Australia.
authors.forename: Antonio
authors.initials: A
authors.lastname: Reverter
authors.affiliation: Embrapa Southeast Livestock, Rodovia Washington Luiz, Km 234, São Carlos, SP, Brazil.
authors.forename: Luciana C A
authors.initials: LC
authors.lastname: Regitano
mesh_terms: D000818:Animals; D001938:Brazil; D002417:Cattle / Q000235:genetics* / Q000254:growth & development*; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D058685:Genetic Pleiotropy; D005838:Genotype; D015810:Linkage Disequilibrium; D008297:Male; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D000069466:Red Meat; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors
keywords: AWM; GWAS; Genotyping; PCIT