Abstract
BackgroundNelore 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.ResultsOur 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s12864-016-2535-3) contains supplementary material, which is available to authorized users.
Highlights
Nelore is the major beef cattle breed in Brazil with more than 130 million heads
Genetic profile of Brazilian Nelore beef cattle After quality control filters we retained genotypes of 449,203 single nucleotide polymorphism (SNP) for linkage disequilibrium and haplotype block analysis, and 224,969 TagSNPs from 780 Nelore animals, including 34 prominent sires and their 746 progeny (Table 1). These genotypes were coupled with genotypes of the same SNP for a sample of 46 Brahman, Hereford and 44 Angus cattle sourced from the Bovine HapMap project [17, 18], and used to calculate a genomic relationship matrix (GRM) that was used in a principal component analysis (PCA) [19]
We suggest that this effect is due to the randomness diversity of the genetic effect of the dams that would bring more related individuals to the center of the figure, indicating that these sires are less related to its half-sib families and even less related to the bulk of more related individuals in the center
Summary
Nelore is the major beef cattle breed in Brazil with more than 130 million heads. 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. Several years later, starting in 1930 but mainly in 1960 and 1962, a Bos indicus cattle breed named Nelore was introduced in Brazil from India and the herd expanded to the majority of the territory due to its good adaptability to tropical climate. With the advent of the Illumina BovineHD BeadChip (Illumina Inc., San Diego, CA), a high density SNP panel comprising over 770,000 markers, we were able to measure the genomic diversity of the Brazilian Nelore from the main commercial sire families and characterize their genomic relationship and genetic profiles across a series of phenotypes. It is known that Nelore breed show moderate heritability for meat quality [7] as well as for growth-related traits [8], which make the application of genomic tools feasible
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