A Validated Whole-Genome Association Study of Efficient Food Conversion in Cattle

Barendse, W.; Reverter, Antônio; Bunch, R. J.; Harrison, B. E.; Barris, Wesley C.; Thomas, Morgane

doi:10.1534/genetics.107.072637

Cited by 177 publications

(191 citation statements)

References 61 publications

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“…In beef cattle, some studies (Barendse et al, 2007;Nkrumah et al, 2007;) have reported associations between markers and RFI. For instance, Barendse et al (2007), using a commercial SNP chip containing approximately 10,000 (10K) SNP, analyzed 8,786 polymorphic SNP in 189 Australian beef cattle, chosen on the basis of being phenotypically high and low for RFI, and they detected 161 SNP associated with RFI at P < 0.01. Development of a commercial 50,000 (50K) SNP chip provided the opportunity to conduct a more powerful genomewide association study (GWAS) for RFI.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association studies for feedlot and growth traits in cattle1

Bolormaa

Hayes²,

Savin

et al. 2011

Journal of Animal Science

150

116

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ABSTRACT:A genome wide-association study for production traits in cattle was carried out using genotype data from the 10K Affymetrix (Santa Clara, CA) and the 50K Illumina (San Diego, CA) SNP chips. The results for residual feed intake (RFI), BW, and hip height in 3 beef breed types (Bos indicus, Bos taurus, and B. indicus × B. taurus), and for stature in dairy cattle, are presented. The aims were to discover SNP associated with all traits studied, but especially RFI, and further to test the consistency of SNP effects across different cattle populations and breed types. The data were analyzed within data sets and within breed types by using a mixed model and fitting 1 SNP at a time. In each case, the number of significant SNP was more than expected by chance alone. A total of 75 SNP from the reference population with 50K chip data were significant (P < 0.001) for RFI, with a false discovery rate of 68%. These 75 SNP were mapped on 24 different BTA. Of the 75 SNP, the 9 most significant SNP were detected on BTA 3, 5, 7, and 8, with P ≤ 6.0 × 10 −5 . In a population of Angus cattle divergently selected for high and low RFI and 10K chip data, 111 SNP were significantly (P < 0.001) associated with RFI, with a false discovery rate of 7%. Approximately 103 of these SNP were therefore likely to represent true positives. Because of the small number of SNP common to both the 10K and 50K SNP chips, only 27 SNP were significantly (P < 0.05) associated with RFI in the 2 populations. However, other chromosome regions were found that contained SNP significantly associated with RFI in both data sets, although no SNP within the region showed a consistent effect on RFI. The SNP effects were consistent between data sets only when estimated within the same breed type.

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Section: Introductionmentioning

confidence: 99%

Genome-wide association studies for feedlot and growth traits in cattle1

Bolormaa

Hayes²,

Savin

et al. 2011

Journal of Animal Science

150

116

View full text Add to dashboard Cite

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“…A direct result of the bovine genome sequencing has been the construction of arrays consisting of tens of thousands of SNP that can be genotyped in parallel (Matukumalli et al 2009; The Bovine HapMap Consortium 2009), which could be used for the practical purpose of identifying quantitative trait loci (Geldermann 1975;Barendse et al 2007) as well as of implementing genomic selection (Goddard and Hayes 2007). Other usages include the estimation of pairwise relatedness between individuals in the absence of pedigree data (Oliehoek et al 2006;Lee et al 2010) and high resolution studies of breed relationships and diversity (Pritchard et al 2000;Patterson et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

et al. 2012

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Abstract. We sequenced the genomes of a Brahman, an Africander and a Tuli bull because tropically adapted breeds of cattle have so far not been well characterised at the level of DNA variation. In excess of 16 Gb of Illumina GA-II sequence was obtained for each animal in the form of 75-bp paired-end reads, generating more than 6· coverage of each genome, and between 86.7 and 88.8% of the bases of each genome sequence was covered by one or more sequence reads. A total of 6.35 million single nucleotide polymorphisms (SNP) were discovered in the three animals, adding 3.56 million new SNP to dbSNP. The Brahman animal had nearly twice as many SNP as either the Tuli or the Africander. Comparing genome sequence to genotypic array data, genotype accuracy from sequencing was more than 98% for homozygotes that had at least six high quality sequence reads and for heterozygotes that had at least two high quality reads containing the alternative allele. Intergenic and intronic SNP were found at higher densities closer to coding sequences, and there was a reduction in numbers of SNP within 5 bp of a splice site, features consistent with genetic selection. On average, slightly more SNP per Mb, and slightly higher average reads per SNP per Mb, were found towards the ends of chromosomes, especially towards the telomeric end of the chromosome. At least one autosome in each animal showed a large stretch of homozygosity, the largest was 58 Mb long in the Tuli, although the animals are not known to have recent inbreeding.

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“…This assertion has been recently confirmed by two molecular studies in which allele substitution effects at several SNP loci distributed across the bovine genome were shown to be associated with RFI and FCR in B. taurus cattle (Barendse et al, 2007;Sherman et al, 2008).…”

Section: Snp Validation In Candidate Bovine Imprinted Genesmentioning

confidence: 64%

A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits

Magee

Berkowicz

Sikora

et al. 2010

Animal

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Genetic (or 'genomic') imprinting, a feature of approximately 100 mammalian genes, results in monoallelic expression from one of the two parentally inherited chromosomes. To date, most studies have been directed on imprinted genes in murine or human models; however, there is burgeoning interest in the effects of imprinted genes in domestic livestock species. In particular, attention has focused on imprinted genes that influence foetal growth and development and that are associated with several economically important production traits in cattle, sheep and pigs. We have re-sequenced regions in 20 candidate bovine imprinted genes in order to validate single nucleotide polymorphisms (SNPs) that may influence important production traits in cattle. Putative SNPs detected via re-sequencing were subsequently re-formatted for high-throughput SNP genotyping in 185 cattle samples comprising 138 performance-tested European Bos taurus (all Limousin bulls), 29 African B. taurus and 18 Indian B. indicus samples. Analysis of the resulting genotypic data identified 117 validated SNPs. Preliminary genotype-phenotype association analyses using 83 SNPs that were polymorphic in the Limousin samples with minor allele frequencies >0.05 revealed significant associations between two candidate bovine imprinted genes and a range of important beef production traits: average daily gain, average feed intake, live weight, feed conversion ratio, residual feed intake and residual gain. These genes were the Ras proteinspecific guanine nucleotide releasing factor gene ( RASGRF1) and the zinc finger, imprinted 2 gene ( ZIM2). Despite the relatively small sample size used in these analyses, the observed associations with production traits are supported by the purported biological function of the RASGRF1 and ZIM2 gene products. These results support the hypothesis that imprinted genes contribute significantly to important complex production traits in cattle. Furthermore, these SNPs may be usefully incorporated into future marker-assisted and genomic selection breeding schemes.

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A Validated Whole-Genome Association Study of Efficient Food Conversion in Cattle

Cited by 177 publications

References 61 publications

Genome-wide association studies for feedlot and growth traits in cattle1

Genome-wide association studies for feedlot and growth traits in cattle1

Next generation sequencing of African and Indicine cattle to identify single nucleotide polymorphisms

A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits

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