Barris W.,ACSIRO Livestock Industries |
Harrison B.E.,ACSIRO Livestock Industries |
McWilliam S.,ACSIRO Livestock Industries |
Bunch R.J.,ACSIRO Livestock Industries |
And 2 more authors.
Animal Production Science | Year: 2012
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. © 2012 CSIRO.
Fortes M.R.S.,ACSIRO Livestock Industries |
Fortes M.R.S.,University of Queensland |
Lehnert S.A.,ACSIRO Livestock Industries |
Bolormaa S.,Australian Department of Primary Industries and Fisheries |
And 6 more authors.
Animal Production Science | Year: 2012
Age at puberty is an important component of reproductive performance in beef cattle production systems. Brahman cattle are typically late-pubertal relative to Bos taurus cattle and so it is of economic relevance to select for early age at puberty. To assist selection and elucidate the genes underlying puberty, we performed a genome-wide association study (GWAS) using the BovineSNP50 chip (∼54000 polymorphisms) in Brahman bulls (n ≤ 1105) and heifers (n ≤ 843) and where the heifers were previously analysed in a different study. In a new attempt to generate unbiased estimates of single-nucleotide polymorphism (SNP) effects and proportion of variance explained by each SNP, the available data were halved on the basis of year and month of birth into a calibration and validation set. The traits that defined age at puberty were, in heifers, the age at which the first corpus luteum was detected (AGECL, h2 ≤ 0.56 0.11) and in bulls, the age at a scrotal circumference of 26 cm (AGE26, h2 ≤ 0.78 0.10). At puberty, heifers were on average older (751 142 days) than bulls (555 101 days), but AGECL and AGE26 were genetically correlated (r ≤ 0.20 0.10). There were 134 SNPs associated with AGECL and 146 SNPs associated with AGE26 (P 0.0001). From these SNPs, 32 (∼22%) were associated (P 0.0001) with both traits. These top 32 SNPs were all located on Chromosome BTA 14, between 21.95 Mb and 28.4 Mb. These results suggest that the genes located in that region of BTA 14 play a role in pubertal development in Brahman cattle. There are many annotated genes underlying this region of BTA 14 and these are the subject of current research. Further, we identified a region on Chromosome X where markers were associated (P 1.00E8) with AGE26, but not with AGECL. Information about specific genes and markers add value to our understanding of puberty and potentially contribute to genomic selection. Therefore, identifying these genes contributing to genetic variation in AGECL and AGE26 can assist with the selection for early onset of puberty. © 2012 CSIRO.