Additional file 2: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Correlation between recombination maps of four cattle breeds using the same sample size. The average correlations were calculated from 1000 repeatedly random samples. Each random sample has the same number of meioses across four cattle breeds. Correlations in males were presented in the top-right triangle and female correlations in the bottom-left. The Holstein data have been published previously [15] and are included for comparison purposes. (DOCX 14 kb

Summary of genome-wide marker and core region (CR) distribution in Chinese Holstein.

a<p>: the number of SNPs involved in core regions of each chromosome.</p

Additional file 1: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Eight breed- and sex-specific recombination maps for Holstein, Jersey, Brown Swiss, and Ayrshire in the two sexes. The columns are SNP name, chromosome number, base pair position, recombination rates between current and preceding SNPs in Holstein females, Holstein males, Jersey females, Jersey males, Brown Swiss females, Brown Swiss males, Ayrshire females, and Ayrshire males, respectively. The Holstein data have been published previously [15] and are included for comparison purposes. (RMAP 7191 kb

Distributions of candidate genes in whole genome.

<p>Distributions of candidate genes in whole genome.</p

Enriched pathway terms when comparing candidate genes to the whole genome using GeneMerge1.2.

<p>This table describes significant pathway terms over-represented in core regions based on GeneMerge1.2 software. Pop-frec describes the frequency of genes in the population with this pathway, and CR-frec describes the frequency of genes in the core regions with this pathway. Ratio is calculated by the comparison of a term within the core regions to that in genome wide. P value here is a Bonferroni corrected P value.</p

Genes within the core regions overlapping with those by genome wide association studies by Jiang et al (2010).

<p>This table describes genes that associated with milk production traits when compared with genome wide association studies, Hap Freq describes the frequency of core haplotype involved in each core region determined by Sweep across genome.</p

Numbers of CNVs identified by three programs and numbers of CNVs overlapped between different programs.

<p>Numbers of CNVs identified by three programs and numbers of CNVs overlapped between different programs.</p

Comparison between results of the current study and results from other studies.

a<p>: CNVRs on Chr Un and mitochondrial sequence are excluded;</p>b<p>: CNVRs on Chr Un are excluded.</p

Enriched GO terms when comparing candidate genes to the whole genome using GeneMerge1.2.

<p>This table describes second GO terms significantly enriched in core regions based on GeneMerge1.2 software. 36 terms are detected to be significant here. Pop-frec describes the frequency of genes in the population with this term, and CR-frec describes the frequency of genes in the core regions with this term. Ratio is calculated by the comparison of a term within the core regions to that in genome wide. P value here is a Bonferroni corrected P value.</p

Summary of whole genome extended haplotype homozygosity tests.

a<p>: Core haplotypes involved in each core region determined by Sweep across genome.</p