Journal: Nature genetics

Article Title: Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks.

doi: 10.1038/ng.3775

Figure Lengend Snippet: Figure 4 Introgression of a novel and complex mutation at the POLLED locus from bovines causes polledness in Mongolian yaks. (a) Mapping of the POLLED locus with Illumina BovineHD BeadChip genotyping data from 36 polled and 40 horned animals. Polledness is modeled as a quantitative trait. The x axis shows genomic positions, and the y axis presents significance measured using the likelihood-ratio test (LRT) statistic. (b) Bovine introgression plot for the first 20 Mb of chromosome 1 based on WGS data. Orange and turquoise dots show the mean frequency of bovine and yak alleles at positions of yak-specific variants in a 70-kb sliding window. The background of each interval is shaded according to read depth, the mean number of reads per 70-kb window, ranging from 0 (dark gray) to >40 (white). Introgressed intervals are identified by a break in the red line (circular binary segmentation of mean allele frequency) and a drop of yak allele frequency below 0.5. Note that YAK13 is homozygous for a bovine introgressed segment encompassing the mapping interval of the POLLED locus (P = 9.7 × 10−9; 95% CI = 1.88–2.20 Mb). This result is independently supported by a reduction in the divergence of the YAK13 genome sequence from the UMD3.1 bovine reference sequence in the POLLED region (0.28%) between positions 1,809,313 and 2,627,891 bp as compared with the average divergence of 1.08% exhibited by both yaks at the genome level. (c) Schematic presenting the nature and location of the three different mutations identified at the POLLED locus in the bovine allele as compared with the wild-type allele. The region displayed ranges from 1,690,000 bp to 2,090,000 bp on chromosome 1 (indicated by dashed lines in b). Red boxes represent segments that are duplicated in the Celtic, Friesian and Mongolian alleles, whereas light and dark gray boxes represent the original segments. Note that none of the three POLLED mutations affect coding regions and that the molecular mechanism underlying polledness remains unknown at the present time. (d) Details of the complex POLLED Mongolian mutation that results in duplication of an 11-bp motif that is entirely conserved among Bovidae and well conserved among vertebrates (Supplementary Figs. 10–13). The region displayed ranges from 1,975,420 bp to 1,976,530 bp on chromosome 1 (indicated by dashed lines in c). Boxes of different color are used to represent segmental duplications.

Article Snippet: For a systematic analysis of cattle introgression in the Mongolian yak population, we investigated Illumina BovineHD BeadChip genotyping data (~777,000 SNPs) for 76 animals originating from different localities (Supplementary Table 1).

Techniques: Mutagenesis, Sequencing