Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic with Human Muscular Dystrophy

Figure 2

Haplotypes of the marbling region. Polymorphic markers define conserved extended C19 ancestral haplotypes: This region on BTAchr19 is bounded by markers SREBF1 and FASN (see [56] for details). The FASN marker is more correctly known as SCT-FSN since the present marker is adjacent to the coding region for FASN, within the segmental duplication containing SECTM1. The map positions of PCR markers and the number and type of alleles at each locus are indicated including the main high frequency and largely breed-specific haplotypes extending from SREBF1 to TCAP. We have extended the haplotyping through the region and plan to develop more markers based on the potential polymorphism revealed by the structural duplications extending from 43 Mb to 52 Mb (figure and below). Note the regions where PCR product polymorphism was not detected [56]. In structural duplications in C19 35-55 Mb region, we used the current cow genome assembly (Bos_tauros_UMD_3.1.1/bostau8 Assembly) on the UCSC Web Browser and searched the chr19 region from 35 Mb to 55 Mb in 500 kb sectors for large structural segmental duplications using standard dot-plotting methods aligning each 500 kb sector against itself (Gepard 1.30) [63]. We found clusters of rolling, sometimes clustered and inverted, segmental duplications in the reference genome on chr19 at 43.51 Mb (~60 kb in length), 43.86 Mb (~90 kb), 48.86 (~57 kb), and 50.846 Mb (~300 kb). We also found a long single imperfect duplication of 103–112 kb at 52.73 Mb and 52.88 Mb. Some of these dot plots are shown as cutaways in the figure. This region has a relatively low density of protein coding genes.