Construction of bovine whole‐genome radiation hybrid and linkage maps using high‐throughput genotyping

S D Mckay,C Li,J Aerts,S S Moore,C P Van Tassell,L K Matukumalli,J F Taylor,J L Williams,P Stothard,C A Gill,Z Wang,C Gao,B M Murdoch,R D Schnabel

doi:10.1111/j.1365-2052.2006.01564.x

Abstract

High-density whole-genome maps are essential for ordering genes or markers and aid in the assembly of genome sequence. To increase the density of markers on the bovine radiation hybrid map, and hence contribute to the assembly of the bovine genome sequence, an Illumina® BeadStation was used to simultaneously type large numbers of markers on the Roslin-Cambridge 3000 rad bovine–hamster whole-genome radiation hybrid panel (WGRH3000). In five multiplex reactions, 6738 sequence tagged site (STS) markers were successfully typed on the WGRH3000 panel DNA. These STSs harboured SNPs that were developed as a result of the bovine genome sequencing initiative. Typically, the most time consuming and expensive part of creating high-density radiation hybrid (RH) maps is genotyping the markers on the RH panel with conventional approaches. Using the method described in this article, we have developed a high-density whole-genome RH map with 4690 loci and a linkage map with 2701 loci, with direct comparison to the bovine whole-genome sequence assembly (Btau_2.0) in a fraction of the time it would have taken with conventional typing and genotyping methods.

Highlights

Radiation hybrid (RH) mapping is a powerful tool that can be utilized for the production of in-depth comparative maps of single chromosomes and whole genomes
The accuracy of typing was confirmed by building the markers into radiation hybrid maps together with 1125 markers that had been conventionally typed on the RH panel
Of the 6738 loci included in the Illumina oligo pooled assays, 5815 (86.3%) were successfully typed and 4690 of the 5815 (80.7%) were assigned to the RH map

Summary

Introduction

Radiation hybrid (RH) mapping is a powerful tool that can be utilized for the production of in-depth comparative maps of single chromosomes and whole genomes. The construction of an RH map relies upon scoring the presence or absence of markers in a hybrid cell panel constructed by fusing irradiated donor cells with recipient rodent cells. Conventional methods for typing markers on RH panels rely on individual or low-complexity multiplex PCR assays for all typed markers on DNA derived from each of the cell lines in the panel, followed by agarose gel electrophoresis to detect the presence or absence of the marker in individual RH cell lines. The accuracy of typing was confirmed by building the markers into radiation hybrid maps together with 1125 markers that had been conventionally typed on the RH panel. With this high-throughput approach, 4690 loci were rapidly mapped. The resulting human–cattle comparative maps have direct comparison to the bovine whole genome sequence assembly (Btau_2.0)

Methods

Results

Discussion

Conclusion