Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

Polina L Perelman,Samantha A Brooks,Rudolf Pichler,Fahad Alshanbari,Pamela A Burger,Denis M Larkin,Heather M Holl,Terje Raudsepp,Kathiravan Periasamy,Anna Gaggl

doi:10.1038/s41598-018-20223-5

Abstract

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.

Highlights

Current genomic resources available for camelids include a comparative chromosome map of the dromedary with humans, cattle and pigs[7], a whole genome cytogenetic map of the alpaca[8,9,10], and genome assemblies at the scaffold level[11,12,13]
We describe the construction and validation of radiation hybrid panels for the dromedary, a useful genomic resource for studies in camelids
Among the 186 radiation hybrids, seven (3.8%) had a mean RF less than 10%, 17 (9.1%) had a mean RF ranging from 10–20%, 124 (66.7%) had a mean RF ranging from 20–70%, while 38 (20.4%) had a mean RF greater than 70%

Summary

Introduction

Current genomic resources available for camelids include a comparative chromosome map of the dromedary with humans, cattle and pigs[7], a whole genome cytogenetic map of the alpaca[8,9,10], and genome assemblies at the scaffold level[11,12,13]. Mapping resources and/or chromosome level assemblies available for camelid genomes. Availability of mapping resources will open up the opportunities for whole genome scans to identify selection signatures, perform linkage analysis, genome-wide association studies, comparative evolutionary genomics and development of genomic tools for breeding and improvement of camels. It has been shown that a combination of RH panels with different levels of resolution produces superior maps[14,15]. We describe the construction and validation of radiation hybrid panels for the dromedary, a useful genomic resource for studies in camelids

Methods

Results

Conclusion