A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

Jan M De Boer,Taco Jesse,Richard Gf Visser,Glenn J Bryan,Herman J Van Eck,Theo Ja Borm,Bart Brugmans,Xiaomin Tang,Jaap Bakker

doi:10.1186/1471-2164-12-594

Abstract

BackgroundPotato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH).ResultsFirst, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map.ConclusionsThe AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.

Highlights

Potato is the world’s third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome
Presented here are the first two genome-wide BAC physical maps of potato, which come from the heterozygous diploid genotype RH89-039-16
These maps serve as an important resource and reference framework for current and future potato research

Summary

Introduction

Potato is the world’s third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The modern cultivated potato (Solanum tuberosum) is a heterozygous autotetraploid (2n = 4x = 48) with an estimated haploid genome size of 850 Mb [1] This polyploid genome configuration reduces the efficiency of potato breeding and makes potato genetics complicated [2]. The published physical maps of plant genomes have shown an evolution of BAC fingerprinting methods over the past decade: starting with agarose gel electrophoresis [11], this was followed by high-resolution sequencing gels [12], which was in turn superseded by multi-colour capillary electrophoresis [13] All of these fingerprint procedures have relied on restriction enzyme digestion of the BAC DNA. The principle of integrating AFLP marker anchoring with BAC AFLP fingerprinting for local physical map construction was reported under the name “KeyMaps” [22,23], but has so far not been applied to a genome-wide physical map

Methods

Results

Conclusion