Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps
Open Access
- 1 November 2013
- journal article
- Published by Oxford University Press (OUP) in G3 Genes|Genomes|Genetics
- Vol. 3 (11), 2031-2047
- https://doi.org/10.1534/g3.113.007153
Abstract
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.This publication has 45 references indexed in Scilit:
- A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid PotatoPLOS ONE, 2013
- The tomato genome sequence provides insights into fleshy fruit evolutionNature, 2012
- A resistance gene against potato late blight originating from Solanum × michoacanum maps to potato chromosome VIITheoretical and Applied Genetics, 2011
- Genome sequence and analysis of the tuber crop potatoNature, 2011
- Assembly algorithms for next-generation sequencing dataGenomics, 2010
- Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technologyChromosome Research, 2009
- Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classificationProceedings of the National Academy of Sciences of the United States of America, 2007
- The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaNature, 2007
- The map-based sequence of the rice genomeNature, 2005
- Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver stainingPlant Molecular Biology Reporter, 2001