Format

Send to

Choose Destination
Genome Biol Evol. 2015 Dec 14;8(1):78-93. doi: 10.1093/gbe/evv250.

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example.

Author information

1
Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
2
Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland.
3
Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland juha.merila@helsinki.fi.

Abstract

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5-2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates.

KEYWORDS:

Lep-MAP2; Pungitius pungitius; RAD-tag; SNP; linkage map; recombination

PMID:
26668116
PMCID:
PMC4758246
DOI:
10.1093/gbe/evv250
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center