Construction of Ultradense Linkage Maps with Lep-MAP2 : Stickleback F-2 Recombinant Crosses as an Example

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Rastas , P , Calboli , F C F , Guo , B , Shikano , T & Merilä , J 2016 , ' Construction of Ultradense Linkage Maps with Lep-MAP2 : Stickleback F-2 Recombinant Crosses as an Example ' , Genome Biology and Evolution , vol. 8 , no. 1 , pp. 78-93 . https://doi.org/10.1093/gbe/evv250

Title: Construction of Ultradense Linkage Maps with Lep-MAP2 : Stickleback F-2 Recombinant Crosses as an Example
Author: Rastas, Pasi; Calboli, Federico C. F.; Guo, Baocheng; Shikano, Takahito; Merilä, Juha
Contributor: University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
Date: 2016-01
Language: eng
Number of pages: 16
Belongs to series: Genome Biology and Evolution
ISSN: 1759-6653
URI: http://hdl.handle.net/10138/208083
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 identity 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 F-2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (similar to 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 (
Subject: linkage map
Lep-MAP2
Pungitius pungitius
RAD-tag
recombination
SNP
QUANTITATIVE TRAIT LOCI
SEX-DETERMINATION
PUNGITIUS-PUNGITIUS
GENETIC ARCHITECTURE
COMPARATIVE GENOMICS
THREESPINE STICKLEBACKS
NINESPINE STICKLEBACKS
GENOTYPING ERRORS
TELEOST FISHES
EVOLUTION
1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
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