Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F₂Recombinant Crosses as an Example

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.

A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

“…Alternatively, this pair of chromosomes might have experienced recurrent fusions in several basal vertebrate taxa. The patterns of conserved synteny in amphibians indicate that a relatively small number of fusions (perhaps none) occurred within the ancestral amphibian lineage, an interpretation that is consistent with the observation of chicken-like karyotypes within basal frog and salamander lineages (Sessions, 2008) and suggests that the relatively compact karyotypes of Xenopus (1N = 10) and newt (1N = 11) are largely the product of convergent evolution.…”

“…Similar to X. tropicalis , the Mexican axolotl ( Ambystoma mexicanum ) and Eastern newt ( Notophthalmus viridescens ) possess karyotypes consisting of relatively small numbers of macrochromosomes and no microchromosomes (1N = 14 and 11, respectively) (Humphrey, 1975; Hutchison and Pardue, 1975; Voss et al, 2011). These patterns suggest the ancestral amphibian karyotype consisted of a large number of chromosomes with two distinct morphologies, both macro- and microchromosomes, with more compact karyotypes representing derived states (Morescalchi et al, 1973; Morescalchi et al, 1974; Sessions, 2008). …”

“…Caecilian karyotypes vary from asymmetric-bimodal karyotypes with higher numbers of chromosomes to symmetric-unimodal karyotypes with fewer chromosomes (Nussbaum and Wilkinson, 1989; Sessions, 2008). Among amphibians, several basal lineages possess karyotypes characterized by the presence of both micro- and macrochromosomes (e.g.…”

The genetic and molecular architecture of phenotypic diversity in sticklebacks

“…One important technique that has now been widely used in evolutionary genomic studies, restriction site-associated DNA sequencing (RAD-seq), was developed using stickleback as one of the test cases [15,16]. Using such next-generation sequencing approaches to create high-density genetic linkage maps has further improved the initial genome assembly in threespine stickleback [17,18] and enabled comparison of the threespine and ninespine stickleback genomes [19]. Finally, transgenic tools have been adapted for use in sticklebacks [20 -22].…”

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

“…linkage map was constructed using Lep-MAP246, a software suite handling thousands of markers and multiple families. All the four full-sib families were used as input, and SNPs showing significant segregation distortion with P-value < 0.01 and a minor allele frequency MAF < 0.05 were excluded.…”