A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination

G3 : Genes - Genomes - Genetics
Philine G D FeulnerOle Seehausen

Abstract

Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).

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Citations

May 12, 2019·GigaScience·Guilhem SempéréPierre Larmande
Jul 21, 2020·Molecular Ecology·Julian JunkerCatherine E Wagner
Aug 8, 2020·Ecology and Evolution·Anna F FellerOle Seehausen
Aug 17, 2018·Nature Reviews. Genetics·Walter Salzburger
Oct 14, 2020·Molecular Ecology·Karen L CarletonThomas D Kocher
Dec 8, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Wenjing TaoThomas D Kocher

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Datasets Mentioned

BETA
SRP136207

Methods Mentioned

BETA
sedation

Software Mentioned

FASTX Toolkit
Pundamilia
ALLMAPS
freebayes
Rqtl
JoinMap
GATK
Picard
UCSC Genome Browser LiftOver
UCSC liftOver

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