Construction of high-resolution recombination maps in Asian seabass

Le Wang,Bin Bai,Zi Yi Wan,Shu Qing Huang,Peng Liu,Baoqing Ye,Elaine Chua,Gen Hua Yue

doi:10.1186/s12864-016-3462-z

Abstract

BackgroundA high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing.ResultsA high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males.ConclusionsThese high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass.

Highlights

A high-density genetic map is essential for de novo genome assembly, fine mapping Quantitative trait locus (QTL) for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution
A high-density genetic map is essential for facilitating genome assembly and examining the accuracy of de novo genome assembly [1]
De novo genome assembly achieved using massively parallel short read sequencing is not perfectly precise due to genome complexity resulting from ancestral vertebrate genome duplications (2R), gene duplications, and occurrences of transposable elements [2, 3]

Summary

Introduction

A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. A high-density genetic map is essential for facilitating genome assembly and examining the accuracy of de novo genome assembly [1]. A robust high-density genetic map is considered as indispensable for studies in the genomic era. Recombination interrupts linkage and allows more effective selection on multiple loci so as to generate complex phenotypic traits [9, 15]. Due to the importance in genetic studies, highdensity genetic maps have been constructed in a few economically important teleosts [18], e.g., Atlantic salmon [19,20,21], Coho salmon [22], channel catfish [23] and Japanese flounder [24], European sea bass [25], Nile tilapia [26], rainbow trout [27] and lake whitefish [28]

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