Construction of high-resolution recombination maps in Asian seabass

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

“…This fact is the main responsible for the length difference between male and female maps of turbot, as reported previously in other fish species 58 , 66–68 . It is tempting to ascribe the different RF between males and females observed in fish 19 , 66 to different crossing-over patterns around heterochromatic blocks. However, other explanations have been proposed for different species, such as the GC content in Asian sea bass 19 ; stronger selection pressure in male gametes during the haploid life stage in zebrafish 66 or in some plants 69 ; and differences in chromatin distribution between sexes as for example in humans 70 .…”

“…It is tempting to ascribe the different RF between males and females observed in fish 19 , 66 to different crossing-over patterns around heterochromatic blocks. However, other explanations have been proposed for different species, such as the GC content in Asian sea bass 19 ; stronger selection pressure in male gametes during the haploid life stage in zebrafish 66 or in some plants 69 ; and differences in chromatin distribution between sexes as for example in humans 70 . More information is needed for a comprehensive explanation to these observations, and indeed, NGS technologies can provide suitable data for this task.…”

“…Genetic maps of bony fish reported to date have been based on a few families, 19 , 38 , 58 and thus, the presence of inter-individual rearrangements affecting marker order has been scarcely addressed. Previous information showed that, despite a general macrosyntenic 1:1 pattern in Acanthopterygii 38 and specifically in Pleuronectiformes, a huge intrachromosomal reorganisation (mainly inversions) has taken place along flatfish evolution 9 , 34 .…”

“…These maps have allowed the identification of genomic regions associated with productive traits 20 , 21 or with adaptation to specific environments 14 , 16 . The pattern of samples and families used in fish for map construction has been quite similar, and only very recently, the number of families has increased 19 , 22 . However, when many families have been analysed, the number of offspring per family has been much smaller (e.g.…”

Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine Medaka Oryzias melastigma

“…Furthermore, it provides a framework for mapping the chromosomal location of single-gene traits and quantitative traits of interest, and helps to facilitate candidate gene cloning, and comparative genomic analysis with some genome information together (Lee et al 2005; Amores et al 2011; Feng et al 2015; Zhu et al 2013; Li et al 2015; Shao et al 2015; Wang et al 2015; Xiao et al 2015; Kanamori et al 2016). A high-density genetic map also plays an important role in assembling whole genome sequences by examining the accuracy of de novo genome assembly (Dukic et al 2016; Rhee et al 2017; Wang et al 2017). Indeed, the importance of a high-density genetic map has been demonstrated during de novo genome assembly in teleost fish, as it was discovered that an additional genome duplication event had occurred (Meyer et al 1999; Meyer et al 2005; Volff, 2005).…”