A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei

Abstract

The Pacific whiteleg shrimp, Litopenaeus vannamei, is the most farmed aquaculture species worldwide with global production exceeding 3 million tonnes annually. Litopenaeus vannamei has been the focus of many selective breeding programs aiming to improve growth and disease resistance. However, these have been based primarily on phenotypic measurements and omit potential gains by integrating genetic selection into existing breeding programs. Such integration of genetic information has been hindered by the limited available genomic resources, background genetic parameters and knowledge on the genetic architecture of commercial traits for L. vannamei. This study describes the development of a comprehensive set of genomic gene-based resources including the identification and validation of 234,452 putative single nucleotide polymorphisms in-silico, of which 8,967 high value SNPs were incorporated into a commercially available Illumina Infinium ShrimpLD-24 v1.0 genotyping array. A framework genetic linkage map was constructed and combined with locus ordering by disequilibrium methodology to generate an integrated genetic map containing 4,817 SNPs, which spanned a total of 4552.5 cM and covered an estimated 98.12% of the genome. These gene-based genomic resources will not only be valuable for identifying regions underlying important L. vannamei traits, but also as a foundational resource in comparative and genome assembly activities.

The Challenge of Genome Sequence Assembly

“…Khatkar et al, [41] and Jones et al, [42] employ the LODE (Locus Ordering by Linkage Disequilibrium) algorithm to position 'orphan' SNPs within genetic linkage map scaffolds. This approach has been shown to improve assembly by locally increasing marker coverage and therefore aiding the positioning of shorter sequence contigs.…”

“…The method is also useful for validating the quality of an assembly by testing the strength of evidence for the positions of SNPs already located in the assembly. Jones et al, [42] applied this approach to develop an integrated linkage and LD map of the Pacific White Shrimp (Litopenaeus vannamei). A linkage scaffold and LD data from 75 individuals was used as the basis to position several hundred SNPs within the scaffold.…”

De novoassembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

“…Modern genomic technologies have significant potential to advance selective breeding programs; however, they require complete, well annotated tissue-specific transcriptomic and genomic datasets. In addition to assisting in genome assembly and creating linkage maps 3 , a complete transcriptome provides a potential resource for differential gene-expression studies 4 ), genome annotation 5 , single nucleotide polymorphism discovery 6 and genome scaffolding 7 .…”

“…Previous research has focussed on hepatopancreas, ovary, heart, muscle and eyestalk tissues 8,9 , in male and female gonads 10 , and in response to infection with Vibrio bacterial species capable of inducing acute hepatopancreatic necrosis disease 11 . In addition to such differential gene-expression studies, genomic data from next generation sequencing (NGS) methods has expanded greatly in recent years, particularly in the study of Pacific white shrimp ( Litopenaeus vannamei ) 3,6,12–23 . Moreover, a transcriptome based on eight tissues was assembled for the less well studied banana shrimp Fenneropenaeus merguiensis 24 , and genes involved in early embryonic specification have been studied in Marsupenaeus japonicus 25 .…”

Genetic mapping in polyploids

“…The disadvantages of targeted approaches have been well explored (particularly regarding ascertainment bias, where the set of targeted SNPs on an array poorly represents the diversity in the samples under investigation due to biased methods of SNP discovery) (Albrechtsen et al, 2010;Moragues et al, 2010;Didion et al, 2012;Lachance and Tishkoff, 2013), although there are advantages and disadvantages to both methods (Mason et al, 2017). Apart from costs, differences exist in the ease of data analysis following genotyping, with sequencing data requiring greater curation and bioinformatics skills (Spindel et al, 2013;Bajgain et al, 2016) as well as potentially containing more erroneous and missing data (Spindel et al, 2013;Jones et al, 2017). In polyploids, SNP arrays have been developed in numerous species, which include both autopolyploid (or predominantly polysomic polyploids) and allopolyploid species.…”