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.

Figure 1

Proportions of Gene Ontology (GO) annotations of the assembled 454 mantle tissue transcripts from Litopenaeus vannamei.

Figure 2

Distribution of SNPs placed using linkage and LODE mapping methods across the 44 linkage groups.

Figure 3

Mean linkage disequilibrium (LD) estimates at different linkage map distances throughout the P. maxima genome for r ² and D′.

Figure 4

Homologous linkage map relationships between the integrated linkage and LODE L. vannamei map and the L. vannamei linkage map produced in Du, et al.. Each dot represents a homologous locus proportional to cM lengths (Kosambi).

Figure 5

Homologous linkage map relationships between the integrated linkage and LODE L. vannamei map and the L. vannamei linkage map produced in Yu, et al.. Each dot represents a homologous locus proportional to cM lengths (Kosambi). Data from Yu, et al. was utilised under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Figure 6

Homologous linkage map relationships between the integrated linkage and LODE L. vannamei map and the P. monodon linkage map produced in Baranski, et al.. Each dot represents a homologous locus proportional to cM lengths (Kosambi). Data from Baranski, et al. was utilised under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Figure 7

Demonstration of synteny analysis between LG4 of the integrated map, LG1 from Du, et al. and LG20 from Baranski, et al.. Only matched markers are listed. Data from Baranski, et al. was utilised under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).