The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs

Abstract

Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i) four landing centres around the east coastline (EC) of India, (ii) survivors of a severe WSSV infection during pond culture (SUR) and (iii) the Andaman Islands (AI) in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. De novo transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp) with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16-129 and 13-130 markers, of length between 139-10.8 and 109.1-10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively) with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits.

Figure 1. Proportion of gene ontology terms related to (A) process, (B) function and (C) category, for transcripts containing linkage mapped SNPs.

Figure 2. Map of the P. monodon mitochondrial genome.

The inner ring shows the location of mitochondrial genes, t-RNA and the control region. The position of assembled contigs are represented by shaded patches in the four concentric rings out from the inner ring (labelled contig IDs) and SNP positions are marked by lines in the outer ring. A double line dividing the top of the outer ring marks the start position for the P. monodon mitochondrial DNA sequence.

Figure 3. Map showing areas from which P. monodon were sampled.

AI, CH, TU and VI represent catch areas covered by landing centres in the Andaman Islands, Chennai, Tuticorin and Vishakhapatnam respectively. BA represents the Bapatla location where shrimp that survived a severe WSSV infection were sampled. Approximate degrees of latitude and longitude are shown.