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.

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

“…Our linkage analysis successfully identified all 73 linkage groups. The linkage map provides high resolution, and the average recombination rate across all linkage groups in E. sinensis is 3.09 cM Mb − 1 , which is much higher than those reported in many other animals, such as mouse (0.5 cM Mb − 1 ), catfish (1.65 cM Mb − 1 ), zebrafish (1.35 cM Mb − 1 ), scallop (1.3 cM Mb − 1 ) and shrimp (1.9 cM Mb − 1 ) (Shimoda et al, 1999;Jensen-Seaman et al, 2004;Kucuktas et al, 2009;Huang et al, 2011;Baranski et al, 2014;Jiao et al, 2014). This suggests that QTLs, if identified, can be narrowed down to quite small genomic region in E. sinensis.…”

A first generation microsatellite-based linkage map of the Chinese mitten crab Eriocheir sinensis and its application in quantitative trait loci (QTL) detection

“…In penaeid shrimps, phenotypic sex has been mapped to a linkage group on the female map (Li et al, 2003;Zhang et al, 2007), suggesting a sex determination system consistent with female heterogamety (ZW) and male homogamety (ZZ). However, the female:male recombination ratios are 1.60:1 in the black tiger shrimp P. monodon (Baranski et al, 2014), 1.28:1 in the white shrimp L. vannamei (Pérez et al, 2004) and 1.23:1 in the Chinese shrimp F. chinensis (Li et al, 2006b), with an exception of 0.55:1 in the kuruma prawn P. japonicas (Li et al, 2003). Our study shows that the estimated genome lengths (G oa ) of the female (2430.9 cM) were close to the male (2658.4 cM), indicating that the recombination rate (0.91:1) does not differ between sexes (i.e., no heterochiasmy) in the mitten crab.…”

“…In fish and shellfish, most linkage maps were developed exclusively using SSR and/or SNP markers (Guyomard et al, 2006;Liu et al, 2013;Sanetra et al, 2009;Song et al, 2012a). Unfortunately, because of a lack of enough SSRs, fully SSR-based linkage maps have not yet been developed in crabs and shrimps, with the exception of a recently reported SNPbased map of the black tiger shrimp Penaeus monodon (Baranski et al, 2014). In our previous study, by taking advantage of the Solexa genomic survey, approximately 15,000 candidate SSR markers were isolated from mitten crabs, and those markers are suitable for construction of a linkage map (Xiong et al, 2012a).…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Genetic linkage maps were constructed also for some other species important for aquaculture, as gilthead sea bream, Sparus aurata (Tsigenopoulos et al, 2014); Asian seabass, Lates calcarifer Sun et al, 2017); mandarin fish, Siniperca chuatsi ; turbot, Scophthalmus maximus (Wang et al, 2015b); Japanese flounder, Paralichthys olivaceus (Castaño-Sánchez et al, 2010;Shao et al, 2015); large yellow croaker, Larimichthys crocea (Ao et al, 2015); black tiger shrimp, Penaeus monodon (Baranski et al, 2014); Pacific white shrimp, L. annamei (Du et al, 2010); Pacific abalone, Haliotis discus hannai (Qi et al, 2010); South African abalone, Haliotis midae (Vervalle et al, 2013) and silver-lipped pearl oyster, Pinctada maxima (Jones et al, 2013). Linkage maps of commercial fish and shellfish have been listed in other review papers (Wenne et al, 2007;Yue, 2014;Abdelrahman et al, 2017).…”