Abstract
The black tiger shrimp, Penaeus monodon, is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.
Highlights
The black tiger shrimp, Penaeus monodon, is naturally distributed in the Indo-West Pacific region and is cultured in much of this region (Motoh, 1985)
At approximately 60 days, the growth traits, including carapace length (CL), body length (BL), body weight (BW), and sex were recorded according to previous descriptions (Motoh, 1985; Sun et al, 2015), and abdominal muscles from the two parents and offspring were preserved in 95% alcohol for genotyping
The sex-averaged consensus genetic map was constructed, and 6524 single nucleotide polymorphisms (SNPs) that were located on 2354 scaffolds (Supplementary Tables S2, S3) were assigned into 44 linkage groups (Figure 2 and Table 1), which contained 2208 unique loci
Summary
The black tiger shrimp, Penaeus monodon, is naturally distributed in the Indo-West Pacific region and is cultured in much of this region (Motoh, 1985). It is commercially important, both in capture fisheries and in aquaculture (Brackishwater Aquaculture Information System, 1988; FAO, 2018), and is the second-most widely cultured shrimp species only after Pacific white shrimp (FAO, 2018). Substantial efforts have been made to improve the quality of the breeding strains. The cultured strains still cannot meet the market needs, especially during severe disease outbreak and negative influences to aquaculture production expansion (Robinson et al, 2014; FAO, 2018). It is necessary to develop genome resources for breeding to achieve sustainable aquaculture
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