Abstract
BackgroundHigh-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.ResultsIn the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8–15.7% of the total growth-traits variation.ConclusionsThe genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.
Highlights
High-resolution genetic linkage map is critical for quantitative trait loci (QTL) mapping, genome sequence assembly and marker-assisted selection in aquaculture species
Genome survey of E. carinicauda We constructed six 270 bp DNA libraries with short paired-end and sequenced them by Illumina Hiseq 4000 platform. 294.46 Gb high-quality reads with 40.01% GC content were obtained in total after sequencing, which covered approximately 31.57-fold the genome size of E. carinicauda
The genome size of E. carinicauda was estimated as 9.33 Gb with remarkably low heterozygosity (0.26%), which were possessed by approximately 76.62% repeat sequences (Table 1)
Summary
High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. The ridgetail white prawn Exopalaemon carinicauda is an important economic shrimp species naturally distributed in the coasts of eastern China and western Korea [1]. Li et al BMC Genomics (2019) 20:598 based on selection of individuals on phenotypic values. Implementation of MAS requires DNA markers that are tightly linked to quantitative trait loci (QTL) for economic traits based on genetic linkage maps [5]. MAS approaches is urgently required for sustainable development in culture of E. carinicauda
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