Abstract
Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.
Highlights
Large-scale loach (Paramisgurnus dabryanus; Cypriniformes; Cobitidae), which distributes naturally in East Asia, is a small bottom-dwelling freshwater fish species (Li et al, 2015)
A K-mer curve illustrated that the main peak appeared at the K-mer depth of 38 (Figure S1), and the genome size of P. dabryanus was estimated as 1.05 Gb with high heterozygosity (0.99%) and approximately 51.90% repeat sequences
The most significant quantitative trait loci (QTL) for almost all the traits related to growth, morphology, and sex were located on the same linkage groups (LGs) LG11 (Figure 5), and these QTLs explained a high percentage of phenotypic variance: from 10.4 to 27.4% (Table 3)
Summary
Large-scale loach (Paramisgurnus dabryanus; Cypriniformes; Cobitidae), which distributes naturally in East Asia, is a small bottom-dwelling freshwater fish species (Li et al, 2015). This species has a diploid chromosome number of 48 (Li, 1983; You et al, 2009), and the cytogenetic evidence and result of sex ratios generally confirmed that the sex determination in large-scale loach was determined by the putative ZZ/ZW system (Chang and Yu, 1997; You et al, 2008); so, it is a promising model for studying the mechanisms of ZW/ZZ sex determination system. The genetic linkage map and QTL mapping have become important MAS breeding tools, because of their abilities to identify molecular markers or candidate genes associated with traits (Sun et al, 2017; Feng et al, 2018)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
