Abstract
BackgroundA high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits.ResultsBy making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation.ConclusionsWe mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.
Highlights
A high-density genetic linkage map is essential for quantitative trait locus (QTL) fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species
Characteristics of several phenotypic traits The mapping family in this study consisted of 200 P. vachelli progeny and their phenotypic growth (e.g., W, total length (TL), head length (HL), body length (BL)/HL, body height (BH), BL, body width (BW)/ED, BL/Snout length (SL)) and hypoxia tolerance-related traits were in concordance with the normal distribution (Kolmogorov-Smirnov test, asymptotic significance > 0.05; Table S1)
With regards to the growth-related traits, BL/HL, condition factor (CF), Eye distance (BW/ED), Eye diameter (BH/ED), and BL/SL were related to body type proportions and W, BL, HL, TL, BW, BH, caudal peduncle length (CL), and caudal peduncle height (CH) were directly related to weight, with these eight traits showing a strong correlation with each other (r = 0.593– 0.967, P < 0.001 for all) (Table 1)
Summary
A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Developed genotyping methods, such as reduced-representation sequencing, SNP arrays, and re-sequencing, have allowed for the discovery and simultaneous scoring of thousands of SNP markers from a single sequencing run for dozens of individuals. These techniques have already been applied in some fish species, such as Ictalurus punctatus [2], Siniperca chuatsi [3], Scophthalmus maximus [4], Paralichthys olivaceus [5], and Megalobrama amblycephala [6]. MAS using QTL analysis is the most effective breeding method for many animals and plant species and it is a direct choice for genotyping the control trait loci
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