A first genetic linage map construction and QTL mapping for growth traits in Larimichthys polyactis

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.

Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.

Construction of Genetic Linkage Maps From a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F₁ family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.