Abstract
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.
Highlights
Large yellow croaker (Larimichthys crocea) has become an important aquaculture species in southeast China, where Mindong and Daiqu are the two major strains farmed
After filtering for segregation errors, minor allele frequency (MAF) and missing genotypes, a final set of 20,186 single nucleotide polymorphisms (SNPs) markers was used for linkage map construction
A consensus genetic linkage map for large yellow croaker was constructed with 20,147 SNPs from RAD sequencing, based on an F1 family from Mindong strain and Daiqu strain
Summary
Large yellow croaker (Larimichthys crocea) has become an important aquaculture species in southeast China, where Mindong and Daiqu are the two major strains farmed. In 2019, the total production of large yellow croaker exceeded 220,000 tons and accounted for more than 12% of the cultured marine fish production of China MAS can be useful for some traits where major QTLs have been identified, most traits of economic importance in aquaculture species (i.e., production traits) are assumed to be polygenic, and often have low-to-moderate heritabilities (Zenger et al, 2019). Application of MAS to improve these complex traits may be inefficient For such polygenic traits, genomic selection is a viable alternative, based on genomic breeding values predicted on a genome-wide scale, allowing even small QTLs to contribute (Meuwissen et al, 2001).
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