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

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.

SUBMITTER: Yu X

PROVIDER: S-EPMC8762270 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND: Chemosensory receptors, which are all G-protein-coupled receptors (GPCRs), come in four types: odorant receptors (ORs), vomeronasal receptors, trace-amine associated receptors and formyl peptide receptor-like proteins. The ORs are the most important receptors for detecting a wide range of environmental chemicals in daily life. Most fish OR genes have been identified from genome databases following the completion of the genome sequencing projects of many fishes. However, it remains unclear whether these OR genes from the genome databases are actually expressed in the fish olfactory epithelium. Thus, it is necessary to clone the OR mRNAs directly from the olfactory epithelium and to examine their expression status. RESULTS: Eighty-nine full-length and 22 partial OR cDNA sequences were isolated from the olfactory epithelium of the large yellow croaker, Larimichthys crocea. Bayesian phylogenetic analysis classified the vertebrate OR genes into two types, with several clades within each type, and showed that the L. crocea OR genes of each type are more closely related to those of fugu, pufferfish and stickleback than they are to those of medaka, zebrafish and frog. The reconciled tree showed 178 duplications and 129 losses. The evolutionary relationships among OR genes in these fishes accords with their evolutionary history. The fish OR genes have experienced functional divergence, and the different clades of OR genes have evolved different functions. The result of real-time PCR shows that different clades of ORs have distinct expression levels. CONCLUSION: We have shown about 100 OR genes to be expressed in the olfactory epithelial tissues of L. crocea. The OR genes of modern fishes duplicated from their common ancestor, and were expanded over evolutionary time. The OR genes of L. crocea are closely related to those of fugu, pufferfish and stickleback, which is consistent with its evolutionary position. The different expression levels of OR genes of large yellow croaker may suggest varying roles of ORs in olfactory function.

Dataset Information

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

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