Abstract
BackgroundYellowtail (Seriola quinqueradiata) are an economically important species in Japan. However, there are currently no methods for captive breeding and early rearing for yellowtail. Thus, the commercial cultivation of this species is reliant upon the capture of wild immature fish. Given this, there is a need to develop captive breeding techniques to reduce pressure on wild stocks and facilitate the sustainable development of yellowtail aquaculture. We constructed a whole genome radiation hybrid (RH) panel for yellowtail gene mapping and developed a framework physical map using a nanofluidic dynamic array to use SNPs (single nucleotide polymorphisms) in ESTs (expressed sequence tags) for the DNA-assisted breeding of yellowtail.ResultsClonal RH cell lines were obtained after ionizing radiation; specifically, 78, 64, 129, 55, 42, and 53 clones were isolated after treatment with 3,000, 4,000, 5,000, 6,000, 8,000, or 10,000 rads, respectively. A total of 421 hybrid cell lines were obtained by fusion with mouse B78 cells. Ninety-four microsatellite markers used in the genetic linkage map were genotyped using the 421 hybrid cell lines. Based upon marker retention and genome coverage, we selected 93 hybrid cell lines to form an RH panel. Importantly, we performed the first genotyping of yellowtail markers in an RH panel using a nanofluidic dynamic array (Fluidigm, CA, USA). Then, 580 markers containing ESTs and SNPs were mapped in the first yellowtail RH map.ConclusionsWe successfully developed a yellowtail RH panel to facilitate the localization of markers. Using this, a framework RH map was constructed with 580 markers. This high-density physical map will serve as a useful tool for the identification of genes related to important breeding traits using genetic structural information, such as conserved synteny. Moreover, in a comparison of 30 sequences in the RH group 1 (SQ1), yellowtail appeared to be evolutionarily closer to medaka and the green-spotted pufferfish than to zebrafish. We suggest that synteny analysis may be potentially useful as a tool to investigate chromosomal evolution by comparison with model fish.
Highlights
Yellowtail (Seriola quinqueradiata) are an economically important species in Japan
Linkage maps were developed for several, commonly cultured species, including Atlantic salmon [3], Atlantic cod [4], common carp [5], and catfish [6]. These maps were created with microsatellite markers and gene-associated single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs)
The modal number of chromosomes was 48. This number is consistent with a previous report that noted the diploid chromosome number in yellowtail gill cells was 48 with a karyotype consisting of one pair of submetacentrics, one pair of subtelocentrics, and 22 pairs of acrocentrics [20]
Summary
Yellowtail (Seriola quinqueradiata) are an economically important species in Japan. there are currently no methods for captive breeding and early rearing for yellowtail. Linkage maps were developed for several, commonly cultured species, including Atlantic salmon [3], Atlantic cod [4], common carp [5], and catfish [6]. These maps were created with microsatellite markers and gene-associated single nucleotide polymorphisms (SNPs) derived from ESTs. SNPs, the most abundant type of DNA sequence polymorphism, are suitable for high-throughput genotyping and provide enhanced possibilities for genetic and breeding applications, linkage map development, assessment of genetic variability, and marker-assisted breeding.
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