Abstract
A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can also facilitate genome sequence assembly. Here, a high density genetic map of Asian seabass was constructed with 3321 SNPs generated by sequencing 144 individuals in a F2 family. The length of the map was 1577.67 cM with an average marker interval of 0.52 cM. A high level of genomic synteny among Asian seabass, European seabass, Nile tilapia and stickleback was detected. Using this map, one genome-wide significant and five suggestive QTL for growth traits were detected in six linkage groups (i.e. LG4, LG5, LG11, LG13, LG14 and LG15). These QTL explained 10.5–16.0% of phenotypic variance. A candidate gene, ACOX1 within the significant QTL on LG5 was identified. The gene was differentially expressed between fast- and slow-growing Asian seabass. The high-density SNP-based map provides an important tool for fine mapping QTL in molecular breeding and comparative genome analysis.
Highlights
A high-density genetic map is essential for comparative genomic studies and fine mapping of quantitative trait loci (QTL), and can facilitate genome sequence assembly
Using the data sets of the parental samples, a catalogue containing 101035 loci was constructed. This catalogue was used as reference for single nucleotide polymorphisms (SNP) discovery and genotyping in the mapping family using the program genotypes. 18262 SNP markers were identified across all the samples, within which, 3928 SNPs were genotyped in more than 80% of progenies
All these genotyped SNPs were used for linkage mapping
Summary
A high-density genetic map is essential for comparative genomic studies and fine mapping of QTL, and can facilitate genome sequence assembly. Various genetic resources have been developed in our group to facilitate the breeding program of this species, such as hundreds to thousands of microsatellite and SNP markers[15,18,19,20,21], linkage and physical maps[15,22,23] and cDNA and BAC libraries[24,25,26] Using these resources, we have conducted QTL mapping and association studies and identified several candidate loci and genes responsible for growth and production traits[15,27,28,29] and disease resistance[30,31]. The low density of markers in our previous linkage maps, in the QTL regions, limited the potential to fine map QTL for important traits and to search for the candidate genes
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