Abstract
BackgroundScatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits.ResultsUsing restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8–19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration.ConclusionsThe first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.
Highlights
High-quality fish breed is the primary prerequisite for large-scale commercial culture
The highest correlation coefficient value was observed between body length (BL) and total length (TL) (r = 0.993), followed by that between body height (BH) and BL (r = 0.906), while the weakest correlation occurred between predorsal length (PD) and BH (r = 0.540)
A high-density genetic linkage map with 6193 single nucleotide polymorphism (SNP) derived from ddRADseq data was constructed for S. argus with an average marker interval of 0.35 cM
Summary
High-quality fish breed (strain) is the primary prerequisite for large-scale commercial culture. In many cultured economic aquatic animals, substantial improvement has been achieved using conventional selective breeding approaches. For genetic improvement of quantitative traits, conventional breeding strategies such as family and individual selection mainly rely on the phenotype and pedigree information [3], whereas the underlying genes showing minor effects usually bring in unwanted nondeterminacy. As a fertile area of research on genetic breeding, QTL mapping based on genotypic data has become an important technique to facilitate the investigations on quantitative traits, and can lay an effective way to understand potential location information and numbers of linked markers for beneficial target traits [5]. It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. A high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits
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