Abstract
BackgroundBoth growth and nutritional traits are important economic traits of Crassostrea gigas (C. gigas) in industry. But few work has been done to study the genetic architecture of nutritional traits of the oyster. In this study, we constructed a high-density genetic map of C. gigas to help assemble the genome sequence onto chromosomes, meanwhile explore the genetic basis for nutritional traits via quantitative trait loci (QTL) mapping.ResultsThe constructed genetic map contained 5024 evenly distributed markers, with an average marker interval of 0.68 cM, thus representing the densest genetic map produced for the oyster. According to the high collinearity between the consensus map and the oyster genome, 1574 scaffold (about 70%) of the genome sequence of C. gigas were successfully anchored to 10 linkage groups (LGs) of the consensus map. Using this high-qualified genetic map, we then conducted QTL analysis for growth and nutritional traits, the latter of which includes glycogen, amino acid (AA), and fatty acid (FA). Overall, 41 QTLs were detected for 17 traits. In addition, six candidate genes identified in the QTL interval showed significant correlation with the traits on transcriptional levels. These genes include growth-related genes AMY and BMP1, AA metabolism related genes PLSCR and GR, and FA metabolism regulation genes DYRK and ADAMTS.ConclusionUsing the constructed high-qualified linkage map, this study not only assembled nearly 70% of the oyster genome sequence onto chromosomes, but also identified valuable markers and candidate genes for growth and nutritional traits, especially for AA and FA that undergone few studies before. These findings will facilitate genome assembly and molecular breeding of important economic traits in C. gigas.
Highlights
Both growth and nutritional traits are important economic traits of Crassostrea gigas (C. gigas) in industry
Though nutritional traits of the oyster were reported to vary with the environment, like the season and sea area [16, 17], the oyster family cultured in the same environment exhibited great phenotype variation of the nutritional traits (Additional file 2, [18]), which indicated obvious genetic effect for nutritional traits
Considering the results from both quantitative trait loci (QTL) mapping and association analysis, we identified markers that were significantly correlated with the traits, and identified candidate genes around these markers utilising the reference genome and annotation file of C. gigas
Summary
Both growth and nutritional traits are important economic traits of Crassostrea gigas (C. gigas) in industry. Few work has been done to study the genetic architecture of nutritional traits of the oyster. The Pacific oyster, Crassostrea gigas (C. gigas) originated in Asia, and has become an important cultured mollusc in many countries as a result of its rapid growth rate and high yield [1, 2]. Growth and nutritional traits are associated with the oyster production and important indicators of oyster quality. Oysters are rich in glycogen, Li et al BMC Genomics (2018) 19:626 importance, breeding work has been performed to improve the quality of C. gigas. Though nutritional traits of the oyster were reported to vary with the environment, like the season and sea area [16, 17], the oyster family cultured in the same environment exhibited great phenotype variation of the nutritional traits (Additional file 2, [18]), which indicated obvious genetic effect for nutritional traits
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