Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
|Alternative Title||Genetic analysis of shell color trait in the bay scallop Argopecten irradians|
|Place of Conferral||北京|
|Keyword||海湾扇贝 壳色 Snp分子标记 简化基因组 转录组|
以一个自交了11代的 “中科红”家系作为实验材料，在其贝壳成色前后两阶段分别取三个重复样，构建了六个（2×3重复）文库，利用Illumina HiSeq2500平台进行双端测序，得到了289,839,646 条reads和70,929个转录本。在SWISSPROT, NR和KOG数据库中比对，最终成功注释到30,896个基因。KEGG和GO 注释，富集到了许多与生物矿化和成色相关的基因。在差异表达分析中，我们发现了黑色素和微量金属元素等相关基因在海湾扇贝贝壳成色后显著上调表达。利用电感耦合等离子体原子发射光谱法（ICP-AES）对海湾扇贝橙色壳和白色壳棱柱层微量金属（Cu, Fe, Mn, Zn）含量进行测定，发现两种壳色的贝壳之间没有显著差异，据此猜测卟啉代谢等相关基因没有参与贝壳的成色过程，而黑色素的作用需进一步实验加以阐释。
|Other Abstract||Historically, bay scallop (Argopecten irradians) was widely distributed in the east coast of the United States and the Gulf of Mexico. In 1980s and 1990s, Argopecten irradians irradians and Argopecten irradians concentricus, both are subspecies of Argopecten irradians, were introduced to China. With the efforts of Chinese scientists from the Institute of Oceanology Chinese Academy of Sciences, bay scallop was cultivated as one of the most important sea products in China and have provoked a boom in mariculture. In order to ramp up production and improve the quality, Chinese researchers cultivated a new bay scallop strain named “Zhongkehong” with wonderful performance. “Zhongkehong” not only has improved survival, growth rate and meat yield, but also has pure orange shell color. In order to understand the genetic control and molecular mechanism of this orange shell color of A. irradians, this study was performed. We employed two main explore methods and one is streamlined restriction site-associated DNA genotyping for genic SNP identification and the other one was transcriptome sequencing for candidate genes associated with orange shell color. The main results were as follows:|
1. Streamlined restriction site-associated DNA genotyping for genic SNP identification
Three self-bred “zhongkehong” family, and three self-bred A. irradians with white shell color (both the lef and right shell) were set up. Genomic DNA from ten individuals of the F2 generation from each family was equally pooled and the restriction-site associated DNA sequencing approach, 2b-RAD, was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for all samples. We identified 14 SNPs associated to orange shell color of A. irradians. To obtain more gene sequences, these 2b-RAD tags were mapped to a genome survey of A. irradians and 9 unique 2b-RAD tags were left for a further verification test. In the verifying experiment, 50 individuals with orange shell color and 50 individuals with white shell color of A. irradians were randomly selected from a workshop’s population and SNP detection of every individual was performed using SNaPshot. The results indicated that five of the nine SNPs were highly associated to orange shell color of A. irradians.
2. Transcriptome sequencing for candidate genes
A selective variety, named as “zhongkehong”, characteristic of consistently orange-color shells were successfully obtained in 2006 and has been propagated for 11 generations in the bay scallop Argopecten irradians. In this study, samples were taken from this variety right before and after the appearance of orange shell color with 3 replications. A total of 6 Transcriptome libraries were used for pair-end sequencing. 289,839,646 paired-end reads were assembled into 70929 transcripts. Annotated against SWISSPROT, NR and KOG database using BLASTX and BLASTN, 30896 Unigenes were successfully annotated. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes classification identified numbers of unigenes involved in biomineralization and pigmentation. The digital gene expression analysis revealed that melanins and trace metal elements may be potentially involved in shell coloration of A. irradians. But the detection of trace metal of prismatic layer revealed no significant difference between orange shell and white shell. This result may eliminate the function of the trace metal in bay scallop shell pigmentation.
Key Words: Argopecten irradians, shell color, SNPs Marker, 2b-RAD, RNA-seq
|Subject Area||水产学 ; 水产学基础学科 ; 水产生物学|
|腾文. 海湾扇贝壳色性状遗传分析[D]. 北京. 中国科学院大学,2017.|
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|海湾扇贝壳色性状遗传分析.pdf（1583KB）||学位论文||开放获取||CC BY-NC-SA||Application Full Text|
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