Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
| Development of high throughput SNP genotyping approach using target sequencing in Pacific white shrimp and its application for genetic study | |
Yu, Yang1,2,4 ; Luo, Zheng1,5; Wang, Quanchao1,3,4; Zhang, Qian1,5; Zhang, Xiaojun1,2,4; Xiang, Jianhai1,2; Li, Fuhua1,2,4,6
| |
| 2020-11-15 | |
| 发表期刊 | AQUACULTURE
 |
| ISSN | 0044-8486 |
| 卷号 | 528页码:8 |
| 摘要 | The Pacific white shrimp Litopeneaus vannamei (L. vannamei) is a worldwide aquaculture species and selection of high performance germplasm is urgently needed. Application of molecular breeding method, such as marker assisted selection (MAS) or genomic selection (GS), is an efficient approach to accelerate the breeding program for high-quality germplasm. However, lack of cost-effective genotyping method is the main obstacle for their applications in shrimp breeding program. In this study, we developed a high throughput SNP genotyping method based on AmpliSeq target sequencing. A total of 581 amplicons including the genome-wide distributed markers, immune-related genes, WSSV resistance related SNPs, growth and sex related SNPs were selected and could be genotyped simultaneously. Totally 10 samples were used for genotyping and 2130 high quality SNPs were genotyped. Through analyzing the genotyped SNPs, the genetic relationship of samples could be accurately reconstructed. Besides, the pooling genotyping method using SNP panel was evaluated. It illustrated that the pooling genotyping method was reliable with read depth at 200. Based on the read depth of each amplicons, the panel was further optimized to 508 amplicons, which will enhance the sequencing uniformity and improve the efficiency of the panel. This study provided a useful genetic tool and a new method for genetic study. It will accelerate the application of MAS and GS in shrimp breeding program. |
| 关键词 | Molecular breeding Pooling genotyping Target sequencing SNP genotyping |
| DOI | 10.1016/j.aquaculture.2020.735549 |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助项目 | National Key R&D Program of China[2018YFD0900303]; National Key R&D Program of China[2018 YFD0901301]; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030105]; China Agriculture Research System-48 |
| WOS研究方向 | Fisheries ; Marine & Freshwater Biology |
| WOS类目 | Fisheries ; Marine & Freshwater Biology |
| WOS记录号 | WOS:000553684000026 |
| 出版者 | ELSEVIER |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 版本 | 出版稿 |
| 条目标识符 | http://ir.qdio.ac.cn/handle/337002/168103 |
| 专题 | 实验海洋生物学重点实验室 |
| 通讯作者 | Li, Fuhua |
| 作者单位 | 1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China 4.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao 266071, Peoples R China 5.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 6.Chinese Acad Sci, Innovat Seed Design, Wuhan, Peoples R China |
| 第一作者单位 | 实验海洋生物学重点实验室; 中国科学院海洋大科学研究中心 |
| 通讯作者单位 | 实验海洋生物学重点实验室; 中国科学院海洋大科学研究中心 |
| 推荐引用方式 GB/T 7714 | Yu, Yang,Luo, Zheng,Wang, Quanchao,et al. Development of high throughput SNP genotyping approach using target sequencing in Pacific white shrimp and its application for genetic study[J]. AQUACULTURE,2020,528:8. |
| APA | Yu, Yang.,Luo, Zheng.,Wang, Quanchao.,Zhang, Qian.,Zhang, Xiaojun.,...&Li, Fuhua.(2020).Development of high throughput SNP genotyping approach using target sequencing in Pacific white shrimp and its application for genetic study.AQUACULTURE,528,8. |
| MLA | Yu, Yang,et al."Development of high throughput SNP genotyping approach using target sequencing in Pacific white shrimp and its application for genetic study".AQUACULTURE 528(2020):8. |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Development of high （1378KB） | 期刊论文 | 作者接受稿 | 限制开放 | CC BY-NC-SA | 浏览 | |
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。
修改评论