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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
Source PublicationAQUACULTURE
ISSN0044-8486
Volume528Pages:8
AbstractThe 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.
KeywordMolecular breeding Pooling genotyping Target sequencing SNP genotyping
DOI10.1016/j.aquaculture.2020.735549
Indexed BySCI
Language英语
Funding ProjectNational 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 Research AreaFisheries ; Marine & Freshwater Biology
WOS SubjectFisheries ; Marine & Freshwater Biology
WOS IDWOS:000553684000026
PublisherELSEVIER
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Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/168103
Collection实验海洋生物学重点实验室
Corresponding AuthorLi, Fuhua
Affiliation1.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
First Author AffilicationKey Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences;  Center for Ocean Mega-Science, Chinese Academy of Sciences
Corresponding Author AffilicationKey Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences;  Center for Ocean Mega-Science, Chinese Academy of Sciences
Recommended Citation
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.
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