Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei

doi:10.1016/j.aquaculture.2024.741375

IOCAS-IR > 实验海洋生物学重点实验室

	Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei
	Yang, Junqing 1,2; Yu, Yang2 ; Zhou, Yizhou 1; Bao, Zhenning 2,3; Liu, Yichen 1; Sun, Jinsheng 1; Li, Fuhua 2,4
	2025-01-15
发表期刊	AQUACULTURE
ISSN	0044-8486
卷号	594 页码:9
通讯作者	Yu, Yang([email protected]) ; Liu, Yichen([email protected])
摘要	Litopenaeus vannamei is one of the most economically productive species in aquaculture. It accounts for about 80% of the world's mariculture production of shrimp. Genetic selection of shrimp is mainly based on family selection. Therefore, accurate pedigree information is essential to ensure the reliability of estimated genetic parameters and the selection of the best broodstock. Recent advances in molecular breeding have facilitated molecular pedigree reconstruction based on SNPs and improved the accuracy of selection. However, breeding populations of aquatic species tend to be large. Therefore, a high-throughput and cost-effective method was needed for the commercial application of parentage assignment. In this study, we developed a low-density SNP panel based on target sequencing. A total of 200 amplicons, evenly distributed across the genome, were captured by multiplex PCR and sequenced by next-generation sequencing. Genotyping of 320 individuals in four ponds including multiple families identified 1,169 SNPs. Based on these SNPs, two softwares including Sequoia and PaternityT were used to reconstruct the sibling information. Consequently, a total of 39 families were accurately identified, and the results of the two software programs were highly consistent. Analysis based on different numbers of amplicons showed that at least 50 amplicons were required for accurate assignment. The identification result was also validated by principal component analysis and phylogenetic analysis. With the development of NGS technology, thousands of individuals could be genotyped with high throughput and low cost, making the method developed in this study affordable for parentage assignment in commercial breeding program. Meanwhile, the low-density SNP panel also has high value and prospects for application in shrimp genetic research.
关键词	Pedigree reconstruction Target sequencing SNP panel Litopeneaus vannamei
DOI	10.1016/j.aquaculture.2024.741375
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2022YFD2400203]; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030105]; Key Research and Development Program of Shandong[2021LZGC029]; Earmarked fund[CARS-48]; Taishan Scholars Program
WOS研究方向	Fisheries ; Marine & Freshwater Biology
WOS类目	Fisheries ; Marine & Freshwater Biology
WOS记录号	WOS:001286044300001
出版者	ELSEVIER
WOS关键词	SINGLE-NUCLEOTIDE POLYMORPHISMS ; PARENTAGE ASSIGNMENT ; TRACEABILITY ; VALIDATION ; SNPS ; MICROSATELLITES ; INFERENCES ; FAMILIES ; DESIGN ; PANELS
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/197672
专题	实验海洋生物学重点实验室
通讯作者	Yu, Yang; Liu, Yichen
作者单位	1.Tianjin Normal Univ, Coll Life Sci, Tianjin Key Lab Anim & Plant Resistance, Tianjin 300387, Peoples R China 2.Chinese Acad Sci, Inst Oceanol, CAS & Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Innovat Seed Design, Wuhan 430072, Peoples R China
推荐引用方式 GB/T 7714	Yang, Junqing,Yu, Yang,Zhou, Yizhou,et al. Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei[J]. AQUACULTURE,2025,594:9.
APA	Yang, Junqing.,Yu, Yang.,Zhou, Yizhou.,Bao, Zhenning.,Liu, Yichen.,...&Li, Fuhua.(2025).Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei.AQUACULTURE,594,9.
MLA	Yang, Junqing,et al."Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei".AQUACULTURE 594(2025):9.