The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster

doi:10.1016/j.aquaculture.2022.739168

IOCAS-IR > 实验海洋生物学重点实验室

	The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster
	Zhang, Kexin 1,2,3; Li, Ao 1,4,5; Qi, Haigang 1,2,5; Yang, Qi 1,6; Du, Mingyang 1,2,3; Wang, Xuegang 1,4,5; Zhang, Ziyan 1,2,3; Wang, Chaogang 1,2,3; Wang, Wei 1,4,5; Zhang, Guofan 1,2,5; Li, Li 1,3,4,5,7
	2023-03-15
发表期刊	AQUACULTURE
ISSN	0044-8486
卷号	566 页码:10
通讯作者	Li, Li(lili@qdio.ac.cn)
摘要	The estuarine oyster (Crassostrea ariakensis), a species native to Asia, is widespread throughout the estuarine region along the northern and southern coasts of China and has important ecological and economic values. Owing to runoff dropping and environmental threats caused by climate change and anthropogenic influences, the natural resources of C. ariakensis have persistently declined. Therefore, breeding oysters with high adaptability, which requires efficient and accurate genotyping tools, is beneficial to restore the germplasm resources and aquaculture. However, targeted genotyping tools are poorly developed for this species and even in other aquatic species. Previously, we have detected some selective regions and genes associated with temperature and salinity adaptation using selection signature analysis and found that the upstream regulatory regions of the environment responsive genes exhibited higher differentiation. In this study, we developed a single nucleotide polymorphism (SNP) targeted genotyping tool for C. ariakensis, which includes 30 K SNPs located in previously identified target regions. The target genomic regions were enriched by hybridization capture using double-stranded DNA (dsDNA) biotin-labeled probes, and sequenced with high depth. A total of 24,541 (81.8%) high-quality SNPs were successfully genotyped in 655 samples. Compared to the genotypes obtained from previous genome-wide resequencing, 74.2% of the SNPs had a consistency rate of 1, with an average consistency rate for each sample of 97.8%. Population structure analysis showed three divergent populations (northern, southern, and middle) on the coast of China, consistent with those constructed using SNPs derived from whole-genome resequencing data. Most of the 30 K SNPs were located in the intergenic and regulatory regions, whereas 7% were located in the coding region. These high-quality SNPs were located in 953 genes, including 100 heat-response and 348 high salinity-responsive genes. Therefore, this panel can be used to evaluate the adaptive divergence between populations, and causative SNPs related to temperature and salinity adaptation in the linkage and association analysis, providing robust support for the molecular breeding of estuarine oyster. To the best of our knowledge, this study proposes the first high-throughput SNP-targeted genotyping tool for studying the genetic basis of environmental adaptation in oyster, and providing insights into the development of targeted SNP genotyping tools for the adaptation study in other aquatic species under climate changes.
关键词	Targeted genotyping SNPs Selective regions Temperature and salinity genes Environmental adaptation Crassostrea ariakensis
DOI	10.1016/j.aquaculture.2022.739168
收录类别	SCI
语种	英语
资助项目	Key Research and Development Program of Shandong[2022LZGC015] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA24030105] ; National Natural Science Foundation of China[32101353] ; Young Elite Sci-entists Sponsorship Program by China Association of Science andTechnology[2021QNRC001] ; Key Technology Research and Industrialization Demonstration Projects of Qingdao[22-3-3-hygg-2-hy] ; Modern Agroindustry Technology Research System[CARS-49]
WOS研究方向	Fisheries ; Marine & Freshwater Biology
WOS类目	Fisheries ; Marine & Freshwater Biology
WOS记录号	WOS:000916119800001
出版者	ELSEVIER
WOS关键词	NONNATIVE CRASSOSTREA-GIGAS ; ARIAKENSIS ; EVOLUTIONARY
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/183383
专题	实验海洋生物学重点实验室
通讯作者	Li, Li
作者单位	1.Chinese Acad Sci, Ctr Ocean Mega Sci, Inst Oceanol, CAS & Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 2.Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao 266237, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Pilot Natl Lab Marine Sci & Technol, Lab Marine Fisheries Sci & Food Prod Processes, Qingdao 266237, Peoples R China 5.Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Peoples R China 6.Qingdao Agr Univ, Coll Life Sci, Qingdao 266109, Peoples R China 7.Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Zhang, Kexin,Li, Ao,Qi, Haigang,et al. The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster[J]. AQUACULTURE,2023,566:10.
APA	Zhang, Kexin.,Li, Ao.,Qi, Haigang.,Yang, Qi.,Du, Mingyang.,...&Li, Li.(2023).The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster.AQUACULTURE,566,10.
MLA	Zhang, Kexin,et al."The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster".AQUACULTURE 566(2023):10.