The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster
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 ant...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/181291 2023-11-12T04:16:18+01:00 The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster Zhang, Kexin Li, Ao Qi, Haigang Yang, Qi Du, Mingyang Wang, Xuegang Zhang, Ziyan Wang, Chaogang Wang, Wei Zhang, Guofan Li, Li 2023-03-15 http://ir.qdio.ac.cn/handle/337002/181291 https://doi.org/10.1016/j.aquaculture.2022.739168 英语 eng ELSEVIER AQUACULTURE http://ir.qdio.ac.cn/handle/337002/181291 doi:10.1016/j.aquaculture.2022.739168 Targeted genotyping SNPs Selective regions Temperature and salinity genes Environmental adaptation Crassostrea ariakensis Fisheries Marine & Freshwater Biology NONNATIVE CRASSOSTREA-GIGAS ARIAKENSIS EVOLUTIONARY 期刊论文 2023 ftchinacasciocas https://doi.org/10.1016/j.aquaculture.2022.739168 2023-10-15T16:07:14Z 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 ... Report Crassostrea gigas Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Aquaculture 566 739168 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
Targeted genotyping SNPs Selective regions Temperature and salinity genes Environmental adaptation Crassostrea ariakensis Fisheries Marine & Freshwater Biology NONNATIVE CRASSOSTREA-GIGAS ARIAKENSIS EVOLUTIONARY |
spellingShingle |
Targeted genotyping SNPs Selective regions Temperature and salinity genes Environmental adaptation Crassostrea ariakensis Fisheries Marine & Freshwater Biology NONNATIVE CRASSOSTREA-GIGAS ARIAKENSIS EVOLUTIONARY Zhang, Kexin Li, Ao Qi, Haigang Yang, Qi Du, Mingyang Wang, Xuegang Zhang, Ziyan Wang, Chaogang Wang, Wei Zhang, Guofan Li, Li The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
topic_facet |
Targeted genotyping SNPs Selective regions Temperature and salinity genes Environmental adaptation Crassostrea ariakensis Fisheries Marine & Freshwater Biology NONNATIVE CRASSOSTREA-GIGAS ARIAKENSIS EVOLUTIONARY |
description |
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 ... |
format |
Report |
author |
Zhang, Kexin Li, Ao Qi, Haigang Yang, Qi Du, Mingyang Wang, Xuegang Zhang, Ziyan Wang, Chaogang Wang, Wei Zhang, Guofan Li, Li |
author_facet |
Zhang, Kexin Li, Ao Qi, Haigang Yang, Qi Du, Mingyang Wang, Xuegang Zhang, Ziyan Wang, Chaogang Wang, Wei Zhang, Guofan Li, Li |
author_sort |
Zhang, Kexin |
title |
The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
title_short |
The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
title_full |
The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
title_fullStr |
The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
title_full_unstemmed |
The development of a 30 K SNP genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
title_sort |
development of a 30 k snp genotyping tool targeting genomic regions of temperature and salinity adaptation in estuarine oyster |
publisher |
ELSEVIER |
publishDate |
2023 |
url |
http://ir.qdio.ac.cn/handle/337002/181291 https://doi.org/10.1016/j.aquaculture.2022.739168 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
AQUACULTURE http://ir.qdio.ac.cn/handle/337002/181291 doi:10.1016/j.aquaculture.2022.739168 |
op_doi |
https://doi.org/10.1016/j.aquaculture.2022.739168 |
container_title |
Aquaculture |
container_volume |
566 |
container_start_page |
739168 |
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1782333436542844928 |