Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker
<i>Larimichthys crocea</i> (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencin...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-07-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/14/7/1508 |
| _version_ | 1797589123452633088 |
|---|---|
| author | Kaifen Zhang Yongdong Zhou Weihua Song Lihua Jiang Xiaojun Yan |
| author_facet | Kaifen Zhang Yongdong Zhou Weihua Song Lihua Jiang Xiaojun Yan |
| author_sort | Kaifen Zhang |
| collection | DOAJ |
| description | <i>Larimichthys crocea</i> (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker. |
| first_indexed | 2024-03-11T01:02:54Z |
| format | Article |
| id | doaj.art-a7c83a5b6fa449b7b1d773febf4d3e40 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T01:02:54Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-a7c83a5b6fa449b7b1d773febf4d3e402023-11-18T19:31:33ZengMDPI AGGenes2073-44252023-07-01147150810.3390/genes14071508Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow CroakerKaifen Zhang0Yongdong Zhou1Weihua Song2Lihua Jiang3Xiaojun Yan4Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, ChinaZhejiang Marine Fisheries Research Institute, Zhoushan 316021, ChinaNational Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaNational Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, ChinaMarine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China<i>Larimichthys crocea</i> (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker.https://www.mdpi.com/2073-4425/14/7/1508<i>Larimichthys crocea</i>RAD-seqgenetic structureselective signalgenetic differentiation |
| spellingShingle | Kaifen Zhang Yongdong Zhou Weihua Song Lihua Jiang Xiaojun Yan Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker Genes <i>Larimichthys crocea</i> RAD-seq genetic structure selective signal genetic differentiation |
| title | Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker |
| title_full | Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker |
| title_fullStr | Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker |
| title_full_unstemmed | Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker |
| title_short | Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker |
| title_sort | genome wide radseq reveals genetic differentiation of wild and cultured populations of large yellow croaker |
| topic | <i>Larimichthys crocea</i> RAD-seq genetic structure selective signal genetic differentiation |
| url | https://www.mdpi.com/2073-4425/14/7/1508 |
| work_keys_str_mv | AT kaifenzhang genomewideradseqrevealsgeneticdifferentiationofwildandculturedpopulationsoflargeyellowcroaker AT yongdongzhou genomewideradseqrevealsgeneticdifferentiationofwildandculturedpopulationsoflargeyellowcroaker AT weihuasong genomewideradseqrevealsgeneticdifferentiationofwildandculturedpopulationsoflargeyellowcroaker AT lihuajiang genomewideradseqrevealsgeneticdifferentiationofwildandculturedpopulationsoflargeyellowcroaker AT xiaojunyan genomewideradseqrevealsgeneticdifferentiationofwildandculturedpopulationsoflargeyellowcroaker |