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Duan B, Kang T, Wan H, Liu W, Zhang F, Mu S, Guan Y, Li Z, Tian Y, Kang X. Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China. Sci Rep 2023; 13:8668. [PMID: 37248314 DOI: 10.1038/s41598-023-35902-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023] Open
Abstract
The swimming crab, Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity of P. trituberculatus in the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420 P. trituberculatus individuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI = 1.374, He = 0.687, and PIC = 0.643) in comparison with wild populations (SI ≥ 1.399, He ≥ 0.692, and PIC ≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations of P. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups of P. trituberculatus were divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.
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Affiliation(s)
- Baohua Duan
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Tongxu Kang
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Haifu Wan
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Weibiao Liu
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Fenghao Zhang
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Yueqiang Guan
- College of Life Sciences, Hebei University, Baoding, 071000, China
| | - Zejian Li
- Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, 061100, China
| | - Yang Tian
- Hebei Fishery Technology Extension Station, Shijiazhuang, 050000, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, 071000, China.
- Institute of Life Science and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Province Innovation Center for Bioengineering and Biotechnology, Baoding, 071000, China.
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Zhang S, Xu Z, Luo L, Gu S, Hu Z, Wan S, Gao Z. Genetic Diversity and Population Structure of Coilia nasus Revealed by 2b-RAD Sequencing. BIOLOGY 2023; 12:biology12040600. [PMID: 37106800 PMCID: PMC10135584 DOI: 10.3390/biology12040600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Coilia nasus is a threatened migratory species in the Yangtze River Basin. To reveal the genetic diversity of natural and farmed populations of C. nasus and the status of germplasm resources in the Yangtze River, the genetic diversity and structure of two wild populations (Yezhi Lake: YZ; Poyang Lake: PY) and two farmed populations (Zhenjiang: ZJ; Wuhan: WH) of C. nasus were analyzed using 44,718 SNPs obtained via 2b-RAD sequencing. The results indicate that both the wild and farmed populations had low genetic diversity, and germplasm resources have undergone varying degrees of degradation. Population genetic structure analyses indicated that the four populations may have come from two ancestral groups. Different amounts of gene flow were identified among WH, ZJ, and PY populations, but gene flow among YZ and other populations was low. It is speculated that the river-lake isolation of Yezhi Lake is the main cause of this phenomenon. In conclusion, this study revealed that genetic diversity reduction and germplasm resource degradation had occurred in both wild and farmed C. nasus, suggesting that conservation of its resources is of great urgency. This study provides a theoretical basis for the conservation and rational exploitation of germplasm resources for C. nasus.
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Affiliation(s)
- Shuangmeng Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zisheng Xu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lifei Luo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shuxin Gu
- Zhenjiang Jiangzhiyuan Fishery Technology Co., Ltd., Zhenjiang 212213, China
| | - Zhen Hu
- Hubei Provincial Aquatic Technology Promotion Station, Wuhan 430060, China
| | - Shiming Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zexia Gao
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Duan B, Mu S, Guan Y, Liu W, Kang T, Cheng Y, Li Z, Tian Y, Kang X. Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus). Front Genet 2022; 13:932173. [PMID: 35923702 PMCID: PMC9340201 DOI: 10.3389/fgene.2022.932173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise FST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.
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Affiliation(s)
- Baohua Duan
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yueqiang Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Weibiao Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Tongxu Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yana Cheng
- College of Life Sciences, Hebei University, Baoding, China
| | - Zejian Li
- Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, China
| | - Yang Tian
- Hebei Fishery Technology Extension Station, Shijiazhuang, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
- Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
- *Correspondence: Xianjiang Kang,
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Wang Q, Liu Y, Wang Y, Jiang S, Zhang C, Li B. GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:32-39. [PMID: 34812992 DOI: 10.1007/s10126-021-10084-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Mesocentrotus nudus is an economically important mariculture species. Identification of sex-related markers and candidate genes has potential implications for sex-control breeding of Mesocentrotus nudus. The aim of this study was to identify the molecular markers and genes associated with the sex of M. nudus. Initial GWAS analysis based on 80 individuals genotyped by using GBS identified 22 sex-related SNPs located on 9 GBS tags. Further targeted sequencing in another population of 124 individuals confirmed that 7 SNPs located on 7 GBS tags displayed complete associations with sex, suggesting a ZW/ZZ sex-determination system in M. nudus. Besides, genome and transcriptome annotations presented that the heat shock protein 75 kDa, mitochondrial (trap1), and protein furry homolog-like (fryl) may be important candidate genes involved in sex determination and differentiation in M. nudus. However, further studies are needed to elucidate the functions of these genes. Overall, the current results not only provide molecular markers that may contribute to the sex-control breeding for M. nudus, but also provide new insights to understand the regulatory mechanism of sea urchin sex.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaoyu Jiang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanxin Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Baoquan Li
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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