Genetic diversity and population structure of the swimming crab (Portunus trituberculatus) in China seas determined by genotyping-by-sequencing (GBS)

Duan, Bing; Mu, Shumei; Guan, Yueqiang; Li, Shuqin; Yu, Yue; Liu, Weibiao; Li, Zejian; Ji, Xindong; Kang, Xianjiang

doi:10.1016/j.aquaculture.2022.738233

Cited by 22 publications

(7 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In terms of expected heterozygosity, this study showed lower genetic diversity of P. trituberculatus in the Bohai Sea ( He = 0.725) than that in the Yellow Sea 47 ( He = 0.814) and the East China Sea 55 ( He = 0.916), which was consistent with the results revealed by SNP markers 14 . It has been shown that when conducting genetic diversity analysis on aquatic animals, the number of SSR loci should be greater than 20 and the sample size should be greater than 45 56 .…”

Section: Discussionsupporting

confidence: 89%

“…To formulate an effective conservation strategy, it is necessary to evaluate the genetic diversity and population structure of P. trituberculatus . In our previous study, SNP markers determined by genotyping-by-sequencing (GBS) revealed a low level of genetic diversity in P. trituberculatus along the coastal waters of China 14 . To evaluate the impact of the massive releases on natural populations, the researchers monitored the temporal variations in genetic diversity and structure in Panjin and Yingkou using microsatellite markers, which suggested that the large-scale stock enhancement of P. trituberculatus presented potential genetic risks to wild populations 15 , 16 .…”

mentioning

confidence: 99%

See 1 more Smart Citation

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Duan

Kang

Wan

et al. 2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 89%

mentioning

confidence: 99%

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Duan

Kang

Wan

et al. 2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…Currently, the development of SSR markers using transcriptome sequences has been further extended and has The populations represented by each cluster number are: 1: Huzhu, 2: Tongde, 3: Maqin, 4: Datong, 5: Menyuan, 6: Qilian, 7: Bama, 8: Huangyuan, 9: Minhe, 10: Guinan. Frontiers in Genetics frontiersin.org been widely used in population genetics, the construction of genetic linkage maps, and analysis of genetic relationships between germplasm and marker-assisted selection breeding (Gong, et al, 2016;Tulsani, et al, 2020;Tian, et al, 2021;Duan, et al, 2022a), RNA-Seq has become an effective method for analyzing transcriptome data. SSR markers have also been developed and applied by Chinese sea buckthorn RNA-seq by previous authors.…”

Section: Discussionmentioning

confidence: 99%

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Liu,

Ye,

2024

Front. Genet.

View full text Add to dashboard Cite

Hippophae rhamnoides subsp. sinensis Rousi is a cold- and drought-tolerant pioneer species with significant economic and ecological value. Evaluating its genetic diversity and population structure is of great importance for guiding the development and utilization of resources. In this study, a total of 41,804 SSRs were generated by transcriptome sequencing of Hippophae rhamnoides subsp. sinensis Rousi. Among the different SSR motif types, mononucleotide repeats (26,972) were the most abundant, followed by trinucleotides, tetranucleotides, and pentanucleotides. 200 pairs of SSR primers were selected to detect polymorphisms, of which 15 pairs primers were selected as validated polymorphic SSRs used for genetic diversity and population structure analysis. A total of 63 alleles were identified with 15 pairs primers, with Nei’s genetic diversity index ranged from 0.27 to 0.83 (average: 0.54), and the expected heterozygosity ranged from 0.16 to 0.73 (average: 0.46). The polymorphism information content ranged from 0.23 to 0.81 (average: 0.48). Genetic structure analyses showed that the 10 populations could be broadly categorized into two groups. AMOVA denoted that genetic variations primarily originated from within the populations, with minimal differences observed between the groups, accounting for only 7% of the total genetic variation. This implies that mutation in H. rhamnoides subsp. sinensis Rousi mainly occurred within the populations. The results showed that the 10 populations of H. rhamnoides subsp. sinensis Rousi are rich in genetic diversity, with low levels of population differentiation and a high degree of gene exchange, which should be taken into consideration for the future work of germplasm resource preservation and seedling breeding.

show abstract

“…Benefitting from the rapid advance of high-throughput sequencing and genotyping technologies, an increasing number of molecular markers are developed and applied to genetic analyses in aquatic species. To date, molecular markers including isozyme ( Fan et al, 2009 ), random amplified polymorphic DNA (RAPD) ( Chi et al, 2010 ), amplified fragments length polymorphism (AFLP) ( Liu et al, 2013 ; Liu et al, 2014 ), mitochondrial DNA ( Guo et al, 2012 ; Shan et al, 2017 ; Hui et al, 2018 ), microsatellites DNA ( Lee et al, 2013 ; Yue et al, 2022 ), and single nucleotide polymorphism (SNP) ( Duan et al, 2022a ) were developed and used in population genetic analysis of P. trituberculatus . Among these markers, microsatellite DNA markers (simple sequence repeats, SSRs) have become an ideal molecular marker in population genetics research because of their co-dominant inheritance, high polymorphism, reproducibility, hyper-variable, transferability, random distribution in the genome, and ease of analysis via PCR ( Gou et al, 2020 ; Pavan Kumara et al, 2020 ; Zhu et al, 2021 ; Lu et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Duan

Guan

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

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.

show abstract

Genetic diversity and population structure of the swimming crab (Portunus trituberculatus) in China seas determined by genotyping-by-sequencing (GBS)

Cited by 22 publications

References 71 publications

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

Contact Info

Product

Resources

About