Characterization and development of SSR markers of Pinctada maxima by RNA-Seq approach

Wang, Ziman; Li, Junhui; Hao, Ruijuan; Adzigbli, Linda; Deng, Yuewen

doi:10.1016/j.aqrep.2019.100230

Cited by 8 publications

(4 citation statements)

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“…The possible reason is that P. trituberculatus has more chromosomes (2n = 106) than shellfish, fish, and other crustaceans ( Liu et al, 2012 ), thus containing more SSR sequences. The average density of SSRs was 1/1.11 kb, which was higher than that in P. maxima (1/29.73 kb) ( Wang et al, 2019a ), sea cucumber ( Apostichopus japonicus ) (1/29.2 kb) ( Du et al, 2012 ), mandarin fish ( Siniperca chuatsi ) (1/26.28 kb) ( Sun et al, 2019 ), large-scale loach ( Paramisgurnus dabryanus ) (1/6.99 kb) ( Li et al, 2015a ), giant wrasse ( Cheilinus undulatus ) (1/5.35 kb) ( Liu et al, 2020 ), burbot ( Lota lota ) (1/4.25 kb) ( Meng et al, 2019 ), and the Bombay duck ( Harpadon nehereus ) (1/3 kb) ( Huang et al, 2021 ), while lower than that of the South African abalone ( Haliotis midae ) (1/0.756 kb) ( Franchini et al, 2011 ), tu-chung ( Eucommia ulmoides ) (1/0.73 kb) ( Huang et al, 2013 ). The differences between SSR frequency and density may be attributed to genome structure, SSR mining tools, dataset size, and search criteria ( Liu et al, 2021c ).…”

Section: Discussionmentioning

confidence: 65%

“…SSR markers acquired from RNA-seq have intrinsic advantages over genomic SSRs because of high efficiency, strong transferability, and correlation with potential genes, as well as their applicability as anchor markers for comparative mapping and evolutionary studies ( Zheng et al, 2014 ; Zhao et al, 2019 ). Transcriptomic SSRs have been extensively explored and applicated in various aquatic species, such as giant freshwater prawn ( Macrobrachium rosenbergii ) ( Jung et al, 2011 ; Yu et al, 2019 ), oriental river prawn ( Macrobrachium nipponense ) ( Ma et al, 2012 ), mud crab ( Scylla paramamosain ) ( Ma et al, 2014 ), Paphia textile ( Chen et al, 2016 ), Penaeus monodon ( Nguyen et al, 2016 ), and pearl oyster ( Pinctada maxima ) ( Wang et al, 2019a ). Transcriptomics have also played an important role in advancing portunid aquaculture ( Waiho et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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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.

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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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Section: Discussionmentioning

confidence: 65%

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.

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“…The Hardy-Weinberg equilibrium (HWE) tests for each locus were estimated by GENEPOP version 3.2 software (Raymond and Rousset 1995) with the Markov chain parameters. The frequencies of null allele were assessed using the software MICRO-CHECKER (Wang et al 2019). Genotype distributions between populations were inspected with the software GENEPOP 3.2 (Raymond and Rousset 1995).…”

Section: Discussionmentioning

confidence: 99%

Genetic structure of the Capoeta aculeata populations inferred from microsatellite DNA loci

Gandomkar

Shekarabi

Abdolhay³

et al. 2020

Biodiversitas

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Abstract. Gandomkar H, Shekarabi SPH, Abdolhay HA, Nazari S, Mehrjan MS. 2020. Genetic structure of the Capoeta aculeata populations inferred from microsatellite DNA loci. Biodiversitas 21: 4565-4570. The present study aimed to investigate the genetic variation of Capoeta aculeata on the basis of DNA microsatellite loci from three rivers (Beshar, Khersan, Maroun) in Kohgiluyeh and Boyer-Ahmad Province in Iran. DNA from fin clips of 120 specimens extracted and was examined with eight microsatellite markers. Genetic differences between the populations were discerned by pairwise comparison based on allelic distribution. The average number of alleles per locus ranged from 4 to 14, while the average observed heterozygosity (Ho) at various loci varied between 0.212 to 0.579, implying that a moderate level of genetic variation. Among three populations, Maroun River population displayed the highest level of variability in terms of heterozygosity. Tests of Hardy-Weinberg showed that the microsatellite loci deviated significantly in the populations. The results indicate that some of the populations were significantly differentiated from one another based on pairwise FST estimates. Genetic distance-based measures supported the clustering of Maroun, Beshar, and Khersan rivers. The neighbor-joining dendrogram topology constructed on the basis of genetic distances among populations supported observed division between the populations. The non-significant differentiation between C. aculeata samples from Beshar and Khersan can be explained by a relative disconnection of these two populations and/or small amounts of gene flow.

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“…Fortunately, due to the rapid advancements in sequencing technologies [13], highly polymorphic microsatellite markers have been developed for numerous aquaculture species, such as Pinctada fucata, pearl oyster (Pinctada maxima), and black amur bream (Megalobrama terminalis) [14][15][16]. Because of its high density, genome-wide distribution, and codominance, microsatellite has been widely used in the survey of genetic diversity and population structure [17,18].…”

Section: Introductionmentioning

confidence: 99%

Parentage Determination of Chinese Hooksnout Carp (Opsariichthys bidens) Based on Microsatellite DNA Markers

Ge,

Xu,

Ren

et al. 2024

Aquaculture Research

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In this study, a panel of 14 microsatellite markers was screened to determine the parentage of 144 progenies in 12 Chinese hooksnout carp (Opsariichthys bidens) full-sib families. The combined exclusion probabilities for 14 loci were 97.6% and 99.9%, respectively, when there was no available parent information or only one parent information was provided. Simulation analysis demonstrated that the power of five loci to exclude false parents exceeded 99.0%, while that of eight loci reached 99.9% based on allele frequency data obtained from full-sib families (168 individuals). Moreover, the cumulative assignment success rate reached 100% with known parental and filial information when utilizing 13 or more loci, even in cases where no parent information was available. The results showed that this set of microsatellite markers proved to be a reliable and efficient tool for parentage determination of O. bidens.

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Characterization and development of SSR markers of Pinctada maxima by RNA-Seq approach

Cited by 8 publications

References 38 publications

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

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

Genetic structure of the Capoeta aculeata populations inferred from microsatellite DNA loci

Parentage Determination of Chinese Hooksnout Carp (Opsariichthys bidens) Based on Microsatellite DNA Markers

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