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Investigating the Genetic Bases of Growth Regulation by E2F3 in Dwarf Surf Clams Mulinia lateralis

Journal of Ocean University of China 2024年第5期23卷 1347-1358页

作者： YAO Ruixing WANG Chen KONG Lingling WANG Yujue bao zhenmin HU Xiaoli MOE Key Laboratory of Marine Genetics and Breeding College of Marine Life Sciences Ocean University of China Laboratory for Marine Fisheries Science and Food Production Processes Qingdao Marine Science and TechnologyCenter Key Laboratory of Tropical Aquatic Germplasm of Hainan Province Sanya Oceanographic Institution Ocean University of China

Bivalve aquaculture plays a crucial role in the aquaculture industry due to the economic value of many bivalve species. Understanding the underlying genetic basis of bivalve growth regulation is essential for enhancing germplasm innovation and ensuring sustainable development of the industry. Though numerous candidate genes have been identified, their functional validation remains challenging. Fortunately, the dwarf surf clam(Mulinia lateralis) serves as a promising model organism for investigating genetic mechanisms underlying growth regulation in bivalves. The GWAS study in the Yesso scallop(Patinopecten yessoensis) has pinpointed the E2F3 gene as a key regulator of growth-related traits. However, the specific role of E2F3 in bivalve growth remains unclear. This study aimed to further confirm the regulatory function of the E2F3 gene in the dwarf surf clam through RNA interference experiments. Our results revealed several genes are associated with individual growth and development, including CTS7, HSP70B2, and PGLYRP3, as well as genes involved in lipid metabolism such as FABP2 and FASN. Functional enrichment analysis indicated that E2F3 primarily modulates critical processes like amino acid and lipid metabolism. These findings suggest that E2F3 likely regulates growth in the dwarf surf clam by influencing amino acid and lipid metabolism. Overall, this study advances our understanding on the function of E2F3 gene in growth regulation in bivalves, providing valuable insights for future research in this field.

关键词： bivalve dwarf surf clam Mulinia lateralis E2F3 growth regulation RNA interference experiment transcriptomic analysis

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Genetic diversity and specific markers in four scallop species, Patinopecten yessoensis, Argopecten irradians, Chlamys nobilis and ***

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Acta Oceanologica Sinica 2005年第4期24卷 107-113页

作者： CHEN Shengping bao zhenmin PAN Jie HU Jingjie College of Marine Life Sciences Ocean University of China Qingdao 266003 China College of Life Sciences Sun Yat-sen University Guangzhou 510275 China

The AFLP （amplified fragrnent length polymorphism）technique was used to analyse the genetic diversity in four scallop species, Patinopecten yessoensis, A rgopecten irradians, Chlamys nobilis and C. farreri. The genetic similarity indexes of these four species are 0.8415, 0.7863, 0.7190 and 0.6731, while Shannon diversity indexes are 43.52, 58.87, 80.16 and 92.83, respectively. As analyzed, the genetic diversities in two native species, i.e., C, farreri and C. nobilis, are higher than those in other two introduced species, A. irradians and P. yessoensis. The results also showed that C. nobilis and C, farreri shared the most common loci. The genetic distance indicated that C. nobilis and C. farreri are closely related. Moreover, out of 510 AFLP markers, 21 specific bands are found to distinguish the four species scallops and these markers may be applied to the specific germplasm characterization and molecular assistant classification in scallops.

关键词： scallops AFLP markers genetic diversity

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Performance Comparison of Two Efficient Genomic Selection Methods(gsbay & MixP ) Applied in Aquacultural Organisms

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Journal of Ocean University of China 2017年第1期16卷 137-144页

作者： SU Hailin LI Hengde WANG Shi WANG Yangfan bao zhenmin College of Marine Life Science Ocean University of China The Center for Applied Aquatic Genomics Chinese Academy of Fishery Sciences

Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

关键词： genomic selection scallop breeding method comparison

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Phylogenetic analysis of Pectinidae (Bivalvia) based on the ribosomal DNA internal transcribed spacer region

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Acta Oceanologica Sinica 2007年第6期26卷 83-90页

作者： HUANG Xiaoting BI Ke HU Jingjie HU Xiaoli bao zhenmin Laboratory of Molecular Genetics and Breeding of Mollusk College of Marine Life Science Ocean University of China Qingdao 266003 China

The ribosomal DNA internal transcribed spacer （ITS） region is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, the molecular phylogenetic analysis of Pectinidae （ Mollusca： Bivalvia） was performed using the nucleotide sequences of the nuclear ITS region in nine species of this family. The sequences were obtained from the scallop species Argopecten irradians, Mizuhopecten yessoensis, Amusium pleuronectes and Mimachlamys nobilis, and compared with the published sequences of Aequipecten opercularis, Chlamys farreri, C. distorta, M. varia, Pecten maximus, and an outgroup species Perna viridis. The molecular phylogenetic tree was constructed by the neighbor-joining and maximum parsimony methods. Phylogenetic analysis based on ITS1, ITS2, or their combination always yielded trees of similar topology. The results support the morphological classifications of bivalve and are nearly consistent with classification of two subfamilies （Chlamydinae and Pectininae） formulated by Waller. However, A. irradians, together with A. opercularis made up of genera Amusium, evidences that they may belong to the subfamily Pectinidae. The data are incompatible with the conclusion of Waller who placed them in Chlamydinae by morphological characteristics. These results provide new insights into the evolutionary relationships among scallop species and contribute to the improvement of existing classification systems.

关键词： bivalve Pectinidae ribosomal DNA ITS phylogeny

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Preliminary Analysis of Population Genetic Diversity of Cultivated Laminaria japonica Sporophyte via AFLP Technique

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Journal of Ocean University of China 2010年第1期9卷 53-58页

作者： YI Heng SUI Zhenghong bao zhenmin Key Laboratory of Marine Genetics Ministry of Education Ocean University of China Qingdao266003 P. R. China Yunnan Henderson Foreign Language School Kunming 650000 P. R. China

The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng,*** methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP *** parameters of the method were *** of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the *** individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers.A total of 21 loci were obtained and 17 of them were *** mean percent age of polymorphic loci of this population was 80.95%.The Nei's gene diversity (H) within this population was 0.3028 and the average Shannon's Information index (I) was 0.4498.A genetic distance matrix among different individuals was constructed as *** this study,an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was *** results of this research also revealed a high level of genetic diversity within the studied population.

关键词： sporophyte Laminariajaponica AFLP genetic diversity

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Isolation and Characterization of Calmodulin Gene of Alexandrium catenella （Dinoflagenate） and Its Performance in Cell Growth and Heat Stress

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Journal of Ocean University of China 2014年第2期13卷 290-296页

作者： Wen, Ruobing Sui, Zhenghong bao, zhenmin Zhou, Wei Wang, Chunyan Key Laboratory of Marine Genetics and Breeding of Ministry of Education of China Ocean University of China Qingdao 266003 P. P. China

Harmful algal blooms （HABs） can occur and then disappear quickly, corresponding to consistent growing and declining of heavy biomasses. The molecular mechanism of blooming remains unclear. In this study, calmodulin gene （cam） of HAB causing species Alexandrium catenella was isolated and characterized, The expression of calmodulin gene was profiled at different growth rates and in heat stress. The full cDNA of cam was 597 nucleotides （nt） in length, including a 25 nt 5＇ untranslated region （UTR）, an 122nt 3＇ UTR, and a 450nt open reading frame （ORF） encoding 149 amino acids. The deduced calmodulin （CAM） was highly conserved in comparison with those of other organisms. As was determined with real-time RT PCR, the abundance of cam transcript varied in a pattern similar to cell growth rate during the whole growing period. The abundance of cam transcript increased by more than 8 folds from lag growth phase to exponential growth phase, and then obviously decreased from exponential growth phase to stationary/decline growth phase. In addition, the relative abundance of cam transcript significantly declined with time during heat shock. Taking CaM function described in other organisms into account, we believe that Ca2- -involved signal transduction, methyla- tion of DNA and toxin precursors underlined the cell growth of this species. The response of cam gene to heat stress in dinoflagellate suggested restrictions in Ca2＋ signal transduction and methylation. These findings are helpful to understand the relationships among growth, cell signal transduction, bloom formation and interaction with environmental stimuli in dinoflagellates.

关键词： harmful algal bloom Alexandrium catenella calmodulin growth rate heat stress

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Chromosomal localization of the major ribosomal RNA genes in scallop Chlamys farreri

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Acta Oceanologica Sinica 2006年第3期25卷 108-115页

作者： HUANG Xiaoting bao zhenmin BI Ke HU Jingjie ZHANG Can ZHANG Quanqi HU Xiaoli Laboratory of Marine Genetics and Breedings Division of Life Science and Technology Ocean University of China Qingdao 266003 China

The chromosomes of Chlamys farreri were analyzed by means of silver staining and fluorescence in situ hybridization （FISH） with 18S-28S rDNA probe. Probe was made by PCR amplification of a DNA fragment containing internal transcribed spacers ITS1 between 18S and 5.8S ribosomal RNA gene, ITS2 between 5.8S and 28S ribosomal RNA gene and 5.8S rRNA gene, and labeled by PCR incorporation of bio-16-dUTP. FISH signals were located on the short arm of subtelocentrie chromosome 10. After silverstaining, nucleolus organizer regions （NORs） could be observed on the telomere of the short arm of chromosome 10. However, one metaphase spread displayed an additional silver spot on the short arm of subtelocentrie chromosome 12.

关键词： rDNA Ag-NORs FISH Chlamysfarreri

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Cytogenetic analysis in two scallops (Bivalvia:Pectinidae) by PRINS and PI banding

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Acta Oceanologica Sinica 2007年第5期26卷 153-158页

作者： ZHANG Lingling bao zhenmin WANG Jue WANG Shi HUANG Xiaoting HU Xiaoli HU Jingjie Laboratory of Marine Genetics and Breeding College of Marine Life Sciences Ocean University of China Qingdao 266003 China

Cytogenetic analysis was performed for the bay scallop （Argopecten irradians Lamarck 1819） and the Japanese scallop （Patinopecten yessoensis Jay 1857 ） by primed in situ labeling （PRINS） and propidium iodide （PI） banding techniques. The PRINS analysis revealed that major rRNA genes were clustered in two loci on the telomeric regions of the short arms on two acrocentric chromosome pairs in A. irradians and on two submetacentric pairs in P. yessoensis. The histone H3 gene sites differed in number and location between these two species. The C-band-like patterns revealed by PI staining varied considerably between these two species. A. irradians displayed terminal bands at long arms on all chromosomes, centromeric bands on some pairs and interstitial bands on five pairs. P. yessoensis exhibited only centromeric bands on all chromosomes. These results would contribute to the better understanding of karyotype evolution in A. irradians and P. yessoensis.

关键词： primed in situ labeling PI banding Argopecten irradians Patinopecten yessoensis

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Assessing genetic diversity of wild populations of Japanese flounderusing AFLP markers

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Acta Oceanologica Sinica 2006年第3期25卷 82-89页

作者： XU Xiaofei ZHANG Quanqi WANG Zhigang QI Jie ZHANG Zhifeng bao zhenmin Heisuke Nakagawa Laboratory of Marine Genetics and Breeding Ocean University of China Qingdao 266003 China Faculty of Applied Biological Science Hiroshima University Higashi - Hiroshima 739 - 8528 Japan

Amplified fragment length polymorphism （AFLP） analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder （Paralichthys olivaceus）. A total of 775 loci （58.32% of which was polymorphic） in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value. The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value （G.,） is 0. 356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

关键词： Paralichthys olivaceus geographical population AFLP genetic diversity

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Development of 101 Novel EST-Derived Single Nucleotide Polymorphism Markers for Zhikong Scallop (Chlamys farreri)

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Journal of Ocean University of China 2013年第3期12卷 403-412页

作者： LI Jiqin bao zhenmin LI Ling WANG Xiaojian WANG Shi HU Xiaoli Key Laboratory of Marine Genetics and Breeding (MGB) Chinese Ministry of EducationCollege of Marine Life SciencesOcean University of China

Zhikong scallop(Chlamys farreri) is an important maricultured species in *** researches on this species,such as population genetics and QTL fine-mapping,need a large number of molecular *** this study,based on the expressed sequence tags(EST),a total of 300 putative single nucleotide polymorphisms(SNPs) were selected and validated using high resolution melting(HRM) technology with unlabeled *** them,101(33.7%) were found to be polymorphic in 48 individuals from 4 *** evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to *** observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505,*** loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of *** gave significant hits for 72 of the 101 polymorphic SNP-containing *** four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons(33 SNPs) or pretermination of translation(1 SNP).The markers developed can be used for the population studies and genetic improvement on Zhikong scallop.

关键词： Zhikong scallop Chlamysfarreri SNP EST HRM

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