+Advanced Search

Advanced Search

Volume 38 Issue 2
. 
Turn off MathJax
Article Contents
Abstract
References
Article Navigation >  Acta Oceanologica Sinica  > 2019  >  38(2): 44-51
XU Binduo, REN Yiping, CHEN Yong, XUE Ying, ZHANG Chongliang, WAN Rong. Optimization of stratification scheme for a fishery-independent survey with multiple objectives[J]. Acta Oceanologica Sinica, 2015, 34(12): 154-169. doi: 10.1007/s13131-015-0739-z
Citation: Wang Yu, Zhang Shoudu, Zhang Guofan, Cong Rihao, Li Li. Molecular mechanism of inbreeding effects based on RNA-Seq analysis of the adductor muscle of bay scallop (Argopecten irradians)[J]. Acta Oceanologica Sinica, 2019, 38(2): 44-51. doi: 10.1007/s13131-019-1351-4
shu

Molecular mechanism of inbreeding effects based on RNA-Seq analysis of the adductor muscle of bay scallop (Argopecten irradians)

doi: 10.1007/s13131-019-1351-4
  • 1.

    CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;Tianjin Bohai Sea Fisheries Research Institute, Tianjin 300457, China;Tianjin Ocean Ranch Technical Engineering Center, Tianjin 300457, China

  • 2.

    National Oceanographic Center, Qingdao 266071, China

  • 3.

    CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao 266071, China;Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China

  • 4.

    CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China

  • Received Date: 2018-02-02
    Abstract
  • Understanding the effects of inbreeding is critical for the long-term viability of shellfish breeding and for understanding inbreeding depression (ID) of the offspring of selfed individuals and full-sib crosses. The bay scallop (Argopecten irradians) is a simultaneous hermaphroditic marine bivalve with distinct male and female gonads and is a species with external fertilization. It is a canonical model invertebrate for analysis of the genetics of ID and evolution of outcrossing mating system. ID in bivalves is well documented with regard to the phenotype and molecular markers aspects, but little is known on how inbreeding affects genome-wide gene expression. Here, we compare the gene expression profiles of adductor muscle of A. irradians lines inbred to F=0.5 with those of its counterpart outbred lines which are originated from the same paternal individual. Inbred and outbred individuals have some differences in growth traits. The shell length and the total weight of inbred scallops are lower than the counterpart of outbred lines. We found that 1 175 genes were up-regulated while 1 390 were down-regulated in inbred lines. Regarding components, differentially expressed genes (DEGs) were concentrated on sarcomeres, contractile filaments, and cell membranes. Among others, whereas regarding their function, the Gene Ontology (GO) was concentrated on transferase, phosphotransferase, peptidase, and others. The DEGs-enriched metabolic pathways mainly belonged to the oxidative phosphorylation pathway and apoptosis pathway. We used another two families to verify our bioinformatic results. The selfed and the outbred family originated from different ancestors, but the selfed family showed obvious ID. By using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we verified that DEGs with inbreeding are involved in the oxidative phosphorylation and cell apoptosis pathways, suggesting that inbreeding may affect energy metabolism and homeostasis.
    • FullText(HTML)
    • References(21)
  • Bijlsma R, Bundgaard J, van Putten W F. 1999. Environmental dependence of inbreeding depression and purging in Drosophila melanogaster. Journal of Evolutionary Biology, 12(6):1125-1137, doi: 10.1046/j.1420-9101.1999.00113.x
    Birchler J A, Riddle N C, Auger D L, et al. 2005. Dosage balance in gene regulation:biological implications. Trends in Genetics, 21(4):219-226, doi: 10.1016/j.tig.2005.02.010
    Charlesworth B, Hughes K A. 1999. The maintenance of genetic variation in life-history traits. In:Singh R S, Krimbas C B, eds. Evolutionary Genetics:from Molecules to Morphology. Cambridge:Cambridge University Press
    Darwin C R. 1876. The Effects of Cross and Self-Fertilization in the Vegetable Kingdom. London:John Murray
    DePristo M A, Weinreich D M, Hartl D L. 2005. Missense meanderings in sequence space:a biophysical view of protein evolution. Nature Reviews Genetics, 6(9):678-687, doi: 10.1038/nrg1672
    Fowler K, Whitlock M C. 1999a. The distribution of phenotypic variance with inbreeding. Evolution, 53(4):1143-1156, doi: 10.1111/evo.1999.53.issue-4
    Fowler K, Whitlock M C. 1999b. The variance in inbreeding depression and the recovery of fitness in bottlenecked populations. Proceedings of the Royal Society B:Biological Sciences, 266(1433):2061-2066, doi: 10.1098/rspb.1999.0887
    Hedgecock D, Sly F. 1990. Genetic drift and effective population sizes of hatchery-propagated stocks of the Pacific oyster, Crassostrea gigas. Aquaculture, 88(1):21-38, doi: 10.1016/0044-8486(90)90316-F
    Huang X, Madan A. 1999. CAP3:A DNA sequence assembly program. Genome Research, 9(9):868-877, doi: 10.1101/gr.9.9.868
    Kristensen T N, Dahlgaard J, Loeschcke V. 2002. Inbreeding affects Hsp70 expression in two species of Drosophila even at benign temperatures. Evolutionary Ecology Research, 4:1209-1216
    Kristensen T N, Dahlgaard J, Loeschcke V. 2003. Effects of inbreeding and environmental stress on fitness-using Drosophila buzzatii as a model organism. Conservation Genetics, 4(4):453-465, doi: 10.1023/A:1024763013798
    Kristensen T N, Sørensen P, Kruhøffer M, et al. 2005. Genome-wide analysis on inbreeding effects on gene expression in Drosophila melanogaster. Genetics, 171(1):157-167, doi: 10.1534/genetics.104.039610
    Longwell A C, Stiles S S. 1973. Gamente cross incompatibility and inbreeding in the commercial American oyster, Crassostrea virginica Gmelin. Cytologia, 38(3):521-533, doi: 10.1508/cytologia.38.521
    Mallet A L, Haley L E. 1983. Growth rate and survival in pure population matings and crosses of the oyster Crassostrea virginica. Canadian Journal of Fisheries and Aquatic Sciences, 40(7):948-954, doi: 10.1139/f83-121
    Newkirk G F, Haley L E. 1983. Selection for growth rate in the European oyster, Ostrea edulis:response of second generation groups. Aquaculture, 33(1-4):149-155
    Pletcher S D, Macdonald S J, Marguerie R, et al. 2002. Genome-wide transcript profiles in aging and calorically restricted Drosophila melanogaster. Current Biology, 12(9):712-723, doi: 10.1016/S0960-9822(02)00808-4
    Reed D H, Briscoe D A, Frankham R. 2002. Inbreeding and extinction:the effect of environmental stress and lineage. Conservation Genetics, 3(3):301-307, doi: 10.1023/A:1019948130263
    Saavedra C. 1997. Low effective sizes in hatchery populations of the European oyster (Ostrea edulis):implications for the management of genetic resources. Journal of Shellfish Research, 16:441-446
    Sangster T A, Lindquist S, Queitsch C. 2004. Under cover:causes, effects and implications of hsp90-mediated genetic capacitance. BioEssays, 26:348-362, doi: 10.1002/(ISSN)1521-1878
    Vermeulen C J, Bijlsma R. 2004a. Changes in mortality patterns and temperature dependence of lifespan in Drosophila melanogaster caused by inbreeding. Heredity, 92(4):275-281, doi: 10.1038/sj.hdy.6800412
    Vermeulen C J, Bijlsma R. 2004b. Characterization of conditionally expressed mutants affecting age-specific survival in inbred lines of Drosophila melanogaster:lethal conditions and temperature-sensitive periods. Genetics, 167(3):1241-1248, doi: 10.1534/genetics.103.023721
    • Relative Articles

  • Relative Articles

    • Supplements(0)
    • Cited By

  • Cited by

    Periodical cited type(17)

    1. Wen Cheng, Chongliang Zhang, Yupeng Ji, et al. Performance evaluation of spatially balanced sampling designs in fishery-independent surveys. Fisheries Research, 2024, 270: 106879. doi:10.1016/j.fishres.2023.106879
    2. Jiao Wang, Binduo Xu, Chongliang Zhang, et al. Effect of sampling design on estimation of phylogenetic diversity metrics of fish community. Oecologia, 2023, 201(1): 129. doi:10.1007/s00442-022-05291-9
    3. Jing Zhao, Keer Yang, Jin Ma. Optimization of Sampling Effort for Different Fishery Groups in the Yangtze River Estuary, China. Marine and Coastal Fisheries, 2022, 14(4) doi:10.1002/mcf2.10214
    4. Xiangyu Long, Rong Wan, Zengguang Li, et al. Sampling Designs for Monitoring Ichthyoplankton in the Estuary Area: A Case Study on Coilia mystus in the Yangtze Estuary. Frontiers in Marine Science, 2022, 8 doi:10.3389/fmars.2021.767273
    5. Ming Sun, Yunzhou Li, Yiping Ren, et al. Using fisheries‐independent survey data to reinforce China’s data‐limited fisheries management: Management strategy evaluation of survey‐based management procedures. Fisheries Management and Ecology, 2021, 28(1): 40. doi:10.1111/fme.12454
    6. Zack S Oyafuso, Lewis A K Barnett, Stan Kotwicki, et al. Incorporating spatiotemporal variability in multispecies survey design optimization addresses trade-offs in uncertainty. ICES Journal of Marine Science, 2021, 78(4): 1288. doi:10.1093/icesjms/fsab038
    7. Chunyang Sun, Yingbin Wang. Impacts of sampling design on the abundance estimation of Portunus trituberculatus using crab pots. Journal of Oceanology and Limnology, 2021, 39(2): 770. doi:10.1007/s00343-020-9296-1
    8. Jiaying Wu, Yang Liu, Haozhi Sui, et al. Using network analysis to identify keystone species in the food web of Haizhou Bay, China. Marine and Freshwater Research, 2020, 71(4): 469. doi:10.1071/MF18417
    9. Jing Wang, Chongliang Zhang, Ying Xue, et al. Comparison of different sampling designs for macrozoobenthos survey in a tidal flat. Regional Studies in Marine Science, 2020, 35: 101113. doi:10.1016/j.rsma.2020.101113
    10. Chunyang Sun, Yingbin Wang. Impacts of the sampling design on the abundance index estimation of Portunus trituberculatus using bottom trawl. Acta Oceanologica Sinica, 2020, 39(6): 48. doi:10.1007/s13131-020-1607-z
    11. Jin Ma, Siquan Tian, Chunxia Gao, et al. Evaluation of sampling designs for different fishery groups in the Yangtze River estuary, China. Regional Studies in Marine Science, 2020, 38: 101373. doi:10.1016/j.rsma.2020.101373
    12. Guosheng Zhang, Jing wang, Ying Xue, et al. Comparison of sampling effort allocation strategies in a stratified random survey with multiple objectives. Aquaculture and Fisheries, 2020, 5(3): 113. doi:10.1016/j.aaf.2020.02.002
    13. Zitao Xiao, Jiaying Wu, Binduo Xu, et al. Uniqueness measure based on the weighted trophic field overlap of species in the food web. Ecological Indicators, 2019, 101: 640. doi:10.1016/j.ecolind.2019.01.042
    14. Jiao Wang, Chongliang Zhang, Ying Xue, et al. Spatio-Temporal Variations in Co-Occurrence Patterns of Fish Communities in Haizhou Bay, China: Null Model Analysis. Journal of Ocean University of China, 2019, 18(6): 1497. doi:10.1007/s11802-019-4119-8
    15. Zitao Xiao, Jiaying Wu, Binduo Xu, et al. Identification of unique species in the marine ecosystem based on the weighted trophic field overlap. MethodsX, 2019, 6: 469. doi:10.1016/j.mex.2019.02.024
    16. Jing Zhao, Jie Cao, Siquan Tian, et al. Evaluating Sampling Designs for Demersal Fish Communities. Sustainability, 2018, 10(8): 2585. doi:10.3390/su10082585
    17. Jing Wang, Binduo Xu, Chongliang Zhang, et al. Evaluation of alternative stratifications for a stratified random fishery-independent survey. Fisheries Research, 2018, 207: 150. doi:10.1016/j.fishres.2018.06.019

    Other cited types(0)

  • Created with Highcharts 5.0.7Amount of accessChart context menuAbstract Views, HTML Views, PDF Downloads StatisticsAbstract ViewsHTML ViewsPDF Downloads2024-052024-062024-072024-082024-092024-102024-112024-122025-012025-022025-032025-0405101520
    Created with Highcharts 5.0.7Chart context menuAccess Class DistributionFULLTEXT: 30.1 %FULLTEXT: 30.1 %META: 69.2 %META: 69.2 %PDF: 0.8 %PDF: 0.8 %FULLTEXTMETAPDF
    Created with Highcharts 5.0.7Chart context menuAccess Area Distribution其他: 1.1 %其他: 1.1 %Australia: 1.1 %Australia: 1.1 %China: 41.4 %China: 41.4 %India: 1.9 %India: 1.9 %Russian Federation: 1.9 %Russian Federation: 1.9 %Thailand: 1.1 %Thailand: 1.1 %United States: 51.5 %United States: 51.5 %其他AustraliaChinaIndiaRussian FederationThailandUnited States

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索
    Get Citation
    PDF
    XML

    Article Metrics

    Article views (669) PDF downloads(456) Cited by(17)
    Proportional views
    Related
    Govern Body: China Association for Science and Technology
    Sponsor: Chinese Society for Oceanography
    Tel: 86-10-62179976
    E-mail: ocean2@hyxb.org.cn
    Website: http://www.aosocean.com/
    京ICP备12043220号-7

    Supported by: Beijing Renhe Information Technology Co. Ltd     百度统计

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return