IDEAS home Printed from https://ideas.repec.org/a/caa/jnlcjg/v56y2020i2id58-2019-cjgpb.html
   My bibliography  Save this article

Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

Author

Listed:
  • Shahril Ab Razak

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Nor Helwa Ezzah Nor Azman

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Rahiniza Kamaruzaman

    (Rice Breeding Program, Rice Research Centre, MARDI Seberang Perai, Kepala Batas, Pulau Pinang, Malaysia)

  • Shamsul Amri Saidon

    (Rice Breeding Program, Rice Research Centre, MARDI Seberang Perai, Kepala Batas, Pulau Pinang, Malaysia)

  • Muhammad Fairuz Mohd Yusof

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Siti Norhayati Ismail

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Mohd Azwan Jaafar

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

  • Norzihan Abdullah

    (Agri-Omic & Bioinformatic Program, Biotechnology and Nanotechnology Research Centre, MARDI Headquarter, Serdang, Selangor, Malaysia)

Abstract

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159-MR167) to 0.723 (MRIA-Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

Suggested Citation

  • Shahril Ab Razak & Nor Helwa Ezzah Nor Azman & Rahiniza Kamaruzaman & Shamsul Amri Saidon & Muhammad Fairuz Mohd Yusof & Siti Norhayati Ismail & Mohd Azwan Jaafar & Norzihan Abdullah, 2020. "Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 56(2), pages 62-70.
  • Handle: RePEc:caa:jnlcjg:v:56:y:2020:i:2:id:58-2019-cjgpb
    DOI: 10.17221/58/2019-CJGPB
    as

    Download full text from publisher

    File URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/58/2019-CJGPB.html
    Download Restriction: free of charge

    File URL: http://cjgpb.agriculturejournals.cz/doi/10.17221/58/2019-CJGPB.pdf
    Download Restriction: free of charge

    File URL: https://libkey.io/10.17221/58/2019-CJGPB?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Youyong Zhu & Hairu Chen & Jinghua Fan & Yunyue Wang & Yan Li & Jianbing Chen & JinXiang Fan & Shisheng Yang & Lingping Hu & Hei Leung & Tom W. Mew & Paul S. Teng & Zonghua Wang & Christopher C. Mundt, 2000. "Genetic diversity and disease control in rice," Nature, Nature, vol. 406(6797), pages 718-722, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Palaniappan, Gomathy & King, Christine A. & Cameron, Don, 2009. "CS - Complexity Of Transition To Alternative Farming Systems," 17th Congress, Illinois State University, USA, July 19-24, 2009 345531, International Farm Management Association.
    2. Nian-Feng Wan & Liwan Fu & Matteo Dainese & Yue-Qing Hu & Lars Pødenphant Kiær & Forest Isbell & Christoph Scherber, 2022. "Plant genetic diversity affects multiple trophic levels and trophic interactions," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. MARCHAND, Sébastien & GUO, Huanxiu, 2014. "The environmental efficiency of non-certified organic farming in China: A case study of paddy rice production," China Economic Review, Elsevier, vol. 31(C), pages 201-216.
    4. Stefan Baumgärtner & Martin F. Quaas, 2007. "Agro-biodiversity as natural insurance and the development of financial insurance markets," Working Paper Series in Economics 61, University of Lüneburg, Institute of Economics.
    5. Kwikiriza, Norman & Katungi, Enid & Horna, Daniela, 2011. "Estimating the role of spatial varietal diversity on crop productivity within an abatement framework: The case of banana in Uganda," IFPRI discussion papers 01051, International Food Policy Research Institute (IFPRI).
    6. Yuying Li & Qiong Wang & Huimin Jia & Kazuya Ishikawa & Ken-ichi Kosami & Takahiro Ueba & Atsumi Tsujimoto & Miki Yamanaka & Yasuyuki Yabumoto & Daisuke Miki & Eriko Sasaki & Yoichiro Fukao & Masayuki, 2024. "An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    7. Wenjiang Jing & Hao Wu & Hanzhu Gu & Zhilin Xiao & Weilu Wang & Weiyang Zhang & Junfei Gu & Lijun Liu & Zhiqin Wang & Jianhua Zhang & Jianchang Yang & Hao Zhang, 2022. "Response of Grain Yield and Water Use Efficiency to Irrigation Regimes during Mid-Season indica Rice Genotype Improvement," Agriculture, MDPI, vol. 12(10), pages 1-18, October.
    8. Francesco Galioto & Irene Criscuoli & Andrea Martelli & Maria Valentina Lasorella & Ilaria Falconi & Danilo Marandola & Giovanni Dara Guccione & Francesca Varia, 2024. "Investigating How Policies and Other Conditions Contribute to Influencing Agricultural GHG Emissions in the EU," Land, MDPI, vol. 13(11), pages 1-16, October.
    9. Stefan Baumgärtner & Martin F. Quaas, 2010. "Managing increasing environmental risks through agrobiodiversity and agrienvironmental policies," Agricultural Economics, International Association of Agricultural Economists, vol. 41(5), pages 483-496, September.
    10. Soleri, Daniela & Cleveland, David A. & Glasgow, Garrett & Sweeney, Stuart H. & Cuevas, Flavio Aragón & Fuentes, Mario R. & Ríos L., Humberto, 2008. "Testing assumptions underlying economic research on transgenic food crops for Third World farmers: Evidence from Cuba, Guatemala and Mexico," Ecological Economics, Elsevier, vol. 67(4), pages 667-682, November.
    11. Yuxin Xie & Yulin Jing & Yajie Wang & Rongchun Zheng & Qiurui Xu & Zhenyu Sun & Tingyu Duan, 2024. "Leguminous Green Manure Intercropping Promotes Soil Health in a Citrus ( Citrus reticulata ) Orchard," Agriculture, MDPI, vol. 14(11), pages 1-20, October.
    12. Peng Zhang & Huize Ren & Xiaobin Dong & Xuechao Wang & Mengxue Liu & Ying Zhang & Yufang Zhang & Jiuming Huang & Shuheng Dong & Ruiming Xiao, 2023. "Understanding and Applications of Tensors in Ecosystem Services: A Case Study of the Manas River Basin," Land, MDPI, vol. 12(2), pages 1-23, February.
    13. Kiros Hadgu & Walter Rossing & Lammert Kooistra & Ariena Bruggen, 2009. "Spatial variation in biodiversity, soil degradation and productivity in agricultural landscapes in the highlands of Tigray, northern Ethiopia," Food Security: The Science, Sociology and Economics of Food Production and Access to Food, Springer;The International Society for Plant Pathology, vol. 1(1), pages 83-97, February.
    14. Papaïx, Julien & Touzeau, Suzanne & Monod, Hervé & Lannou, Christian, 2014. "Can epidemic control be achieved by altering landscape connectivity in agricultural systems?," Ecological Modelling, Elsevier, vol. 284(C), pages 35-47.
    15. Chen, Shiliang & Liu, Xiang & He, Qiang & Zhou, Shurong, 2022. "Higher-order interactions on disease transmission can reverse the dilution effect or weaken the amplification effect to unimodal pattern," Ecological Modelling, Elsevier, vol. 474(C).
    16. R. Amayo & Teddy Oparok & Jimmy Lamo & Silue Drissa & Richard Edema & Geoffrey Tusiime, 2024. "Rice Blast Prevalence in Smallholder Rice Farmlands in Uganda," Journal of Agricultural Science, Canadian Center of Science and Education, vol. 12(10), pages 105-105, April.
    17. Dedeurwaerdere, Tom & Hannachi, Mourad, 2019. "Socio-economic drivers of coexistence of landraces and modern crop varieties in agro-biodiversity rich Yunnan rice fields," Ecological Economics, Elsevier, vol. 159(C), pages 177-188.
    18. Bai, Wei & Sun, Zhanxiang & Zheng, Jiaming & Du, Guijuan & Feng, Liangshan & Cai, Qian & Yang, Ning & Feng, Chen & Zhang, Zhe & Evers, Jochem B. & van der Werf, Wopke & Zhang, Lizhen, 2016. "Mixing trees and crops increases land and water use efficiencies in a semi-arid area," Agricultural Water Management, Elsevier, vol. 178(C), pages 281-290.
    19. Samuel E. Wuest & Lukas Schulz & Surbhi Rana & Julia Frommelt & Merten Ehmig & Nuno D. Pires & Ueli Grossniklaus & Christian S. Hardtke & Ulrich Z. Hammes & Bernhard Schmid & Pascal A. Niklaus, 2023. "Single-gene resolution of diversity-driven overyielding in plant genotype mixtures," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    20. Layla Höckerstedt & Elina Numminen & Ben Ashby & Mike Boots & Anna Norberg & Anna-Liisa Laine, 2022. "Spatially structured eco-evolutionary dynamics in a host-pathogen interaction render isolated populations vulnerable to disease," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:caa:jnlcjg:v:56:y:2020:i:2:id:58-2019-cjgpb. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Ivo Andrle (email available below). General contact details of provider: https://www.cazv.cz/en/home/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.