Advance Search
Wagutu Godfrey Kinyori, Njeri Henry Kariuki, Fan Xiang-Rong, Chen Yuan-Yuan. Development and transferability analysis of SSR primers in wild rice Zizania latifolia (Poaceae)[J]. Plant Science Journal, 2020, 38(1): 105-111. DOI: 10.11913/PSJ.2095-0837.2020.10105
Citation: Wagutu Godfrey Kinyori, Njeri Henry Kariuki, Fan Xiang-Rong, Chen Yuan-Yuan. Development and transferability analysis of SSR primers in wild rice Zizania latifolia (Poaceae)[J]. Plant Science Journal, 2020, 38(1): 105-111. DOI: 10.11913/PSJ.2095-0837.2020.10105
shu

Development and transferability analysis of SSR primers in wild rice Zizania latifolia (Poaceae)

  • 1. Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;

  • 2. University of Chinese Academy of Sciences, Beijing 100049, China;

  • 3. Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China;

  • 4. College of Science, Tibet University, Lhasa 850000, China;

  • 5. Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, China

Funds: 

This work was supported by a grant from the Talent Program of Wuhan Botanical Garden, Chinese Academy of Sciences (Y855291B01).

More Information
  • Received Date: April 01, 2019
  • Revised Date: June 14, 2019
  • Available Online: October 31, 2022
  • Published Date: February 27, 2020
    Graphical Abstract
    • Abstract
  • Zizania latifolia Turcz., also known as Manchurian wild rice, is a member of the tribe Oryzeae, and a major wild ecological and genetic resource. In this study, nuclear SSR primers were developed in silico based on part of the existing genome sequences of Z. latifolia. Five wild populations of the species from different regions across China were selected to screen 64 developed primers. Results showed that 15 primer pairs were polymorphic in at least one population. In addition, we identified a total of 84 alleles, with an average of 5.6 alleles per locus. For the different populations, the level of observed and expected heterozygosity ranged from 0.000 to 0.941 and 0.072 to 0.625, respectively. Relatively high genetic differentiation between populations (FST=0.432) was found, as evidenced by low levels of gene flow (Nm=0.576) among populations. These newly developed markers will facilitate further study of the level and pattern of genetic diversity, and the development of germplasm resource conservation strategies for natural extant Z. latifolia populations. In the cross-species transferability test, eight and nine of the 15 loci were successfully amplified in Oryza sativa L. and O. rufipogon Griff., respectively.
    • FullText(HTML)
    • References (21)
  • [1]
    Chen Y, Long L, Lin X, Guo W, Liu B. Isolation and characterization of a set of disease resistance-gene analogs (RGAs) from wild rice, Zizania latifolia Griseb. I. Introgression, copy number lability, sequence change, and DNA methylation alteration in several rice-Zizania introgression lines[J]. Genome, 2006, 49(2):150-158.
    [2]
    Terrell E, Peterson P, Reveal J, Duvall M. Taxonomy of North American species of Zizania (Poaceae)[J]. Sida, 1997, 17:533-549.
    [3]
    Xu X, Walters C, Antolin MF, Alexander ML, Lutz S, et al. Phylogeny and biogeography of the eastern Asian-North American disjunct wild-rice genus (Zizania L., Poaceae)[J]. Mol Phylogenet Evol, 2010, 55(3):1008-1017.
    [4]
    Peng SL, You WH, Qi G, Yang FL. Nitrogen and phosphorus uptake capacity and resource use of aquatic vegetables floating bed in the eutrophicated lake[C/OL]//2013 Third International Conference on Intelligent System Design and Engineering Applications. (2013-01-01)[2019-09-05]. DOI: 10.1109/ISDEA.2012.237.
    [5]
    Chen YY, Liu Y, Fan XR, Li W, Liu YL. Landscape-scale genetic structure of wild rice Zizania latifolia:The roles of rivers, mountains and fragmentation[J]. Front Ecol Evol, 2017, 5:17.
    [6]
    Guo HB, Li SM, Peng J, Ke WD. Zizania latifolia Turcz. cultivated in China[J]. Genet Resour Crop Evol, 2007, 54(6):1211-1217.
    [7]
    Chen YY, Chu HJ, Liu H, Liu YL. Abundant genetic diversity of the wild rice Zizania latifolia in central China revealed by microsatellites[J]. Ann Appl Biol, 2012, 161(2):192-201.
    [8]
    Wang HM, Wu GL, Jiang SL, Huang QN, Feng BH, et al. Genetic diversity of Zizania latifolia Griseb. from Poyang lake basin based on SSR and ISSR analysis[J]. J Plant Genet Resour, 2015, 16(1):133-141.
    [9]
    Fan XR, Ren XR, Liu YL, Chen YY. Genetic structure of wild rice Zizania latifolia and the implications for its management in the Sanjiang Plain, Northeast China[J]. Biochem Syst Ecol, 2016, 64:81-88.
    [10]
    Zhao Y, Zhong L, Zhou K, Song Z, Chen J, Rong J. Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China:Implications for neo-domestication as a grain crop[J]. AoB Plants, 2018, 10(6):ply072.
    [11]
    Quan Z, Pan L, Ke W, Liu Y, Ding Y. Sixteen polymorphic microsatellite markers from Zizania latifolia Turcz. (Poaceae)[J]. Mol Ecol Resour, 2009, 9(3):887-889.
    [12]
    Guo LB, Qiu J, Han ZJ, Ye ZH, Chen C, et al. A host plant genome (Zizania latifolia) after a century-long endophyte infection[J]. Plant J, 2015, 83(4):600-609.
    [13]
    Li Q, Wan JM. SSRHunter:Development of a local searching software for SSR sites(in Chinese)[J]. Hereditas, 2005, 27:808-810.
    [14]
    Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI. FastPCR:An in-silico tool for fast primer and probe design and advanced sequence analysis[J]. Genomics, 2017, 109(3/4):312-319.
    [15]
    Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochem Bull, 1987, 19:11-15.
    [16]
    Peakall ROD, Smouse PE. GENALEX 6:Genetic analysis in Excel. Population genetic software for teaching and research[J]. Mol Ecol Notes, 2006, 6:288-295.
    [17]
    Goudet J. FSTAT ver 2.9.4, a program to estimate and test gene diversities and fixation indices[EB/OL]. (2005-08-23)[2019-09-05]. https://www2.unil.ch/popgen/softwares/fstat.htm.
    [18]
    Kumar S, Stecher G, Tamura, K. MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7):1870-1874.
    [19]
    Hamrick JL, Godt MJW. Effects of life history traits on genetic diversity in plant species[J]. Philos Trans R Soc Lond B Biol Sci, 1996, 351(1345):1291-1298.
    [20]
    Xu XW, Ke WD, Yu XP, Wen J, Ge S. A preliminary study on population genetic structure and phylogeography of the wild and cultivated Zizania latifolia (Poaceae) based onAdh1a sequences[J]. Theor Appl Genet, 2008, 116(6):835-843.
    [21]
    Wright S. Evolution and the Genetics of Populations:the Theory of Gene Frequencies[M]. Illinois:University of Chicago Press, 1969.
    • Related Articles

  • Related Articles

    [1]Jia Xiande, Lü Haiying, Wu Limei, Yang Yinan, Huang Renhao, Wang Hao, Niu Xin. Response of leaf functional traits and anatomical structure to altitude in Crataegus songarica K. Koch in Tianshan wild fruit forest[J]. Plant Science Journal, 2024, 42(2): 150-159. DOI: 10.11913/PSJ.2095-0837.23157
    [2]Liu Xiong-Sheng, Xiao Yu-Fei, Wang Yong, Huang Rong-Lin, Jiang Ying, Liu Fei, Jiang Yi. Anatomical structures of vegetative organs of Keteleeria fortunei (Murr.)Carr.var. cyclolepis (Flous) Silba and its ecological adaptability[J]. Plant Science Journal, 2020, 38(1): 39-46. DOI: 10.11913/PSJ.2095-0837.2020.10039
    [3]Jiang Ya-Ting, Duan Guo-Min, Tian Min, Wang Cai-Xia, Zhang Ying. Anatomical structure of the vegetative organs of Calanthe tsoongiana and their ecological adaptation[J]. Plant Science Journal, 2019, 37(3): 271-279. DOI: 10.11913/PSJ.2095-0837.2019.30271
    [4]Liu Xiong-Sheng, Xiao Yu-Fei, Jiang Yi, Li Juan, Lin Jian-Yong, Liang Rui-Long. Anatomical structures of the vegetative organs of Phoebe bournei (Hemsl.) Yang and ecological adaptability[J]. Plant Science Journal, 2018, 36(2): 153-161. DOI: 10.11913/PSJ.2095-0837.2018.20153
    [5]Li Na, Guo Xue-Min, Li Ming, Bai Lan. Comparison of leaf anatomical structures between female and male Broussonetia papyrifera(L.) Vent.[J]. Plant Science Journal, 2017, 35(2): 164-170. DOI: 10.11913/PSJ.2095-0837.2017.20164
    [6]WU Yan-Fang, ZHANG Jian, LEI Jing, XU Feng, WU Li-Li. Anatomical Structure of Vegetative Organs of Ginkgo biloba L.[J]. Plant Science Journal, 2016, 34(2): 175-181. DOI: 10.11913/PSJ.2095-0837.2016.20175
    [7]SHEN Shi-Kang, ZHANG Xin-Jun, WU Fu-Qin, YANG Guan-Song, WANG Yue-Hua, SUN Wei-Bang, LIN Ru-Tao. Study on the Anatomical Structures of Rhododendron protistum var. giganteum with an Extremely Small Population[J]. Plant Science Journal, 2016, 34(1): 1-8. DOI: 10.11913/PSJ.2095-0837.2016.10001
    [8]YANG Zhi-Jian, FENG Jin-Ling, CHEN Hui. Study on the Anatomical Structures in Development of the Nurse Seed Grafted Union of Camellia oleifera[J]. Plant Science Journal, 2013, 31(3): 313-320. DOI: 10.3724/SP.J.1142.2013.30313
    [9]LU Chang, WANG Fang, ZHANG Xiao-Ping. Leaf Comparation on Anatomical Structure and Epidermal Characteristics of Pteroceltis tatarinowii Maxim. in Different Areas[J]. Plant Science Journal, 2012, 30(4): 337-351. DOI: 10.3724/SP.J.1142.2012.40337
    [10]TAO Yong, JIANG Ming-Xi. Study on Anatomical Structure Adaptation of Stem of Alternanthera philoxeroides (Mart.) Griseb to Various Water Condition[J]. Plant Science Journal, 2004, 22(1): 65-71.

  • Cited by

    Periodical cited type(10)

    1. 林协全，王宁，汪其双，陈春锦，刘锦航，邹双全，邹小兴. 福建金线莲的环境因子分析及生境适宜性评价. 山东农业大学学报(自然科学版). 2023(02): 201-207 .
    2. 林志强，马铁成. 新疆灌溉定额空间分布规律浅析. 水资源开发与管理. 2023(09): 69-74 .
    3. 艾拉努尔·卡哈尔，王鹏军，逯永满，袁祯燕，买买提明·苏来曼. 基于MaxEnt生态位模型预测木灵藓科三属植物在新疆的潜在分布区. 华中师范大学学报(自然科学版). 2022(03): 487-496+540 .
    4. 李雪，高广磊，孙桂丽，史浩伯，赵芳芳，马龙. 基于MaxEnt预测梭梭和白梭梭在新疆的潜在适生区. 西部林业科学. 2021(01): 145-152 .
    5. 祖丽米热·买买提依明，维尼拉·伊利哈尔，艾拉努尔·卡哈尔，吾热古丽·艾买提，买买提明·苏来曼，刘永英. 基于最大熵模型的真藓属植物在新疆的潜在分布预测. 森林工程. 2021(04): 1-10+21 .
    6. 古丽妮尕尔·穆太力普，夏尤普·玉苏甫，袁祯燕，买买提明·苏来曼. 阿尔金山国家级自然保护区的对齿藓属(Didymodon Hedw.)植物调查. 东北林业大学学报. 2020(01): 34-43 .
    7. 张梅，禄彩丽，魏喜喜，马珊，刘伟峰，宋健，彭瑞，李建贵. 基于MaxEnt模型新疆枣潜在适生区预测. 经济林研究. 2020(01): 152-161 .
    8. 周亚东，Mwangi Brian Njoroge，Ndungu John Mbari，王生位，胡光万，王青锋. 基于MaxEnt模型模拟肯尼亚茜草科河骨木属植物的潜在分布及其在植物志中的应用初探(英文). 植物科学学报. 2020(05): 636-643 . 本站查看
    9. 杨冬臣，王佳颖，李静，杨一洲，张金林. 基于Maxent生态位模型的外来入侵植物刺果瓜在我国的适生区预测. 河北农业大学学报. 2019(03): 45-50 .
    10. 赵儒楠，何倩倩，褚晓洁，鲁志强，祝遵凌. 气候变化下千金榆在我国潜在分布区预测. 应用生态学报. 2019(11): 3833-3843 .

    Other cited types(15)

Catalog

    Get Citation
    PDF
    XML
    Article views (610) PDF downloads (651) Cited by(25)
    Turn off MathJax
    Article Contents
    Abstract
    References
    Related Articles
    Copyright © 2022 Plant Science Journal 鄂ICP备05004779号-3
    Address：No. 201, Jiufeng 1st Road, Donghu High tech Zone, WuhanPostal Code：430074

    Supported by: Beijing Renhe Information Technology Co., Ltd.  Baidu Analytics

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return