2025-4-4- 7
Home > Archive>Volume 24, Issue 4, 2023 >1106-1113. DOI:10.13430/j.cnki.jpgr.20221221001
PDF HTML XML Export Cite reminder
Identification and Evaluation Method for Genome-wide DNA Fingerprinting of Rice Germplasm
Author:
Affiliation:

1.Institute of Crop Sciences， Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement， Beijing 100081;2.Smartgenomics Technology Institute， Tianjin 301700

Fund Project:

Foundation projects： National Key Research and Development Program of China （2021YFD1200500）； The CAAS Science and Technology Innovation Program； Protective Program of Crop Germplasm of China （2018NWB036-01， 2018NWB036-12-2）； The National Infrastructure for Crop Germplasm Resources （NICGR2018-001）

  • Article
    • | |
  • Metrics
    • |
  • Reference [17]
    • | | | |
  • Comments
    Abstract:

    DNA fingerprinting analysis that enables assigning uniform identity information for each rice germplasm is of great significance for identifying the genetic basis of rice germplasm resources， improving their utilization efficiency and protecting the intellectual property rights of the seed industry in China. In this study， using 5374 rice accessions that have been genotyped by the whole-genome resequencing， two sets of genome-wide DNA fingerprinting standards were established through the selection of reference sample resources， analysis of high-quality SNP loci， and selection of the optimal number of SNPs and SNP combinations. Through principal component analysis and phylogenetic tree analysis， SNPs in the collection of fingerprinting standards 1 and 2 could represent 94，197 high-quality population common SNPs applicable for the population genetic diversity. In addition， population genetic similarity analysis verified the effectiveness of fingerprinting standards 1 and 2 to uncover the genetic similarity identification of rice germplasm resources. This study is expected to provide technical support for the conservation and utilization of rice germplasm resources and the protection of intellectual property rights in the seed industry， and to provide reference for the development of DNA fingerprinting standards for other crops.

    Reference
    [1] Jeffreys A J, Wilson V, Thein S L. Hypervariable minisatellite regions in human DNA. Nature, 1985, 314(6006):67-73
    [2] 刘旭, 李立会, 黎裕. 方沩. 作物种质资源研究回顾与发展趋势. 农学学报, 2018 (1): 1-6Liu X, Li L H, Li Y, Fang W. Crop germplasm resources advances and trends. Journal of Agriculture, 2018 (1): 1-6
    [3] 韩龙植. 水稻种质资源基础性工作研究进展. 植物遗传资源学报,2013, DOI:10.13430/j.cnki.jpgr.2013.01.023Han L Z. Research progress of basic work on rice germplasm resources. Journal of Plant Genetic Resources, 2013, DOI: 10.13430/j.cnki.jpgr.2013.01.023
    [4] Surridge C. Rice cultivation: Feast or famine？ Nature, 2004, 428(6981):360-361
    [5] 庄杰云, 施勇烽, 吕波, 陈能, 杨坤, 应杰政, 曾瑞珍. NY/T 1433-2007, 水稻品种鉴定 DNA指纹方法. 北京:中国农业出版社,2007Zhuang J Y, Shi Y F, Lv B, Chen N, Yang K, Ying J Z, Zeng R Z. NY/T 1433-2007, Identification of rice (Oryza sativa L.) varieties using microsatellite markers. Beijing: China Agriculture Press, 2007
    [6] 徐群, 魏兴华, 庄杰云, 吕波, 袁筱萍, 刘平, 张新明, 余汉勇, 堵苑苑. NY/T 1433-2014, 水稻品种鉴定技术规程 SSR标记法. 北京:中国农业出版社,2014Xu Q, Wei X H, Zhuang J Y, Lv B, Yuan X P, Liu P, Zhang X M, Yu H Y, Du Y Y. NY/T 1433-2014, Protocol for identification of rice varieties-SSR marker method. Beijing: China Agriculture Press, 2014
    [7] 魏兴华, 刘丰泽, 韩斌, 徐群, 冯旗, 赵妍, 支巨振, 周泽宇, 杨窑龙, 冯跃, 任雪贞, 王珊, 章孟臣. NY/T 2745-2021, 水稻品种真实性鉴定 SNP标记法. 北京:中国农业出版社,2021Wei X H, Liu F Z, Han B, Xu Q, Feng Q, Zhao Y, Zhi J Z, Zhou Z Y, Yang Y L, Feng Y, Ren X Z, Wang S, Zhang M C. NY/T 2745-2021, Rice (Oryza sativa L.) varieties genuineness identification-SNP based method. Beijing: China Agriculture Press, 2021
    [8] 彭海, 方治伟, 李论, 马爱进, 周俊飞, 温常龙, 李甜甜, 唐浩, 陈红, 崔野韩, 张嘉楠, 贾英民, 徐娜, 宋书峰, 胡美霞, 符习勤, 赵治海, 梁勇, 徐振江, 高利芬, 陈利红, 韩瑞玺, 张蝶, 张静, 余进文. GB/T 38551-2020, 植物品种鉴定 MNP标记法. 北京:中国标准出版社,2020Peng H, Fang Z W, Li L, Ma A J, Zhou J F, Wen C L, Li T T, Tang H, Chen H, Cui Y H, Zhang J N, Jia Y M, Xu N, Song S F, Hu M X, Fu X Q, Zhao Z H, Liang Y, Xu Z J, Gao L F, Chen L H, Han R X, Zhang D, Zhang J, Yu J W. GB/T 38551-2020, Identification of plant varieties-MNP marker method. Beijing: China Standards Press, 2020
    [9] Chen S, Zhou Y, Chen Y, Gu J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 2018, 34(17):i884-i890
    [10] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 genome project data processing subgroup. The sequence alignment/map format and SAMtools. Bioinformatics, 2009, 25(16):2078-2079
    [11] Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009, 25:1754-1760
    [12] van der Auwera G A, Carneiro M O, Hartl C, Poplin R, Angel G D, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella K, Altshuler D, Gabriel S, DePristo M A. From FastQ data to high confidence variant calls: The genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics, 2013, 43(1110):11.10.1-11.10.33. DOI: 10.1002/0471250953.bi1110s43
    [13] Yang J, Lee S H, Goddard M E, Visscher P M. GCTA: A tool for genome-wide complex trait analysis. The American Journal of Human Genetics, 2011, 88:76-82
    [14] Vilella A J, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. Ensembl compara gene trees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research, 2009, 19:327-335
    [15] Han B, Cui D, Ma X D, Cao G L, Zhang H, Koh H J, Han L Z. Evidence for evolution and selection of drought-resistant genes based on high-throughput resequencing in weedy rice, Journal of Experimental Botany, 2022, 73(7): 1949-1962
    [16] Cui D, Zhou H, Ma X D, Lin Z C, Sun L H, Han B, Li M M, Sun J C, Liu J, Jin G X, Wang X J, Cao G L, Deng X W, He H, Han L Z. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of geng/japonica rice cultivars. Plant Communications, 2022, 3(3):100325
    [17] 马静,安永平,王兴盛,孙建昌.宁夏水稻品种微卫星标记数据库的建立.植物遗传资源学报, 2016,17(2):226-232Ma J, An Y P, Wang X S, Sun J C. Establishment of Ningxia rice microsatellite marker database. Journal of Plant Genetic Resources, 2016, 17 (2):226-232
    Related
    Cited by
    Comments
    Comments
    分享到微博
    Submit
Get Citation

Copy
Share
Article Metrics
  • Abstract:213
  • PDF: 1113
  • HTML: 161
  • Cited by: 0
History
  • Received:December 21,2022
  • Revised:December 26,2022
  • Online: June 13,2023
  • Published: June 14,2023
Article QR Code
You are the 604152th visitor 京ICP备09069690号-23
® 2025 All Rights Reserved
Supported by:Beijing E-Tiller Technology Development Co., Ltd.
Firefox, Chrome, IE10, IE11 are recommended. Other browsers are not recommended.