中国农业科学 ›› 2022, Vol. 55 ›› Issue (23): 4567-4582.doi: 10.3864/j.issn.0578-1752.2022.23.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

半糯粳稻品种核心标记的筛选及DNA指纹图谱的构建

赵春芳1(),赵庆勇1,吕远大2,陈涛1,姚姝1,赵凌1,周丽慧1,梁文化1,朱镇1,王才林1,张亚东1,*()   

  1. 1江苏省农业科学院粮食作物研究所/国家耐盐碱水稻技术创新中心华东中心/江苏省优质水稻工程技术研究中心,南京 210014
    2江苏省农业科学院种质资源与生物技术研究所,南京 210014
  • 收稿日期:2022-07-25 接受日期:2022-09-09 出版日期:2022-12-01 发布日期:2022-12-06
  • 联系方式: 赵春芳,E-mail:czhao@jaas.ac.cn。
  • 基金资助:
    江苏省农业科技自主创新资金(CX[20]2002);江苏省重点研发计划(BE2021301);现代农业产业技术体系建设专项资金(CARS-01)

Screening of Core Markers and Construction of DNA Fingerprints of Semi-Waxy Japonica Rice Varieties

ZHAO ChunFang1(),ZHAO QingYong1,LÜ YuanDa2,CHEN Tao1,YAO Shu1,ZHAO Ling1,ZHOU LiHui1,LIANG WenHua1,ZHU Zhen1,WANG CaiLin1,ZHANG YaDong1,*()   

  1. 1Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice/Jiangsu High Quality Rice R&D Center, Nanjing 210014
    2Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014
  • Received:2022-07-25 Accepted:2022-09-09 Published:2022-12-01 Online:2022-12-06

摘要: 目的 构建一套基于水稻重要性状基因标记的品种DNA指纹鉴定体系,为加强主栽优良食味半糯粳稻品种的种质管理与品种保护奠定基础。方法 以34个江浙沪主栽优良食味半糯粳稻品种为供试材料,通过已知标记多态性鉴定、公共数据库基因序列比对、基因组重测序等多种方法对水稻重要性状调控基因的关键差异位点进行筛选,开发核心SNP或InDel标记;利用As-PCR技术将SNP标记发展为依据电泳条带鉴别的简单PCR标记,通过电泳条带特征化和类型分析获得基因型信息,构建半糯粳稻品种的DNA指纹图谱库。结果 筛选出来源于40个水稻重要性状调控基因的54个核心标记,包括18个SNP标记和36个InDel标记;54个标记在20个品种中共检测到155个有效特征化条带,转化为155个0/1数据位点,建立各品种的DNA指纹数据库,可区分全部供试品种。遗传多样性分析表明,品种间遗传相似性变异范围为0.47—0.90,其中,南粳7718与苏香粳100的相似性系数最小,而南粳9308与南粳9036的相似性系数最大,二者存在8个数据位点差异。亲缘关系分析可将供试品种划分为6个分支,其中,南粳7718为独立分支,表明其与其他品种间的亲缘关系较远。核心标记鉴定效果的进一步验证表明,该套标记可以对14个半糯粳稻新品种进行有效区分,聚类图显示其分布于Ⅱ、Ⅲ和Ⅳ 3个类群,证实各品种间基因型信息的差异性;并利用该套标记鉴定了一个未知半糯水稻的品种真实性,根据基因型和聚类分析,将其判定为南粳9108。结论 经优化筛选,获得可准确区分当前主推半糯粳稻品种的54个核心标记,并发展为可电泳检测的简单PCR标记,利用该套标记组合构建了34个江浙沪地区主栽优良食味半糯粳稻品种的DNA指纹图谱。

关键词: 水稻, 半糯粳稻, DNA指纹图谱, 分子标记

Abstract:

【Objective】 A set of variety DNA fingerprint identification system based on the core markers of genes regulating rice important traits was constructed, which will establish a foundation for strengthening the germplasm management and protection of the mainly promoted semi-waxy japonica rice varieties with high eating quality.【Method】 34 semi-waxy japonica rice varieties mainly cultivated in Jiangsu, Zhejiang and Shanghai were used as the test materials. The key differential sequence sites in genes regulating rice important traits were screened and core SNP or InDel markers were developed through multiple methods such as polymorphism testing of existing markers, gene sequence alignment from public databases and genome resequencing. SNP markers were developed into simple PCR markers based on electrophoretic bands by As-PCR technology. Genotype information was obtained by electrophoretic band characterization and type analysis, and the DNA fingerprint database of the semi-waxy japonica rice varieties was constructed..【Result】 54 core markers derived from 40 key genes regulating rice important traits were obtained, including 18 SNP and 36 InDel markers; 155 characteristic and effective bands were identified by 54 markers in the tested rice varieties, which were transformed into 155 0/1 data sites. The DNA fingerprint database of each variety was established and could distinguish it from all tested varieties. Genetic diversity analysis showed that the variation range of genetic similarity among varieties was 0.47-0.90, among which the lowest similarity coefficient was detected between Nanjing 7718 and Suxiangjing 100, while the highest similarity coefficient was detected between Nanjing 9308 and Nanjing 9036, among which there were 8 differential data sites. Genetic relationship analysis indicated that 34 varieties were divided into 6 branches, of which Nanjing 7718 was an independent branch, suggesting it has a distant relationship from other varieties. Further verification of the identification effect of core markers showed that the set of markers could effectively distinguish 14 new semi-waxy japonica rice varieties. The cluster diagram showed that they were distributed in three groups of Ⅱ, Ⅲ and Ⅳ, confirming the differences of genotype information among varieties; using this set of markers, the authenticity of an unknown semi-waxy rice variety was also identified. According to genotype and cluster analysis, it was determined as Nanjing 9108.【Conclusion】 After optimization and screening, 54 core markers that could accurately distinguish all the tested semi-waxy japonica varieties were obtained, and developed into simple PCR markers detected by electrophoresis. Using this set of marker combinations, the DNA fingerprints of 34 semi-waxy japonica varieties in Jiangsu, Zhejiang and Shanghai were constructed.

Key words: rice (Oryza sativa L.), semi-waxy japonica rice, DNA fingerprints, molecular markers