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作物学报 ›› 2019, Vol. 45 ›› Issue (2): 316-321.doi: 10.3724/SP.J.1006.2019.82037

• 研究简报 • 上一篇    

东乡野生稻与日本晴多态性标记的开发

马小定1,唐江红2,张佳妮2,崔迪1,李慧3,黎毛毛3,*(),韩龙植1,*()   

  1. 1中国农业科学院作物科学研究所 / 农作物基因资源与基因改良国家重大科学工程, 北京 100081
    2重庆师范大学, 重庆 401331
    3江西省农业科学院水稻研究所, 江西南昌330200
  • 收稿日期:2018-07-09 接受日期:2018-10-08 出版日期:2019-02-12 网络出版日期:2018-11-06
  • 通讯作者: 黎毛毛,韩龙植
  • 基金资助:
    本研究由国家重点研发计划项目(2016YFD0100101);本研究由国家重点研发计划项目(2016YFD0100301);国家自然科学基金项目(31501287);国家自然科学基金项目(31671664);国家科技支撑计划项目(2015BAD01B01-1);中国农业科学院科技创新工程项目;国家农作物种质资源保护项目(2017NWB036-01);国家农作物种质资源保护项目(2017NWB036-12-2);国家农作物种质资源平台资助(NICGR2017-001)

Development of molecular markers polymorphic between Dongxiang wild rice and Geng rice cultivar ‘Nipponbare’

Xiao-Ding MA1,Jiang-Hong TANG2,Jia-Ni ZHANG2,Di CUI1,Hui LI3,Mao-Mao LI3,*(),Long-Zhi HAN1,*()   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
    2 Chongqing Normal University, Chongqing 401331, China
    3 Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
  • Received:2018-07-09 Accepted:2018-10-08 Published:2019-02-12 Published online:2018-11-06
  • Contact: Mao-Mao LI,Long-Zhi HAN
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0100101);This study was supported by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31501287);the National Natural Science Foundation of China(31671664);the National Key Technology Support Program of China(2015BAD01B01-1);the Agricultural Science and Technology Innovation Program of CAAS;the National Crop Germplasm Conservation Project(2017NWB036-01);the National Crop Germplasm Conservation Project(2017NWB036-12-2);and the National Crop Germplasm Resources Platform Project(NICGR2017-001)

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摘要：

东乡野生稻是分布于全球最北端的一种普通野生稻, 与亚洲栽培稻基因组差异较大, 目前缺少覆盖其全基因组的分子标记。本文以东乡野生稻和日本晴为材料, 通过筛选已有的1017个标记, 并利用东乡野生稻基因组重测序信息设计的217个InDel标记, 共检测出203个标记在东乡野生稻与日本晴间呈现多态性。这些标记均匀分布于12条染色体, 平均间隔1.9 Mb, 基本覆盖东乡野生稻全基因组区域。通过对籼粳亚种的检验分析, 发现该套多态性分子标记在东乡野生稻与粳稻杂交后代群体基因型分析上具有较高的应用价值。本研究结果为发掘东乡野生稻的有利基因以及分子标记辅助选择育种提供了有力的工具。

关键词: InDel标记, 基因组重测序, 粳稻

Abstract:

Dongxiang wild rice is a type of common wild rice (Oryza rufipogon) that has the northernmost natural distribution of any wild rice species. The genome of Dongxiang wild rice differs from that of modern cultivated rice varieties (Oryza sativa). At present, a set of molecular markers that covers the entire genome of Dongxiang wild rice is lacking. In this study, we used Dongxiang wild rice and the Geng rice variety “Nipponbare” as research materials. By screening the existing collection of 1017 SSR and InDel markers and the 217 InDel markers which were designed using Dongxiang wild rice genome resequencing information, we obtained a set of 203 markers polymorphic between Dongxiang wild rice and ‘Nipponbare’, which were relatively uniformly distributed on the 12 rice chromosomes, and basically covered the entire genome, with an average inter-locus distance of 1.9 Mb. Through the genotyping of five Xian and five Geng varieties, we concluded that those 203 polymorphic molecular markers have a high application value in genotype analysis of Dongxiang wild rice and Geng rice offspring population. These results provide a powerful tool for exploring beneficial genes from Dongxiang wild rice as well as marker-assisted breeding and selection.

Key words: InDel marker, genome re-sequencing, Geng rice

图1

多态性分子标记筛选 1: 东乡野生稻; 2: 日本晴; 3: 东乡野生稻/日本晴杂合体; M: 标准分子量。"

表1

各染色体多态性标记分布"

染色体
Chromosome		 染色体长度
Chromosome length (kb)		 标记数量
Number of marker		 平均标记间隔
Mean interval
(kb)
1 43270 23 1881
2 35937 22 1633
3 36413 30 1213
4 35502 17 2088
5 29958 16 1872
6 31248 18 1736
7 29697 16 1856
8 28443 13 2187
9 23012 14 1643
10 23207 9 2578
11 29021 13 2232
12 27531 12 2294

图2

多态性分子标记在染色体上的分布图谱 每条染色体左边数字表示引物的物理位置(单位Mb)。"

图3

多态性分子标记在籼粳亚种中的应用 1: 东乡野生稻; 2: 日本晴; 3: 辽盐241; 4: 松粳8; 5: 吉粳88; 6: 淮稻9号; 7: 合系6号; 8: 黄花占; 9: 白玉丝苗; 10: 扬稻6号; 11: 湘晚籼12号; 12: 鄂中5号。"

表2

多态性标记籼梗亚种基因型鉴定一致性分析"

亚种
Subspecies		 鉴定总数
Number of
identification		 东乡野生稻基因型数目
Number of Dongxiang wild rice genotype		 日本晴基因型数目
Number of Nipponbare genotype		 杂合基因型数目
Number of heterozygous genotype		 其他基因型数目
Number of others
genotype
粳 295 (5×59) 34 (11.6%) 250 (84.7%) 6 (2.0%) 5 (1.7%)
籼 295 (5×59) 218 (73.9%) 40 (13.5%) 5 (1.7%) 32 (10.9%)
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