基于SSILP、InDel和SSR标记的杂草稻籼粳分类

doi:10.3969/j.issn.10017216.2012.06.008

中国水稻科学 ›› 2012, Vol. 26 ›› Issue (6): 686-692.DOI: 10.3969/j.issn.10017216.2012.06.008

基于SSILP、InDel和SSR标记的杂草稻籼粳分类

徐群¹,许红云² ,魏兴华^1，* ,汤圣祥¹,李东宣² ,陈丽娟²

¹中国水稻研究所水稻生物学国家重点实验室，浙江杭州 310006； ²云南农业大学稻作研究所，云南昆明650201；

收稿日期:2012-01-16 修回日期:2012-04-17 出版日期:2012-11-10 发布日期:2012-11-10
通讯作者: 魏兴华1，*
基金资助:
国家自然科学基金资助项目（30860057）；国家973计划资助项目（2011CB100401）。

SSILP, InDel and SSR Markersbased indicajaponica Classification for Weedy Rice

XU Qun¹ , XU Hongyun ² , WEI Xinghua ^1,* , TANG Shengxiang ¹ , LEE Dongsun ² , CHEN Lijuan ²

¹ State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China；² Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China；

Received:2012-01-16 Revised:2012-04-17 Online:2012-11-10 Published:2012-11-10
Contact: WEI Xinghua1,*

摘要/Abstract

摘要： 采用40对SSILP、30对InDel和43对SSR标记对来自斯里兰卡的28份杂草稻和14栽培稻，来自国内外的9份籼型栽培稻、7份粳型栽培稻和4份代表性杂草稻进行遗传多样性分析。SSILP、InDel和SSR标记分别检测到84、61和213个等位基因，其平均多态性信息含量(PIC)分别为0.257、0.255和0.543。聚类分析显示供试的42份斯里兰卡杂草稻和栽培稻均为籼型。SSILP与InDel标记的相关性很高（r=0.989），而它们与SSR标记相关性较低（0.812和0.808）。结果表明，SSILP和InDel标记可高效鉴别各类稻种资源的籼粳属性，而SSR标记更适用于亚种内的分类。

关键词: 杂草稻, 栽培稻, 分子标记, 籼粳分类

Abstract: Forty SSILP, 30 InDel and 43 SSR markers were used to compare genetic diversity of 42 weedy and cultivated rice entries from Sri Lanka, 9 indica and 7 japonica rice cultivars as well as four representatives of weedy rice from China and other countries(regions). There were 84, 61 and 213 alleles identified by SSILP, InDel and SSR markers, with average polymorphism information content (PIC) values 0.257, 0.255 and 0.543, respectively. The NJ clusters analysis indicated all 42 Sri Lanka weedy and cultivated rice entries belonged to indica type. The genetic distances of SSILP and InDel markers revealed highly correlation (r=0.989). Meanwhile the associations between SSR markers and the other two markers (SSILP and InDel) were lower as 0.812 and 0.808, respectively. With the rising reliability and accuracy of indicajaponica classification resulted from the development of more subspeciesspecific markers, SSILP and InDel markers can be applied extensively for the indicajaponica classification of rice germplasm. And SSR markers can classify better in the subspecies.

Key words: weedy rice, cultivated rice, molecular marker, indicajaponica classification

中图分类号:

徐群1,许红云2 ,魏兴华1，* ,汤圣祥1,李东宣2 ,陈丽娟2. 基于SSILP、InDel和SSR标记的杂草稻籼粳分类[J]. 中国水稻科学, 2012, 26(6): 686-692.

XU Qun1 , XU Hongyun2 , WEI Xinghua1,* , TANG Shengxiang1 , LEE Dongsun2 , CHEN Lijuan2. SSILP, InDel and SSR Markersbased indicajaponica Classification for Weedy Rice[J]. Chinese Journal of Rice Science, 2012, 26(6): 686-692.

参考文献

\[1\]Melchinger A E, Messmer M M, Lee M, et al. Diversity and relationships among UnitedStates maize inbreds revealed by restriction fragment length polymorphisms. Crop Sci, 1991, 31: 669678.

\[2\]Wei X H, Yuan X P, Yu H Y, et al. Temporal changes in SSR allelic diversity of major rice cultivars in China. J Genet Genom, 2009, 36, 363370.

\[3\]于萍, 袁筱萍, 徐群, 等. 中国常规稻主栽品种的遗传结构及籼粳组分变化.中国水稻科学， 2011, 25(4): 387391.

\[4\]Zhang H L, Sun J L, Wang M X, et al. Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR. Genome， 2007, 50: 7283.

\[5\]张晓丽，郭辉，王海岗，等. 中国普通野生稻与栽培稻种SSR多样性的比较分析. 作物学报，2008, 34(4): 591597.

\[6\]赵伟，夏寒冰，章淑杰，等. 籼粳特异插入/缺失分子标记揭示的稻属植物遗传分化. 复旦学报: 自然科学版，2008，47(3): 281287.

\[7\]Wang X S, Zhao X Q, Zhu J, et al. Genomewide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res, 2005, 12: 417427.

\[8\] Zhao X Q, Yang L, Zheng Y, et al. Subspeciesspecific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.). J Genet Genom, 2009, 36: 435442.

\[9\]Suh H S. Weedy rice. Wild Crop Germplasm Center & Yeungnam University, Korea, 2008: 1317.

\[10\]王黎明，陈勇. 杂草稻研究现状及利用展望. 植物保护, 2009, 35(5): 1417.

\[11\]Suh H S, Sato Y I, Morishima H. Genetic characterization of weedy rice (Oryza sativa L.) based on morphophysiology, isozymes and RAPD markers. Theor Appl Genet, 1997, 94:316321.

\[12\]Chen L J, Suh H S, Lee D S. Evolutionary significance of Chinese weedy rice “Lutao”. SABRAO J Breed Genet， 2001， 33(2): 99109.

\[13\]Panaud O, Chen X L, McCouch S R. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet, 1996, 252: 597607.

\[14\]Liu K, Muse S V. Power Marker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 2005, 21： 21282129.

\[15\]Patzak J. Comparison of RAPD, STS, ISSR and AFLP molecular methods used for assessment of genetic diversity in hop (Humulus lupulus L.). Euphytica, 2001, 121: 918.

\[16\]Peakall R, Smouse P E. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes, 2006, 6(1): 288295.

\[17\]Excoffier L, Laval L G, Schneider S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol Bioinform Online, 2005, 1: 4750.

\[18\]Yu G Q, B Y, Shi C H, Dong C Q, et al. Genetic diversity and population differentiation of Liaoning weedy rice detected by RAPD and SSR markers. Biochem Genet, 2005, 43: 261270.

\[19\]Zhang L J, Dai W M, Wu C, et al. Genetic diversity and origin of japonica and indicalike rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China. Genet Resour Crop Evol, 2012,59:399410.

\[20\]Cho Y G, Blair M W, Panaud O, et al. Cloning and mapping of variety specific rice genomic DNA sequences amplified length fragment polymorphisms (AFLP) from silverstained polyacrylamide gels. Genome, 1995, 39: 373378.

\[21\]Bres P C, Bangratz M, Ghesquiere A. Genetic diversity and population dynamics of weedy rice in the Camargue. Genet Select, 2001, 33(1): 425440.

\[22\]Garcia A A F, Benchimol L L, Barbosa A M M, et al. Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genet Mol Biol, 2004, 27: 579588.

\[23\]Heckenberger M, van der Voort J R, Melchinger A E, et al. Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties: Ⅱ. Genetic and technical sources of variation in AFLP data and comparison with SSR data. Mol Breeding， 2003, 12: 97106.

\[24\]Huang M, Xie F M, Chen L Y, et al. Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers. Rice Sci, 2010, 17(4):257268.

\[25\]Xu X M, Liang K J, Zhang S G, et al. Analysis of indicajaponica differentiation in rice parents and derived lines using ILP markers. Agric Sci China， 2009, 8(12): 14091418.

[1]	肖乐铨, 李雷, 戴伟民, 强胜, 宋小玲. 转cry2A/bar*基因水稻与杂草稻杂交后代的苗期生长特性[J]. 中国水稻科学, 2023, 37(4): 347-358.
[2]	王石光, 陆展华, 刘维, 卢东柏, 王晓飞, 方志强, 巫浩翔, 何秀英. 应用CRISPR/Cas9技术与分子标记辅助选择创制广东丝苗米新种质[J]. 中国水稻科学, 2023, 37(1): 29-36.
[3]	陈涛, 赵庆勇, 朱镇, 赵凌, 姚姝, 周丽慧, 赵春芳, 张亚东, 王才林. 利用分子标记辅助选择培育优良食味、低谷蛋白香粳稻新品系[J]. 中国水稻科学, 2023, 37(1): 55-65.
[4]	董铮, 王雅美, 黎用朝, 熊海波, 薛灿辉, 潘孝武, 刘文强, 魏秀彩, 李小湘. 基于MAGIC群体的水稻镉含量全基因组关联分析[J]. 中国水稻科学, 2022, 36(1): 35-42.
[5]	降好宇, 曾盖, 郝明, 黄湘桂, 肖应辉. 广谱抗稻瘟病种质75-1-127的褐飞虱抗性基因鉴定及分子标记辅助选择育种[J]. 中国水稻科学, 2019, 33(3): 227-234.
[6]	张宏根, 仲崇元, 司华, 刘巧泉, 顾铭洪, 汤述翥. 分子标记辅助选择改良C418对红莲型粳稻不育系的恢复力[J]. 中国水稻科学, 2018, 32(5): 445-452.
[7]	曾生元, 李闯, 杜灿灿, 孙立亭, 景德道, 林添资, 余波, 钱华飞, 姚维成, 周义文, 龚红兵. Pigm特异性选择标记的开发及其在粳稻穗颈瘟抗性育种中的利用[J]. 中国水稻科学, 2018, 32(5): 453-461.
[8]	梁燕, 季芝娟, 曾宇翔, 张翠真, 吴晗霖, 杨长登. 超级早稻中早39稻瘟病抗性的系谱分析[J]. 中国水稻科学, 2017, 31(4): 441-446.
[9]	汪文娟, 周继勇, 汪聪颖, 苏菁, 封金奇, 陈炳, 冯爱卿, 杨健源, 陈深, 朱小源. 八个抗稻瘟病基因在华南籼型杂交水稻中的分布[J]. 中国水稻科学, 2017, 31(3): 299-306.
[10]	井文, 章文华. 水稻耐盐基因定位与克隆及品种耐盐性分子标记辅助选择改良研究进展[J]. 中国水稻科学, 2017, 31(2): 111-123.
[11]	李威, 圣忠华, 朱子亮, 魏祥进, 石磊, 邬亚文, 唐绍清, 王建龙, 胡培松. 粳稻柱头外露率QTL定位[J]. 中国水稻科学, 2017, 31(1): 23-30.
[12]	丁国华, 孙健, 杨光, 张凤鸣, 白良明, 孙世臣, 姜树坤, 王彤彤, 郑洪亮, 夏天舒, 沈希宏, 马殿荣, 陈温福. 干旱胁迫下杂草稻和栽培稻根系基因表达差异研究[J]. 中国水稻科学, 2016, 30(5): 458-468.
[13]	袁筱萍, 王彩红, 邓宏中, 徐群, 冯跃, 余汉勇, 王一平, 魏兴华. 亚洲栽培稻遗传变异分析最少SSR引物数的研究[J]. 中国水稻科学, 2015, 29(6): 578-586.
[14]	徐霞, 张晓波, 施勇烽, 王惠梅, 黄奇娜, 奉保华, 李小红, 郭丹, 吴建利. 水稻褐色颖壳新等位基因OsFBX310^bh6的克隆鉴定[J]. 中国水稻科学, 2015, 29(4): 335-342.
[15]	刘洋, 刘二宝, 曾思远, 普伟, 刘强明, 梁利君, 刘佩睿, 张琪梦, 洪德林. 杂交粳稻亲本米质性状配合力的分子标记区段检测[J]. 中国水稻科学, 2015, 29(4): 373-381.

基于SSILP、InDel和SSR标记的杂草稻籼粳分类

SSILP, InDel and SSR Markersbased indicajaponica Classification for Weedy Rice

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics