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Acta Agron Sin ›› 2016, Vol. 42 ›› Issue (06): 932-941.doi: 10.3724/SP.J.1006.2016.00932

• RESEARCH NOTES • Previous Articles    

Development of 295 InDel Markers for Indica andJapanicaRice

CHU Zhi-Zhan1,GUO Hai-Bin2,ZENG Dong-Chang1,LIU Yao-Guang1,*?   

  1. 1 College of Life Sciences, South China Agricultural University/ State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou 510642, China;2Center of Experimental Teaching for Common Basic Course, South China Agricultural University,Guangzhou 510642,China
  • Received:2015-11-09 Revised:2016-01-11 Online:2016-06-12 Published:2016-03-14
  • Contact: 刘耀光, E-mail: ygliu@scau.edu.cn E-mail:chuben@scau.edu.cn
  • Supported by:

    This study was supported by the Open Fund Project of State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources(SKL-CUSAb-2013-04)and the Natural Science Fund of Guangdong Province-the Launch Program for Doctor (2015A030310485).

Abstract:

Insertion/Deletion (InDel) markers have advantages of simplicity and reliability for genotyping.We selected 634 candidate InDelmarkers distributing throughout the 12 chromosomes of riceby comparing genome sequences between the japonica cultivarNipponbare and the indica cultivar 93-11. PCR results of these candidate markers betweentwojaponica(Nipponbare and Taizhong 65) and twoindica(9311 and Huanghuazhan)cultivars revealed that295 InDelmarkersdisplayed common polymorphisms between the japonica and indicacultivars which is useful for gene mapping and molecular breeding involving inindica andjaponicasubspecies.

Key words: InDel marker, Rice, Gene mapping

[1]Jeon J S, An G. Gene tagging in rice: a high throughput system for functional genomics. Plant Sci, 2001, 161: 211–219
[2]Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, Wang G, Qian L L, Li X, Yu Q B, Liu H J, Chen D H, Gao J H, Huang H, Shi T L, Yang Z N.Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.Plant Physiol, 2004, 135: 1198–1205
[3]王林友, 张礼霞, 勾晓霞, 范宏环, 金庆生, 王建军. 利用InDel标记鉴定浙优系列杂交稻籼粳属性和预测杂种优势. 中国农业科学, 2014, 47: 1243–1255
Wang L Y, Zhang L X, Gou X X, Fan H H, Jin Q S, Wang J J. Identification of indica-japonica attribute and prediction of heterosis of Zheyou hybrids rice using indel molecular markers.SciAgric Sin, 2014, 47: 1243–1255(in Chinese with English abstract)
[4]Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res, 2001, 11: 1441–1452
[5]McCouch S R, Teytelman L, Xu Y, Lobos K B, Clare K, Walton M, Fu B Y, Maghirang R, Li Z K, Xing Y Z, Zhang Q F, Kono L, Yano M, Fjellstrom R, DeClerck G, Schnbeider D, Cartinhour S, Ware D, Stein L. Development and mapping of 2240 new SSR markers for rice (Oryza sativaL.). DNA Res, 2002, 9: 199–207
[6]International Rice Genome Sequencing Project. The map-based sequence of the rice genome.Nature, 2005, 436: 793–800
[7]冯芳君, 罗利军, 李荧, 周立国, 徐小艳, 吴金, 陈宏伟, 陈亮, 梅捍卫. 水稻InDel和SSR标记多态性的比较分析. 分子植物育种, 2005, 3: 725–730
Feng F J, Luo L J, Li Y, Zhou L G, Xu X Y, Wu J, Chen H W, Chen L, Mei H W. Comparative analysis of polymorphism of InDel and SSR markers in rice. Mol Plant Breed, 2005, 3: 725–730(in Chinese with English abstract)
[8]Guillemaut P, Mardchal-Drouard L. Isolation of plant DNA: A fast, inexpensive, and reliable method. Plant Mol Biol Rep, 1992, 10: 60–65
[9] Bassam B J, Caetano-Anollés G, Gresshoff P M. Fast and sensitive silver staining of DNA in polyacrylamide gels. AnalBiochem, 1991, 196: 80–83
[10] 王明军, 王云月, 陆春明, 杨慧, 王云涛. 利用籼粳稻特异InDe标记分析云南糯稻品种的籼粳特性. 云南农业大学学报(自然科学版), 2010, 25: 333–337
Wang M J, Wang Y Y, LuC M, Yang H, Wang Y T. Characteristic of Yunnan Glutinous rice varieties revealed by the indica-japonica specified Insertion/Deletion (InDel) molecular markers. J Yunnan AgricUniv(Nat Sci), 2010, 25: 333–337(in Chinese with English abstract)
[11] 姚国新, 黄文超. 利用水稻籼粳分化InDel标记鉴定育种材料的籼粳属性. 杂交水稻, 2013, 28(3): 53–57
Yao G, Huang W. Identifying indica-japonica characteristic of rice breeding materials with indica-japonica differentiation InDel markers. Hybrid Rice, 2013,28(3): 53–57(in Chinese with English abstract)
[12] Qian H R, Zhuang J Y, Lin H X, Lu J, Zheng K L. Identification of a set of RFLP probes for subspecies differentiation in Oryza sativa L. Theor Appl Genet, 1995, 90: 878–884
[13] Dudley J W, Maroof M A, Rufener G K. Molecular markers and grouping of parents in maize breeding programs. Crop Sci, 1991, 31: 718–723
[14] Joshi S P, Gupta V S, Aggarwal R K, Ranjekar P K, Brar D S. Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet, 2000, 100: 1311–1320
[15] Moreno S, Martín J P, Ortiz J M. Inter-simple sequence repeats PCR for characterization of closely related grapevine germplasm. Euphytica, 1998, 101: 117–125
[16] Prevost A, Wilkinson M J. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet, 1999, 98: 107–112

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