Scientia Agricultura Sinica ›› 2011, Vol. 44 ›› Issue (18): 3701-3708.doi: 10.3864/j.issn.0578-1752.2011.18.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS •     Next Articles

Application of High-Resolution Melting Curve Analysis for Molecular Marker Genotyping in Rice

ZHAO  Jun-Liang, ZHANG  Shao-Hong, LIU  Bin   

  1. 1. 广东省农业科学院水稻研究所
  • Received:2011-01-12 Revised:2011-03-08 Online:2011-09-15 Published:2011-09-15

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Abstract: 【Objective】 In order to test the feasibility and reliability of high-resolution melting curve analysis (HRM) for molecular marker genotyping in rice crop, SSR, InDel and SNP genotyping of a rice recombinant inbred line (RIL) population and their parents were conducted using HRM. 【Method】 A japonica cultivar Lijiangxintuanheigu (LTH), an indica cultivar Sanhuangzhan 2 (SHZ-2) and their derived RIL populations were used. The amplicons of the two molecular markers, a SSR marker and an InDel marker, which could not be differentiated by non-denaturing polyacrylamide gels electrophoresis (PAGE), and the amplicons of a G/A transition SNP marker, were subjected to HRM analysis. The reference homozygous DNA from LTH was added before PCR. 【Result】 By adding reference DNA, the heterozygous and two different homozygous genotypes generated from SSR, InDel and SNP, respectively, could be distinguished by HRM. The best discrimination for the three genotypes was given when the amount of reference DNA was equal to 20% template DNA. The genotypes of two parents and their derived RI lines based on HRM were perfectly consistent with those based on denaturing PAGE. 【Conclusion】 HRM can be used for SSR, InDel and SNP genotyping in rice. Comparing with PAGE, HRM has the advantages of high resolution, high through-put, simplicity and safety. It is a promising technology for molecular marker analysis in rice.

Key words: rice, SSR, Indel, SNP, HRM

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