InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes

Abstract

Abstract: High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed.

Key words: rice, molecular marker, insertion-deletion length polymorphism, single nucleotide polymorphism, bioinformatics, gene mapping, rolled leaf gene

PAN Cun-hong, LI Ai-hong, DAI Zheng-yuan, ZHANG Hong-xi, LIU Guang-qing, WANG Zi-bin, MA Yu-yin, YIN Yue-jun, ZHANG Ya-fang, ZUO Shi-min, CHEN Zong-xiang, PAN Xue-biao. InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes[J]. RICE SCIENCE, 2008, 15(4): 251-258 .

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