Abstract With the development of functional genomics, expressed sequence tags (ESTs) has become an important resource of PCR-based molecular markers for plants. This paper briefly reviews advancement in functional molecular markers for plants in the functional genomics era, including EST-SSR, CAPS, SNP, SRAP and TRAP. Compared with conventional markers, the EST-derived markers are a novel type of molecular tool with remarkable advantages, such as being easily to develop, more informative, and highly transferable, especially for preferential targeting ORFs. Applications of the new functional molecular markers in plants genetics and breeding are summarized in this paper, such as construction of genetic linkage maps, important trait gene tagging location, comparative mapping, genetic diversity, cultivars identification and marker-assisted selection breeding.
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