Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping

  • Rajeev K VarshneyEmail author


Development and application of molecular markers derived from genes, commonly called genic markers or sometimes functional markers, is gaining momentum in plant genetics and breeding. Availability of large amount of sequence data coming from genome/transcriptome sequencing projects as well as advent of next generation sequencing technologies together with advances in bioinformatics tools, marker discovery is becoming cheaper and faster. The availability of inexpensive high-density SNP-genotyping arrays is encouraging the plant genetics and breeding community to undertake genome-wide marker genotyping for a variety of applications. For instance, high-throughput and low cost genotyping assays for gene-based markers offers the possibility to accelerate the trait mapping based on high-density linkage mapping as well as genome-scanning based association mapping approaches in addition to facilitate physical mapping, comparative mapping, phylogenetic studies and understanding genome organization in crop plant species. Marker discovery, genotyping and molecular breeding practices would be routine in near future for crop improvement in many crop species. Advances in the area of marker discovery and genotyping using highly parallel genomics assays and also a few applications have been discussed in this chapter.


Single Nucleotide Polymorphism Marker Cleave Amplify Polymorphic Sequence Cleave Amplify Polymorphic Sequence Marker Single Nucleotide Polymorphism Locus Generation Sequencing Technology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Thanks are due to Generation Challenge Programme (GCP), National Fund of Indian Council of Agricultural Research, Pigeonpea Genomics Initiative under Indo-US Agricultural Knowledge Initiative (AKI) and Department of Biotechnology (Government of India) for funding the research of author on development of genic molecular markers in legume species at ICRISAT.


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© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  2. 2.Generation Challenge Programme (GCP) CIMMYTMexicoMexico

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