Biotechnology Letters

, Volume 36, Issue 3, pp 417–426 | Cite as

From genomics to functional markers in the era of next-generation sequencing

  • R. K. SalgotraEmail author
  • B. B. Gupta
  • C. N. StewartJr.


The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of “perfect” markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.


Crop plants Functional markers Genomic selection Next generation DNA sequencing Plant biotechnology, plant breeding, polymorphisms 



R. K. Salgotra is thankful to the Department of Science and Technology (DST) of Government of India for providing BOYSCAST Fellowship to carry out research at Plant Molecular Genetics Laboratory, University of Tennessee, USA.


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • R. K. Salgotra
    • 1
    Email author
  • B. B. Gupta
    • 1
  • C. N. StewartJr.
    • 2
  1. 1.Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, ChathaJammuIndia
  2. 2.Plant Molecular Genetics, Department of Plant SciencesUniversity of TennesseeKnoxvilleUSA

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