3 Biotech

, 8:95 | Cite as

Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.)

  • B. Kalyana BabuEmail author
  • Salej SoodEmail author
  • Dinesh Kumar
  • Anjeli Joshi
  • A. Pattanayak
  • Lakshmi Kant
  • H. D. Upadhyaya
Original Article


Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.


Cross-genera transferability Barnyard millet SSR markers Population structure Orthologs 



The authors thank Indian Council of Agricultural Research for financial support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13205_2018_1118_MOESM1_ESM.docx (271 kb)
Supplementary material 1 (DOCX 270 kb)
13205_2018_1118_MOESM2_ESM.docx (14 kb)
Supplementary material 2 (DOCX 13 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • B. Kalyana Babu
    • 1
    • 3
    Email author
  • Salej Sood
    • 1
    • 4
    Email author
  • Dinesh Kumar
    • 1
  • Anjeli Joshi
    • 1
  • A. Pattanayak
    • 1
  • Lakshmi Kant
    • 1
  • H. D. Upadhyaya
    • 2
  1. 1.ICAR-Vivekananda Parvatiya Krishi Anusanthan SansthanAlmoraIndia
  2. 2.International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  3. 3.ICAR-Indian Institute of Oil Palm ResearchWest GodavariIndia
  4. 4.ICAR-Central Potato Research InstituteShimlaIndia

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