Transcriptomes of Indian barnyard millet and barnyardgrass reveal putative genes involved in drought adaptation and micronutrient accumulation

  • Murukarthick Jayakodi
  • Manimekalai Madheswaran
  • Karthikeyan Adhimoolam
  • Sampath Perumal
  • Dhasarathan Manickam
  • Thangaraj Kandasamy
  • Tae-Jin YangEmail author
  • Senthil NatesanEmail author
Original Article


Indian barnyard millet (Echinochloa frumentacea) is a rich source of dietary fiber, minerals and protein. The lack of genetic resources has slowed the discovery of genes involved in its nutrient accumulation and climate resilience. Here, we present the first transcriptomes of E. frumentacea [97,065 transcripts, including 65,276 protein-coding transcripts, over 90% of which have been functionally annotated, and 31,789 long noncoding RNA (lncRNA) transcripts] and its wild relative E. crus-galli (93,725 transcripts, including 68,480 protein-coding transcripts, 89% of which have been annotated). Comparative transcriptome analysis identified 4159 protein-coding and 2258 lncRNA transcripts in Indian barnyard millet that showed either up- or down-regulated expression when compared with E. crus-galli, and 3489 protein-coding transcripts unique to Indian barnyard millet were also detected. Additional analysis revealed that photosynthesis is likely crucial in the drought adaptation of Indian barnyard millet. We then identified possible genes regulation responsible for drought tolerance and Fe and Zn accumulation. Moreover, based on the simple sequence repeat (SSR)-containing sequence, 30 SSR primer pairs were arbitrarily selected, synthesized and used to screen the 30 E. frumentacea accessions. Of these, 10 SSR primers were polymorphic. Collectively, our results enhance the knowledge of micronutrient accumulation and drought tolerance in Indian barnyard millet, as well as of the genetic diversity of Echinochloa species.


Drought Simple sequence repeats Indian barnyard millet Micronutrients 



All the authors wish to acknowledge National Agricultural Development Programme (NADP)/Rashtriya Krishi Vikas Yojana (RKVY)—Tamil Nadu Govt, for providing financial support. Thanks to Centre of Innovation (CI), Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, for providing instrumentation facilities.

Compliance with ethical standards

Conflict of interest

The authors have declared that no competing, or conflicts of interest exist.

Supplementary material

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Supplementary file1 (XLSX 32 kb)
11738_2019_2855_MOESM2_ESM.doc (1.5 mb)
Supplementary file2 (DOC 1540 kb)


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Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2019

Authors and Affiliations

  • Murukarthick Jayakodi
    • 1
  • Manimekalai Madheswaran
    • 2
  • Karthikeyan Adhimoolam
    • 3
  • Sampath Perumal
    • 4
  • Dhasarathan Manickam
    • 3
  • Thangaraj Kandasamy
    • 2
  • Tae-Jin Yang
    • 1
    Email author
  • Senthil Natesan
    • 3
    • 5
    Email author
  1. 1.Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
  2. 2.Department of Plant Breeding and Genetics, Agricultural College and Research InstituteTamil Nadu Agricultural UniversityMaduraiIndia
  3. 3.Department of Biotechnology, Agricultural College and Research InstituteTamil Nadu Agricultural UniversityMaduraiIndia
  4. 4.Agriculture and Agri-Food CanadaSaskatoonCanada
  5. 5.Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and BiotechnologyTamil Nadu Agricultural UniversityCoimbatoreIndia

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