Indian efforts towards whole genome sequencing of crop plants
Authors: S. V. Amitha Mithra*, Amolkumar U. Solanke and Basavaprabhu L. Patil
ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi
*Corresponding author:

India entered the international arena of plant genomics research with the prestigious International Rice Genome Sequencing Project (IRGSP), with the responsibility of sequencing long arm of chromosome 11 of rice which wasfunded by Department of biotechnology (DBT), Government of India. National Research Centre on Plant Biotechnology (NRCPB) under Indian Council of Agricultural Research (ICAR), and University of Delhi South Campus (UDSC) successfully generated gold standard sequence of rice chromosome 11 in the interval of 57.3 to 110.1 cM which harbours R-genes governing disease resistance in high density. The high quality rice whole genome information was published in 2005 and is now being used for functional and comparative genomics, and mapping and cloning of agriculturally important genes across the globe with the ultimate aim of breeding better rice varieties. Subsequent to this, India was the obvious choice in the International Tomato Genome Sequencing Consortium, for sequencing the 5th chromosome of tomato. ICAR and UDSC were responsible for sequencing the long arm of chromosome 5 in the interval of 73 to 119 cM, which was accomplished successfully by these institutes. From these ventures, Indian scientists gained the necessary expertise and established required infrastructure to take up greater challenges in the field of plant genomics and decided to give emphasis to dig into the genomes of crops that are economically important and indigenous to the country. In this endeavor, pigeonpea was the first plant genome sequenced entirely through a network of 31 Indian scientists from ICAR institutes and other Indian Universities. This effort was led by NRCPB, New Delhi culminating in the publication of pigeonpea draft genome in the year 2012. Subsequent to this, in 2018, the improved genome of pigeonpea was also published by the same network of scientists. In 2017, draft genome of dark jute, cv. Navin (Corchorus olitorius), and an indigenous high volume crop (in terms of produce) of the country was published. The longer merged reads from Illumina MiSeq platform facilitated economical de-novo assembly of jute genome into 52,373 contigs (377.3 Mbp) covering 90.8% of the estimated genome size. Recently, the draft genome of mango cv. Amrapali, another high volume and economically important fruit crop of India has been generated and the data is drafted for a publication. Currently Indian scientists are working on decoding the genome of clusterbean, an important indigenous and industrially important legume crop of which India is the major producer. Another international collaboration resulted in 2013 in the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Wheat genome is the largest amongst cultivated crop species with genome size of 17 Gb packed in 21 chromosomes. Punjab Agricultural University, ICAR-NRCPB and UDSC became partners in International Wheat Genome Sequencing Consortium (IWGSC) for generating the gold standard sequence of wheat chromosome 2A. Draft genome sequence of wheat was generated and published in 2012 while the complete genome is under preparation. Owing to these developments over the last two decades, India now has improved capabilities with skilled human resource and infrastructure in the field of genomics, bioinformatics and computational biology.


  • International Rice Genome Sequencing Project, (2005) The map-based sequence of the rice genome. Nature, 436: 793-800.
  • Mahato A et al., (2018) An improved draft of the pigeonpea ( Cajanus cajan (L.) Millsp.) genome. Data Brief. 16: 376–380.
  • Sarkar d, Mahato A, Sathya P et al., (2017) The draft genome ofCorchorus olitorius cv. JRO-524 (Navin). Genomics Data 12: 151-154 (2017)
  • Singh NK et al., (2012) The first draft of the pigeonpea genome sequence. J. Plant Biochem. Biotechnol. 21: 98–112.
  • The International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum) genome. Science 345 (6194: 1251788
  • The Tomato Genome Consortium (2012) Tomato genome sequencing and comparative analysis reveal two consecutive triplications that spawned genes influencing fruit characteristics. Nature, 485: 635-641.
  • Varshney R. K. et al., (2012) Draft genome sequence of pigeonpea ( Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 33: 83-89
  • Varshney R. K. et al., (2013) Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement. Nature Biotechnology 31: 240–246

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