Authors: Amolkumar U. Solanke*, S. V. Amitha Mithra and Basavaprabhu L. Patil
ICAR-National Research Centre on Plant Biotechnology (NRCPB),
LBS Centre, IARI , Pusa Campus, New Delhi, 110012, India
*Corresponding author: Amol.Solanke@icar.gov.in
Plant genomics is a multidisciplinary approach to unravel the structure, function and evolution of genomes in plants to answer fundamental biological questions regarding plant evolution, domestication and utilization. Genomics includes sequencing of genomes, determination of the complete set of transcripts and proteins encoded by the genome and identification of function of genes and metabolic pathways in an organism. Arabidopsis being the first sequenced plant genome plays the pivotal role of serving as a model plant for characterization of many genes in crop plants. Rice has the distinction of the first crop genome sequenced in the world. With the advent of Next Generation Sequencing (NGS) technologies, by now, more than 100 plant species have been sequenced and many more are in pipeline.
Genomics has several practical applications in crop improvement. Genomics is useful in identification and characterization of agronomically important genes, mining of superior alleles, comparative genomics for orphan crops or crops with large and complex genomes, development of DNA markers, molecular tagging of useful traits, marker assisted selection, genome-wide association mapping, Quantitative trait loci (QTL) identification, development of transgenic crops and understanding evolution. The availability of genomic resources and advances in our understanding of gene function along with the available natural genetic variation will equip the plant breeders to design crops with enhanced yield, quality and better survival under adverse environmental conditions.
Arabidopsis thaliana genome was unraveled in 2000 (AGI, 2000) followed by the draft genome of both subspecies of rice, Oryza japonica and indica, the most important staple food for more than half of the world in 2002 (Goff et al., 2002; Yu et al., 2002). Subsequently, the high-quality genome sequence of Oryza japonica rice was published by the International Rice Genome Sequencing Consortium in 2005. Later, tomato, a representative species for half of the vegetable crops, was undertaken by the international research community for sequencing. Though tomato was initially sequenced with the traditional Sanger sequencing method, the development of Next Generation Sequencing (NGS) platforms provided a major thrust to sequencing efforts (The Tomato Genome Consortium, 2012). Later NGS became the integral part of all whole genome sequencing projects. It has also enabled sequencing of bread wheat (Triticum aestivum), the most important cereal crop next to rice, despite having a very huge and complex genome. Till date, more than 100 plant genomes are sequenced and almost a new genome is decoded every month. Recently, Beijing Genomics Institute (BGI) has launched the 3-Million Genomes Project targeting genomes of a million plants, animals and microbes. Apart from whole genome sequencing, generation of transcriptome data has become a routine exercise, augmenting the resources to more than 75 million ESTs from around 25000 organisms in the NCBI dbEST domain (https://www.ncbi.nlm.nih.gov).
- Goff S.A., et al., 2002. A draft sequence of the rice genome ( Oryza sativa L. ssp. japonica). Science, 296: 92-100.
- The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
- 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.
- Yu J., et al., 2002. A draft sequence of the rice genome ( Oryza sativa L. ssp. indica). Science ,296: 79-92.
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