India in the Gene Pool of Crops

In 2010, India became the sixth country in the world to map the entire human genome. Decoding the human genome in entirety entailed the sequencing of 3.1 billion nucleotide (that in a certain sequence forms the gene) and identify all the approximately 20,000-25,000 genes in human DNA.

The International Wheat Genome Sequencing Consortium (IWGSC) has been working since 2005 to produce a high quality reference genome sequence for hexaploid (similar chromosomes in sets of six) bread wheat. Its aim is to generate a publicly available resource that provides an accurate representation of the structure and organization of sequence along individual chromosomes, enabling the identification of the position of genes, regulatory elements, sequence-based markers, and other features. Twenty three laboratories from 15 different countries are engaged in the project under the leadership of International Wheat Genome Sequencing Consortium (IWGSC). Today 80% of the wheat genome is represented in physical maps and around 15% is represented by high quality reference sequence.

Mapping the wheat genome

In nature, the bread wheat used today evolved after cross hybridization of three different but closely related species. This evolutionary process led to the accumulation of the largest content of DNA among all the food crops, making wheat genetics more complex than other food crops. Obtaining a high quality sequence for bread wheat is technically challenging. The genome is very large (17 Gb), 5 times larger than the human genome. Ten years back wheat was considered one of the toughest crops to decode due to its genome size of 17000 million base pairs, and presence of three sets of highly similar chromosomes in the genome and a very large proportion of repetitive DNA (ranging from 80- 90%). Dr Akhilesh Tyagi, Director of National Institute of Plant Genome Research has been at the helm of gene-mapping in case of crops. He says, ‘The blue print assembles only about 60 percent of the genome and we expect to assemble complete genome in next three years.

Completion of the wheat genome reference sequence is essential to accelerate breeding and the rapid identification of genes underlying complex traits such as yield, disease and pest resistance and non-biological stress tolerance. The genome sequence will aid breeders by enabling new strains to be developed. There would be decrease in time consumption from discovery to commercialization of new varieties for farmers.’  So far, chromosome map sequencing has been completed for only 3 chromosomes.

The genome reference sequence presents a benchmark for pitching the differences between varieties that are associated with different traits, and provide breeders and plant scientists with a molecular tool kit or marker-based selection, high throughput screening and the association of traits with specific genes and proteins. It can usher the production of a new generation of wheat varieties that will enable higher yields and improved sustainability of wheat production systems.

For each gene in wheat there are three copies, one from each of the three genomes, and in most cases only one copy expresses. How the plant decides which copy of the gene to express is most intriguing question in wheat biology. Availability of chromosome based sequence has opened new horizons for researching this issue.

The Tomato Story: slicing the genome

Very often you have cribbed over tomato perishing too fast. Perhaps such days will soon be over. In 2012, the Tomato Genome Consortium (TGC), a group organized in 2003 in Washington, consisting of over 300 scientists from fourteen countries sequenced the genomes of the domesticated tomato, Solanum lycopersicum. The Indian contribution harped on decoding the genomic sequence of specific regions of chromosome 5 of tomato by implementing Next Generation Sequence (NGS) technology. In India, the Initiative on Tomato Genome Sequencing (IITGS) was coordinated by Prof. A.K.Tyagi along with team members from University of Delhi, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute and National Institute of Plant Genome Research.

This achievement is expected to lower costs and speed up efforts to improve the worldwide tomato production, making it better equipped to combat the pests, pathogens, drought and diseases and of course the yield, quality, shelf-life and nutrition.  India happens to be the third largest producer of a variety of tomatoes after China and USA.

Why know the genetic buildup?

Dr Vijay Raghavan, secretary with the Ministry of Biotechnology is upbeat about the achievement, ‘Indian researchers took up the analysis of specific genes / gene families related to ripening, nutrition, disease resistance and abiotic stress tolerance based on transcriptome data and comparative genomics. The genomic resources generated are expected to greatly accelerate improvement of tomato by functional genomics and molecular breeding.’

 The sequences provide a detailed overview at the functional portions of the tomato genome and its closest relative, revealing the order, orientation, types and relative positions of their 35000 genes. The sequences will help researchers to decipher the relationships between tomato genes and its traits to exemplify the impact of genetic and environmental factors that interplay to determine the field crop’s health and viability.

Tomato factoid

Tomato is a member of the Solanacae or nightshade family, and the new sequences are expected to provide reference points helpful for identifying important genes in tomato’s relatives. The group includes potato, pepper, eggplant and petunia to constitute the world’s most prominent vegetable plant family in terms of both economic value and production volume. Solanacae members serve as sources of food, spices, medicines and ornamentals.

Tomato family contains 17 species. The wild ancestors of modern tomato still grow in Chile, Peru and Ecuador. Modern domesticated tomato belongs to the species S. Lycopersicum. Spanish explorers brought tomatoes to Europe in 1500s and to Asia subsequently. A large number of varieties were bred in North America in early 1800s onwards by great scientists like Charles Rick.

The genomic sequences offer insight into how tomatoes have diversified and adapted to new environments. They show that the tomato genome expanded abruptly about 60 million years ago, at a time close to one of the large mass extinctions.

Recognizing Chickpea gene-pool

In 2013, India along with 10 countries decoded the entire chickpea genome of 29000 genes located in 8 pairs of chromosomes. India is the largest producer, almost 70 percent of chickpea in the world. But the yield is less than 1 tonne per hectare. Now Indian Centre of Agriculture and Research (ICAR) is aiming to produce varieties with molecular breeding. But somehow no time-frame has been assigned. Their aim is to alter the genes for traits like early maturing, salinity tolerance and mineral content. Why hasn’t India harped on cracking sugarcane that is more beneficial to society, instead of groundnut? Prof Tyagi says, ‘Sugarcane has a huge genome making it a much more difficult task than groundnut.’

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