Saturday, November 19, 2011

'Arhar' genome decoded

Varanasi, November 4, 2011: A group of thirty-one Indian scientists from ICAR Institutes, State Agricultural Universities and Banaras Hindu University, led by Prof. Nagendra Kumar Singh from ICAR’s National Research Centre on Plant Biotechnology in New Delhi have decoded the genome of 'Arhar', the second most important pulse crop of India. This is the first plant genome sequenced entirely through a network of Indian institutions and it will provide highly valuable resource for variety improvement of pigeonpea.

Average pulse crop productivity in India has remained low at about 650 kg per hectare for the last six decades leading to soaring ‘Dal’ prices with increasing demands. Lack of high yielding, disease and pest resistant varieties is a major factor for the stagnant pulse productivity. Slow progress in breeding high yielding Arhar varieties is attributed to dearth of genetic information coupled with large crop duration and intractable pod borer problem and poor utilization of wild germplasm resources. Development of DNA markers tightly linked to important agronomic traits is a prerequisite for undertaking molecular breeding in crops. Availability of the Arhar genome sequence will accelerate development of new varieties and hybrids with enhanced productivity by making use of germplasm resources, in a way similar to the rice genome experience.

The genome of popular Arhar variety ‘Asha’ was assembled using long sequence reads of 454-FLXsecond generation sequencing technology resulting in 511 million base pairs of high quality genome sequence information. The scientists have identified 47,004 protein coding genes in the Arhar genome, of which 1,213 genes are for disease resistance and 152 genes for tolerance to drought, heat and salinity that make it a hardy crop. In contrast to soybean, Arhar has fewer number of genes for oil biosynthesis and larger number of genes for cellulose biosynthesis which make it an oil-free woody plant. The genome sequence was used to develop a large number of ‘Arhar’ DNA markers which were experimentally validated for high rate of variation among the pigeonpea varieties. These markers will be useful for DNA fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications.

Until a couple of years ago pigeonpea was considered an orphan legume crop because developed countries would not invest in the research due to the crop being cultivated mainly in the tropical and subtropical countries but now substantial amount of genomic resources have been generated, largely due to the efforts of Indo-US Agricultural Knowledge Initiative (AKI) and Network Project on Transgenics in Crops (NPTC) both with funding support from the ICAR.

Pigeonpea or red gram (‘Arhar’ or ‘Tur’) is an important grain legume (Pulse) crop of India. About 85% of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. India imports pigeonpea from Myanmar which is the second largest producer. The world acreage of pigeonpea is about 4.90 mha with annual production of about 4.22 mmt worth about 1.5 billion US dollars. India is the largest producer, consumer and importer of pigeonpea with annual production of 3.07 mmt, followed by Myanmar (0.72 mmt) and Malawi (0.15 mmt) (FAOSTAT 2008).

Know More….

How is Arhar genome going to benefit the Indian farmers and general public?

Presently, India is importing about 3 million tones of pulses at cost of about Rs. 7000 crores every year. The large demand supply gap has led to soaring prices of Dal and food inflation. The decoding of Arhar genome has unfolded its complete genetic information content which will help faster development of high yielding, disease resistant and insect resistant varieties of Arhar for higher productivity on the farmer’s field and lower prices of Dal in the market for the general public.

What is the Arhar genome project about?

The Arhar genome project was initiated under Indo-US AKI to generate all kinds of genomic resources in pigeonpea including EST sequences, trait mapping populations, mutant lines, BAC libraries, information databases and finally the complete physical map of the genome. Knowledge of location of each and every gene in the genome will help faster discovery of genes for important agronomic traits such as yield, disease resistance, insect resistance, water logging tolerance and breeding of improved variety of Arhar similar to rice and wheat.

Who funded the Arhar genome project?

The project was supported for four years (2005-06 to 2009-10) through the Education Division of ICAR. For the last two years (2010-11 and 2011-12) the project is being supported by the Crop Science Division of ICAR under NPTC project (Functional Genomics Component). The total cost of generating the first draft of Arhar genome sequence, including the support to AKI partners for arhar genomics resources has been about Rs. 11 crores over the last six years. ICAR is now putting heavy emphasis on the genomics of important indigenous crop plants untouched by the global genomics research.

What was the role of ICRISAT and USA in the Arhar genome project?

Dr. R.K. Varshney from ICRISAT Hyderabad supported by ICAR and GCP projects and Prof. Dough Cook from University of California, Davis USA, supported by an NSF grant were involved in the first phase of the Indo-US AKI project in generating EST resources and BAC-end sequences and SSR markers but after the conclusion of Indo-US AKI in 2009-10, they have not been associated with the Indian Arhar genome sequencing network.

What is the basic genetic information on Arhar?

Number of chromosomes: 11 pairs

Genome size (Physical): 858 Mb (million base pairs)

Genome size (Genetic): 1057 cM (centi Morgan)

How are plants different from animals in terms of total number of genes?

Plants seem to have higher number of genes than animals mainly due to genome duplications (polyploidy), but they also perform additional biological functions of converting solar energy to chemical energy and non-living matter into organic compounds. Also they need a large number of defense genes to survive in the open nature as they cannot run away. Animals on the other hand have more number of genes for highly developed senses and locomotion related functions. For defense they are able created more proteins from less number of genes due to post transcriptional processing of antibody genes.

Press release from PPP Cell-BHU

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