The document discusses the sequencing of the pigeonpea genome by Indian scientists. It provides background on pigeonpea and describes the key aspects of the genome sequencing project, including that it was led by Indian scientists and funded by ICAR. It sequenced the genome of the popular Indian variety Asha, identifying over 47,000 genes including some for traits like disease resistance. The sequencing work has implications for crop improvement and utilizes genetic resources conserved in gene banks. However, it notes some controversy as two Indian research groups claimed to have independently sequenced the genome.

1. Submitted To:-
Prof. Dr. Rajesh Singh
Submitted By:-
Utkarsh Jamindar
ID- 14169
B.Sc.(Ag) Part-I
PIGEONPEA GENOME SEQUENCING

2.  Pigeonpea (Cajanus cajan (L.) Millspaugh) belongs to family Fabaceae with chromosome no. 2n=22 and
genome size of 858 Mbp
 A major source of protein to about 20% of the world population (Thu et al., 2003).
 An abundant source of minerals and vitamins (Saxena et al., 2002).
 Most versatile food legume with diversified uses such as food, feed, fodder and fuel.
 It is hardy, widely adaptable crop with better tolerance to drought and high temperature.
 Plays an important role in sustaining soil productivity by fixing atmospheric nitrogen.
 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).
Pigeon pea

3. Decoding of Pigeon pea
• 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 (Agricultural Knowledge Initiative) 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.
• Variety selected for the project?
• The genome of popular Arhar variety ‘Asha’ was assembled using long sequence reads of 454-FLX
second 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.

4. Decoding of Pigeon pea
• What was the role of Indian Scientists?
• 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 at 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.
• Institutions involved
• National Research Centre on Plant Biotechnology (ICAR), New Delhi
• Indian Agricultural Research Institute (ICAR), New Delhi
• Indian Institute of Pulse Research (ICAR), Kanpur, UP
• Banaras Hindu University, Varanasi, UP
• Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra
• University of Agricultural Sciences, Dharwad, Karnataka

5. Decoding of Pigeon pea
• 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.

6. Basic genetic information on
Pigeon pea
• Number of chromosomes=11 pairs
• Genome size (Physical)=858 Mb(million base pairs)
• Genome size (Genetic)=1057 cM (centi Morgan)
(as per ICAR database)

7. Research implications
• Several genes, unique to pigeonpea, that have been identified for
drought tolerance. Future research may find ways of transferring
these genes to other legumes in the pigeonpea family such as
soybean, cowpea, and common bean, so that these crops will also
become drought resistant - a significant asset in view of the
increasingly drier climates in these crops' production areas.
• Genes for other agronomically important traits can also be
identified and used to enhance not only pigeonpea but other
legumes too.
• Genomewide association studies can now be created to assess
thousands of pigeonpea accessions held in collections around the
world. The genebank at ICRISAT alone holds more than 13,600
accessions. The potential diversity of genes among these yet-to-
be-studied accessions can now be explored at much lower cost
and much more quickly. The chances are also higher of finding
variant genes whose superiority is such that they can be used to
improve not only pigeonpea but also other legumes.

8. Research implications
• With the genome sequence as a reference, it would be faster
and cheaper to screen ‘good genes’ from seed collections
stored in genebanks. This would also help cut down on the
time taken to breed new varieties from 6-10 years to just
about 3 years.
• Transferring genes from the crop's close relatives, and even
other, more distant, legumes to pigeonpea varieties will
become more practical, thus helping to broaden the crop's
genetic diversity.
• The decoding of the genome will also help clarify the roles
that certain gene families have played in the evolution and
domestication of pigeonpea and its ancestors and relatives.

9. Controversy
• Two separate groups of Indian scientists have laid claim on cracking
the genome of the pigeonpea — called the poor man’s meat —
sparking off a controversy on the prestigious genome projects.
• The ICAR scientists reported their finding online1 on October 25, 2011
and posted a press statement on the ICAR website on November 2. The
ICRISAT group, partnering with Chinese and American organisations,
published their paper 12 days later on November 6, 20112 but an
embargoed press release was doing the rounds on November 1.
• The major difference between the two sequencing projects is that while
the ICRISAT-led team has assembled 605.78 Mb out of the 833.07 Mb
(about 72.5%) of the genome, the ICAR team has captured 511 Mb
(about 61%). Both groups have submitted their data to the US-based
National Centre for Biotechnology Information (NCBI) Genbank, an
open access, annotated collection of all publicly available nucleotide
sequences and their protein translations.