The first draft of the pigeonpea genome sequence

Area of Science:

• Genomics
• Plant Science
• Agricultural Science

Background:

• Pigeonpea (Cajanus cajan) is a vital legume crop for food and nutritional security, particularly in India.
• India produces and consumes over 85% of the world's pigeonpea.
• Understanding the pigeonpea genome is crucial for crop improvement.

Purpose of the Study:

• To present the first draft genome sequence of the pigeonpea variety 'Asha'.
• To identify genes related to disease resistance, abiotic stress tolerance, and biosynthesis pathways.
• To develop molecular markers for pigeonpea germplasm analysis and breeding.

Main Methods:

• Genome assembly using long sequence reads (454 GS-FLX) with >550 bp read length and >10-fold coverage.
• Gene prediction for protein-coding genes and transposable elements.
• Identification of disease resistance, abiotic stress tolerance, and comparative gene content analysis with soybean.
• Scaffold anchoring to chromosomes using genic-SNP markers.
• Development and validation of hypervariable 'Arhar' simple sequence repeat (HASSR) markers.

Main Results:

• A high-quality pigeonpea genome sequence of 510,809,477 bp was assembled.
• 47,004 protein-coding genes and 12,511 transposable element genes were predicted.
• 1,213 disease resistance genes and 152 abiotic stress tolerance genes were identified.
• Pigeonpea exhibits fewer lipid biosynthesis genes and more cellulose synthesis genes compared to soybean.
• Eleven chromosomes were anchored, showing synteny with soybean chromosomes.
• 437 HASSR markers were validated for polymorphism, useful for breeding.

Conclusions:

• The first draft genome sequence of pigeonpea provides a valuable resource for genetic improvement.
• The identified genes and markers will facilitate breeding for enhanced food and nutritional security.
• This achievement represents a significant milestone for Indian agricultural research institutions.