Specific goal: Public availability of genome-wide molecular markers for ICRISAT's crops for use in molecular tagging and selection programs

Outputs:

1. At least 2000 PCR-based markers for each species
2. Low-cost, high-throughput assay marker assays
3. Global, public database with marker information

The major objective of ICRISAT's efforts in structural and functional genomics applications is to identify, isolate and manipulate gene sequences for traits of interest in ICRISAT's mandated crops. To accomplish this, it is necessary to have a number of genomic resources available. Molecular markers of various types (eg, RFLPs, AFLPs, SSRs, SNPs and DArTs) are necessary for analyzing the molecular diversity in a species, and for locating specific genes and QTLs in the genome. Markers such as AFLPs can be developed from generic resources available commercially, while markers such as RFLPs, SSRs and SNPs require significant investment to develop. For ultimate ease of use in breeding, marker types based on simple PCR techniques (SSRs, SNPs and DArTs) are desirable. The availability of each of the more important marker types for each mandated crop is listed in the following table.

For crops such as sorghum and chickpea, a large number of molecular markers are already available and the number is expected to continue to increase. This is true especially for sorghum, where it has recently been announced by the US Department of Energy that the sorghum genome will be sequenced starting in 2006. Pearl millet and groundnut have a number of markers available, although a much larger number is required to provide adequate coverage of the genome, especially in the portion of the genome far from the centromere that is insufficiently covered in pearl millet. For pigeonpea and most of the minor millets, the number is extremely limited and considered inadequate for most mapping and breeding purposes.

Molecular markers can be developed via a number of different strategies (eg, from EST and/or BAC libraries). The specific strategy to be employed will depend on the status of various other genomic resources in the targeted species. In some cases, it will be desirable to target specific genomic regions to saturate a region known to contain gene(s) of interest. Some targeting could benefit from a comparative approach using a species such as rice, maize or soybean that have available high-density maps. It is envisioned that marker development would be developed in partnership with public (and private) collaborators in developed and developing countries (eg, sorghum and pearl millet with USA; chickpea and pigeonpea with India; groundnut with Brazil, India and USA, DArTs with DArT P/L in Australia).  

For further information, contact Rajeev Varshney, Dave Hoisington, S Senthivel