Resources
Germplasm Collection
Genomic Resources
Genetic Mapping
QTL Mapping
Comparative Genomics
Transcriptomics
Genome Sequencing
Genome Manuscript
International Pearl Millet Genome Sequencing Consortium (IPMGSC)

Project Director : Rajeev K. Varshney
                                      Research Program Director – Grain Legumes
                                      Director – Centre of Excellence in Genomics
                                      International Crops Research Institute for the Semi-Arid Tropics  (ICRISAT),
                                      Hyderabad, India

                                      E-mail: r.k.varshney@cgiar.org

Pearl millet (Pennisetum glaucum L.) is a fifth most important cereal primarily grown for food grain, fodder and construction material by smallholder farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. The crop occupies approximately 30 million hectares annually, providing nutritious staple food grains for more than 100 million households – especially the poorest rural households in some of the hottest, driest rainfed farming regions. Pearl millet can be considered as “neglected” as compared to rice, maize, wheat, barley and sorghum, for which there is a much larger global scientific community at work.

In order for producers and consumers of this dryland cereal to benefit from recent technological advances in genetics and plant breeding, it is essential that minimum genomic tool kits be developed for this crop. In this context, restriction fragment length polymorphism (RFLP)-based marker-assisted backcrossing with the elite donor parent ICMP 451 was used to add downy mildew resistance to the male parent H 77/833-2. RFLP technology is expensive and cumbersome as compared to modern genomics tools such as simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs) and genotyping-by-sequencing (GBS). Though some efforts in pearl millet have been made in the recent past to develop genomic tools such as SSRs (700) and DArT markers (15,360), the marker repertoire is still very poor as compared to other cereal crops.

With the objective to develop ample genomic resources for enhancing breeding efficiency, ICRISAT has established an informal consortium of research organizations with expertise in genome sequencing, crop genomics and pearl millet research with the overall objective to sequence the pearl millet genome. The consortium members include the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT, http://www.icrisat.org); L’institut de recherché pour le développement in France (IRD, http://www.ird.fr); the Indian Council of Agricultural Research in India (http://www.icar.org.in/); the University of Georgia (http://www.uga.edu); Cornell University (http://www.cornell.edu/); University of Florida (http://agronomy.ifas.ufl.edu) in the USA; L'Institut Sénégalais de Recherches Agricoles (ISRA; http://www.isra.sn/) and Pioneer Overseas Corporation, India (http://www.pioneer.com/web/site/india); Recently Fort Valley State University, USA (http://www.fvsu.edu); University of Vienna, Austria (http://www.univie.ac.at); Oklahoma State University, USA (http://biochemistry.okstate.edu) and Consiglio Nazionale delle Ricerche, Italy (http://www.cnr.it/sitocnr/home.html) has joined the consortium.

Tift 23D2B1, the global reference genotype and an important ancestral genotype of many seed parents of pearl millet hybrids in use for forage and grain in the USA as well as dual-purpose hybrids in India, has been chosen for developing the draft genome sequence. A high quality draft genome assembly is being developed using a hybrid sequence assembly approach (whole genome shotgun sequence (WGS) data and BAC sequencing data together with a restriction site associated DNA (RAD) sequence tag based genetic map). In parallel, re-sequencing of 993 pearl millet germplasm lines (including 606 B and R-lines and 387 pearl millet inbred genotypes association panel; PMiGAP lines) by using whole genome re-sequencing (WGRS) and/or RAD-sequencing is in progress. Further, to enhance precision in gene prediction and gene annotation, ICRISAT, in collaboration with IRD and UGA has developed a comprehensive transcriptome assembly.

In collaboration with several international partners, we are in the process of assembling and analyzing the pearl millet genome. These data are primarily meant for consortium members. Consortium members can download these data by clicking here.

In addition to basic genome analysis (e.g., genome organization, gene prediction and annotation, and comparison of the genome with other sequenced cereals), large scale and genome-wide simple sequence repeat (SSRs) and single nucleotide polymorphism (SNPs) will be identified that will be readily available to the pearl millet genetics and breeding community.

Click here to download the Supplementary information.

Consortium members (key colleagues from different participating institutes)
ICRISAT, India: Mahendar Thudi, Anu Chitikineni, Rachit K Saxena, Krishnamohan Katta, Rakesh Srivastava, SK Gupta, Trushar Shah, Abhishek Rathore & Stefania Grando
                              Kenya: Damaris Odoeny
                              Mali: C Tom Hash, Falalou Hamidu
Beijing Genomics Institute (BGI), Shenzhen, China:
                              Xin Liu, Xun Xu, Wang Jun
Institut de recherché pour le developpement (IRD), France:
                              Yves Vigouroux
Cornell University, USA:
                              Jason Wallace, Edward Buckler
University of Georgia, USA:
                              Peggy Ozias-Akins, Katrein Devos, Jeff Bennetzen
University of Florida, USA:
                              Jianping Wang
Senegalese Agricultural Research Institute (ISRA), Senegal:
                              Ndjido Kane, Mame Codou Gueye
Indian Council of Agricultural Research (ICAR), India:
                              Swapan K Datta, AICRP Coordinator- Pearl Millet
Pioneer Overseas Corporation, India:
                              RS Mahala
Fort Valley State University, USA:
                              Somashekar Punnuri, Bharat Singh
University of Vienna, Austria:
                              Palak Chaturvedi, Arindam Ghatak, Wolfram Weckwerth
Oklahoma State University, USA:
                              Ramanujulu Sunkar
Consiglio Nazionale delle Ricerche, Italy:
                              Francesca Sparvoli

Consortium members
ICRISAT ICAR FLORIDA IRD CSHL BGI CORNELL
GCP PIONEER BMGf FVSU UNIVIE OKSTATE CNR
Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
© Center of Excellence in Genomics. 2008