Finger Millet Group Image Finger Millet

Resource Development for Finger Millet

Finger millet, Eleusine coracana subsp. coracana, is an important important staple upon which millions depend for food and rural household incomes in eastern Africa. It is more nutritious than other cereals and, when malted, is particularly valued as a weaning food because it provides more energy per feed than those based on gelatinized starch.  It is also a nourishing food for invalids and diabetics. Finger millet grows well with minimal inputs in marginal environments and it is often the only reliable food source for the very poor in times of drought and crop failure. The crop was domesticated from the wild species E. coracana subsp. africanaE. coracana is an allotetraploid with genome composition AABB.  The A genome was contributed by the diploid species E. indica while the B genome donor is unknown.  Very little is known about the genetics of finger millet.  We have two complementary projects funded by the Bill and Melinda Gates PEARL Program and NSF BREAD to develop genetic and genomic resources for finger millet with the aim of improving the crop for a number of traits, including resistance to the fungal pathogen Magnaporthe oryzae, the causal organism to blast disease.  These projects build on earlier work on the assembly and characterization of a finger millet germplasm, funded by BioInnovate Africa.

To date, little work has been done to improve this orphan crop, which typically yields only one third of its genetic potential of 6 ton/ha (Oduori, 2008). This is because most finger millets found in farmers' fields are landraces and these unimproved varieties are routinely challenged by the devastating blast disease, caused by the fungus Magnaporthe oryzae, which results in up to 90% yield losses in combination with other abiotic stresses. The main focus of our projects is on enhancing our understanding of the diversity and virulence/aggressiveness of finger millet infecting races of the blast fungus Magnaporthe orzyae in eastern Africa. This information will be used as a launch pad to enhance finger millet cultivars for blast resistance.

The combined aims of the two projects are:

(1) To collect and sequence 200 finger millet blast strains from across Eastern Africa to provide insight into the distribution and virulence/aggressiveness of finger millet blast pathotypes. The blast genome sequences will be mined to identify candidate effector genes using an effector prediction pipeline that incorporates common characteristics of known effectors (secretion and high polymorphism levels).

(2) To conduct an association analysis between already available genotyping-by-sequencing (GBS) data in a set of 120 finger millet accessions and their blast resistance phenotypes identified for two monoconidial blast isolates to identify markers linked to blast resistance for use in marker-assisted breeding.

(3) To conduct comparative sequence analyses of finger millet infecting strains with strains that are pathogenic to other grasses to determine to what degree knowledge gained in rice (and other grass) blast can be extrapolated to finger millet blast. Both rice blast and finger millet blast are caused by the same species, Magnaporthe oryzae, but display high host specificity and vary at the DNA sequence level.

(4) To generate a high quality assembly of the finger millet genome and resequence ~30 finger millet accessions.

(5) To analyze the blast-finger millet interaction transcriptome using RNA-Seq to identify genes that are induced at early stages of infection. Genes encoding secreted proteins will be identified from the RNA-Seq experiment and cross-referenced to those identified using the effector prediction pipeline. Host genes that are differentially expressed will be compared between compatible and incompatible interactions, and with genes that are differentially expressed during early stages of blast infection in rice.

(6) To develop a nested association mapping panel of some 4000 RILs derived from 21 diverse parents using a double round robin design. This population will represent the first mapping resource that captures substantial diversity present in finger millet germplasm and has a high quantitative trait loci detection power. 

Project participants:

Santie de Villiers (PI PEARL, Co-PI BREAD) - Pwani University, Kenya
Katrien M. Devos (PI BREAD, Co-PI PEARL) - University of Georgia, Athens, USA
Kassahun Tesfaye (Co-PI BREAD/PEARL) - Addis Ababa University, Ethiopia
Matthews Dida (Co-PI BREAD/PEARL) - Maseno University, Kenya
John Takan (Co-PI PEARL) - NaSSARI, Uganda
Chang Hyun Khang (Co-PI BREAD) - University of Georgia, Athens, USA
Mike Schatz (Co-PI BREAD) - Johns Hopkins University, USA
Damaris Odeny (Co-PI BREAD) - ICRISAT, Nairobi, Kenya
Justin Ringo (Co-PI BREAD) - Mikocheni Agricultural Research Institute, Tanzania

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