Integrating genomics and mapping approaches to improve pearl millet productivity in drought prone regions of Africa and Asia

Declining water resources and unpredictable rainfall are serious threats to crop productivity throughout the world. Climate change scenarios indicate that water shortage and shortening of the effective growing season will be increasingly likely in sub-Saharan Africa and South Asia increasing the need for short-duration cereals such as pearl millet with enhanced drought tolerance. Although pearl millet is better adapted to water stress compared to other cereals, drought remains one of the most important factors in reducing yield and yield stability of this staple food grain crop of the world's poorest people. Improving pearl millet's tolerance to drought offers a sustainable route to alleviate poverty and food insecurity of pearl millet farmers in sub-Saharan Africa and South Asia. Efficient breeding for drought-prone environments, however, requires selection strategies that are sufficiently independent of the variation inherent in the natural environment to permit identification and use of true genetic differences. Molecular markers linked closely to traits such as pearl millet grain and stover yield during drought will provide increased reliability for selecting and breeding of these traits. The proposed research will conduct targeted genetic mapping of a genomic region on linkage group 2 known to be associated with a major drought tolerance QTL in pearl millet, in combination with precision phenotyping. A large population that is segregating only for the target drought tolerance QTL will be studied with the aim to delimit this QTL and identify closely-spaced markers. In addition, a large and diverse pearl millet germplasm panel will be used to identify additional favourable alleles/haplotypes associated with this QTL, using association genetic analysis. This association mapping is complementary to the targeted mapping approach and will identify more generic gene-based markers within the QTL. These markers would then be available for use in the transfer of this important drought tolerance QTL into a number of elite genetic backgrounds adapted to locations in Africa and Asia, using marker assisted back crossing, in collaboration with participating NARS scientists. Such material would be available as pre-breeding lines for future variety development in different parts of Africa and Asia, and involvement of NARS scientists in the process of this research, will ensure both training as well as the technology transfer. We will also explore potential physiological drought tolerance traits in near isogenic line pairs with and without the LG2 QTL to determine which traits relate to the field drought tolerance in this material. Such physiological information will help design new ideotypes of pearl millet (and other cereals) for drought-prone environments and enhance the understanding of the physiological mechanisms underlying this QTL. The direct beneficiaries of this project will be resource poor subsistence farmers in areas of Africa and Asia where pearl millet is the staple cereal and for whom food security is a very big issue. Marker-assisted breeding methods have the potential to dramatically improve the efficiency of breeding pearl millet hybrids that have improved drought tolerance together with local adaptation requirements combined with locally-preferred grain quality and improved yield attributes. The output of the proposed project will also provide a ground for map based cloning of drought tolerance gene(s) in future studies. While immediately applicable to pearl millet, generic knowledge and methodologies developed in this project will contribute to the global pool of knowledge in the important research area of drought tolerance and facilitate increased and sustainable crop production in water-limited environments globally.

Pearl millet [Pennisetum glaucum (L.) R. Br.] is the staple cereal crop grown by subsistence farmers in the hottest, driest regions of sub-Saharan Africa and the Indian subcontinent where rain-fed crop production is possible. Unreliable and scant rainfall is the most important factor contributing to low grain and straw yields and poor yield stability of this crop. Efficient breeding for drought-prone environments requires selection strategies that are sufficiently independent of the variation inherent in the natural environments to permit identification and use of true genetic differences. The project will conduct targeted genetic mapping of a genomic region associated with a major drought tolerance QTL on LG 2 in pearl millet and identify closely-spaced gene-based markers associated with this QTL. An agronomically-elite near-isogenic population that segregates only for the genomic region associated with the drought tolerance QTL will be mapped with a wide range of novel markers identified using comparative mapping methods. In a complementary approach, association of these markers to the drought tolerance QTL will be tested by conducting association genetic analysis to identify more generic gene-based markers within the QTL. The tightly linked gene-based markers associated with the drought tolerance QTL thus identified will then be used to transfer this important QTL into a number of elite genetic backgrounds adapted to locations in Africa and Asia, using marker assisted back crossing. The near-isogenic lines developed will also be evaluated at various sites in Africa and Asia to confirm the effect of the QTL in a range of environments and to identify morpho-physiological traits associated with improved drought tolerance. Generic knowledge and methodologies developed in this project will contribute to the global pool of knowledge in this important research area and facilitate increased crop production in water-limited environments globally.