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et al. 2006; Garcia‐Lara et al. 2009; Krakowsky et al. 2004), making marker assisted selection (MAS) a
potentially viable strategy to improve resistance to these pests.
However, few molecular markers are being used in breeding programs, largely because little effort has
been put into breeder‐friendly marker development. This requires the establishment of a fine‐mapping
pipeline that will identify usable polymorphisms tightly linked to the genes of interest. Recent
reductions in the cost of genotyping have made the use of marker‐assisted selection (MAS) for this
purpose feasible for small commercial and public breeding programs in Africa. A systematic pipeline
designed to deliver breeder‐ready markers for these and other leaf and ear diseases and storage pests
should now be established to support rapid conversion of elite drought‐tolerant and other inbred lines
to higher levels of biotic stress resistance.
CIMMYT has developed several populations that can be used for marker identification, validation, and
fine mapping. These need to be phenotyped in multiple environments and genotyped at high density to
to identify suitable markers for use in selection. Marker development depends on good phenotypic data
to make reliable marker trait associations. To collect quality phenotypic disease data suitable for marker
identification, CIMMYT has established disease phenotyping hubs in southern Africa and Mexico and
equipped them with misting systems to create ideal microclimatic conditions for foliar disease
development. These are being used to screen elite inbred lines that form part of an association mapping
panel for resistance to GLS, NCLB, and SCLB. There are plans to establish similar hubs in West Africa and
Asia. Initial QTL localization will be done with these panels, which will also identify donors for use in
subsequent fine‐mapping. Marker development will benefit from use of standardized disease
establishment and scoring protocols across CIMMYT, IITA, NARSs and commercial partners.
Researchable issues
Further refinement of target regions with the greatest return to investment in drought tolerance
breeding, and specific needs of resource‐poor women and men in those regions.
The physiological and genetic (mostly polygenic) bases for improved yield under drought, nitrogen,
waterlogging, acid soils and heat stress, permitting the development of new selection systems and
marker–trait associations useful for accelerating breeding progress.
Determining the extent to which germplasm, selected for tolerance to single stresses such as
drought, is tolerant to the same stress in combination with other stresses such as heat, and
understanding the mechanisms for combined stress tolerance.
Understanding the genetic control of key adaptive traits (mostly oligogenic biotic stress resistance
traits).
Improved high‐throughput phenotyping approaches for component traits (spectral reflectance for
growth analysis, water and nutrient uptake, rhizotron facility for root system analysis, isotope
enrichment for water use efficiency (WUE), image analysis for growth and production, electrical
conductivity and spectral reflectance for site characterization).
Tagging genes/QTLs for key adaptive diseases (MSV, GLS, TLB, PFSR) and identification of breederready
markers for incorporating biotic stress resistance in elite germplasm.
Harmonizing phenotyping assays for important biotic stresses to reliably identify donors and
breeding materials with resistance to the target diseases.
Gene‐by‐germplasm and gene‐by‐environment interaction of individual native and transgenic genes
for stress tolerance with strong effect.
Use of crop models and genetic analysis to assess the relevance and design of managed abiotic
stress screening, and high‐throughput phenotyping and genotyping to maximize genetic gains in the
target environment and as climates change.
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