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Comparative genomics to improve cereal yields in high-aluminium and low-phosphorous soils

Product Delivery Coordinator: Leon Kochian

Executive summaries:

The Comparative Genomics Challenge Initiative was officially launched in May 2010 at a workshop held Eldoret, Kenya. Current projects in this CI are:

G3007.04: Tailoring superior alleles for abiotic stress genes for deployment into breeding programmes: a case study based on association analysis of AltSB, a major aluminium tolerance gene in sorghum (PI: Jurandir Vieira Magalhaes, EMBRAPA)
G3008.04: Drought from a different perspective: Improved tolerance through Phosphorous acquisition (PI: Sigrid Heuer, IRRI)
G4008.10: Assessment of the breeding value of superior haplotypes for AltSB, a major Al tolerance gene in sorghum: linking upstream genomics to acid soil breeding in Niger and Mali (ALTFIELD) (PI: Robert Schaffert, EMBRAPA)
G4008.41: Application and validation of the major QTL phosphate uptake 1 (Pup1) (PI: Sigrid Heuer, IRRI)
G7009.07: Cloning, characterization and validation of AltSB/Al tolerance in rice (PIs: Susan McCouch/Leon Kochian, Cornell University and USDA-ARS)
G7010.03.01: Cloning, characterization and validation of PUP1/P efficiency in maize (PI: Leon Kochian, USDA-ARS/Cornell University)
G7010.03.02: Validation of ZmMATEs as genes underlying major Al tolerance QTLs in maize (PI: Claudia Guimaraes, EMBRAPA)
G7010.03.03: Establishing a molecular breeding program based on the aluminum tolerance gene, AltSB, and the P efficiency QTL, Pup-1, for increasing sorghum production in Sub-Saharan Africa -(SorghumMB) (PI: Eva Weltzien, ICRISAT - Mali)
G7010.03.04: Developing Rice with Dual Tolerance of Phosphorus Deficiency and Aluminum Toxicity: Marker-Assisted Pyramiding of Pup1 with Novel Tolerance QTLs (PI: Sigrid Heuer, IRRI)
G7010.03.05: Marker-assisted breeding for improving phosphorus-use efficiency and tolerance to aluminum toxicity in maize (PI: Samuel Gudu, Moi University/KARI, Kenya)
G7010.03.06: Improving phosphorus efficiency in sorghum by the identification and validation of sorghum homologs for Pup1, a major QTL underlying phosphorus uptake in rice (SorghumPup1) (PI: Jurandir Magalhaes, EMBRAPA)

Past events

Comparative Genomics CI Launch workshop, 14–15 May 2010, Eldoret, Kenya

Workshop materials (link to program & pdfs)

Research Initiatives

GCP's crop research is based on seven crop- and crop cluster-based Research Initiatives (RIs). Each RI is led by a Product Delivery Coordinator. At their formation, the RIs were known as Challenge Initiatives (CIs). Access the individual Research Initiative InfoCentres (on the left-hand menu) for further information including research databases, research products, facts and figures, feature stories, blogposts, videos and more.

The seven Research Initiatives

cassava-sky n-palmer ciat-square-small legume diversity ciat web-square-small  maize-diversity x-fonseca cimmyt-web1-square-small  rice-paddy n.palmer ciat-square-small  sorghum s-sridharan-square-small  wheat-field cimmyt-square-small  n.palmer ciat-maize-rice-sorghum-web-square-small
1. Cassava –
yield in Africa's
2. Legumes –
tropical legume
productivity for
in sub-Saharan
Africa and
South Asia

(beans, chickpeas,
cowpeas, groundnuts)
3. Maize –
tolerance in
maize for Asia
4. Rice –
in rice
for Africa
5. Sorghum –
in sorghum
for Africa
6. Wheat –
in wheat
for Asia
7. Comparative
to improve
cereal yields in

(maize, rice
& sorghum)

The seventh RI in comparative genomics takes advantage of knowledge in model crops to facilitate gene discovery in other genomes – one of the challenges GCP is supposed to address. The main objective of this RI is to build on the Phase I characterisation of genes identified in Phase I (Alt1 and Pup1) to identify orthologous gene(s) for aluminium tolerance in rice and sorghum, and to improve phosphorus uptake efficiency in sorghum and maize.

All in all, each RI features the following:

  • A first component on the phenotypic characterisation of contrasting and diverse set of germplasm (eg, reference sets, introgression lines, synthetics, etc). The main output will be germplasm, with new elite alleles for agronomic traits, for prebreeding activities.
  • A strong molecular breeding component – the core of RI activities – focusing primarily on marker-assisted recurrent selection, marker-assisted selection mainly for cassava and some of modified backcross-based nested association mapping (BCNAM) populations for sorghum. The main output will be improved germplasm for breeding activities.
  • A strategic data management component to ensure scientists plan for sufficient time and resources to appropriately analyse store and label the data generated during the five years of the second phase. The main output will be a user-friendly dataset accessible to, and useable by, colleagues within and without GCP.
  •  A significant capacity-building component, at both the human and infrastructure level, to ensure that developing-country partners can conduct field experiments, and appropriately manage and analyse project data. The main output will be a network of partners able to use modern breeding tools in a sustainable manner and a set of molecular breeding communities of practice.