This document summarizes several maize projects focused on improving phosphorus use efficiency and tolerance to aluminum toxicity through marker-assisted breeding and gene discovery. Key activities include phenotyping maize panels to identify genes associated with root architecture traits and phosphorus efficiency, developing near-isogenic lines carrying tolerance genes, and generating hybrid varieties with improved tolerance for testing and release in Kenya. Looking ahead, the projects aim to validate additional aluminum tolerance genes, genotype novel sources of tolerance, and conduct joint studies of root architecture genes that may also improve drought tolerance.

1. Maize Projects in the Comparative
Genomics Challenge Initiative
• G7010.03.02: Validation of ZmMATE’s as genes underlying major Al
tolerance QTLs in maize - COMPLETED
•G7010.03.01: Cloning, characterization and validation of PUP1/P efficiency
in maize – NEARLY COMPLETED
• G7010.03.05: Marker-assisted breeding for improving phosphorus-use
efficiency and tolerance to aluminum toxicity in maize – NEARLY COMPLETED
COMPLETION STRATEGY
• G7010.03.01 – Maize PUP1 Genes Project: Need to phenotype Buckler
association panel in lab for 3D root system architecture traits and in the field
at JIRCAS for P efficiency traits on low P and sufficient P soils for association
analysis work. Also phenotype the Embrapa diversity and RIL panels for 3D
RSA traits. Completed by mid 2015.
• G7010.03.0 – Maize MABC for Al Tolerance and P Efficiency Genes Project :
Complete generation of Al tolerant and P efficient top cross hybrids. Then
assess at multiple national field sites in Kenya for national registration and
release to farmers. Completed by end of 2015

2. PRODUCTS
•Validation of major maize Al tolerance gene, ZmMATE1 which underlies
major QTL on chr 6.
- Markers linked to ZmMATE1 and chr 6 Al tolerance QTL.
- Near-isogenic lines and NIL-hybrids introgressed with Al tolerance QTL.
- Elite Brazilian & Kenyan lines characterized for Al tolerance and ZmMATE1 expression: new
sources of superior alleles
- Possible source of novel Al tolerance loci in very Al tolerant Kenyan maize line.
• Maize P efficiency QTL & Genes
- RIL population segregating for P efficiency and RIL backcross and testcross populations.
- P efficiency QTL - overlap of P efficiency QTL with root trait QTL.
- NILs for specific P efficiency QTL in different backgrounds.
- Candidate P efficiency genes (OsPSTOL1 homologs) based on localization with P efficiency
and/or root trait QTL and “appropriate” gene expression properties.
• MABC of Al tolerance & P efficiency
- Al tolerant and P efficient top cross hybrids developed – some have been registered in Kenya
for release to farmers with others in the pipeline.
- Single cross hybrids tolerant to both Al toxicity/P deficiency
- Three different sets of locally adapted Kenyan germplasm introgressed with ZmMATE1 gene
from Brazilian maize

3. Looking to the Future
• Develop markers that are diagnostic for the very high expression ZmMATE1
alleles (that are 3 copies in tandem).
• We have intriguing molecular and genetic evidence for novel Al tolerance
genes in Brazilian germplasm. Identification and validation of these new Al
tolerance genes for introduction into our MABC pipelines.
• Evidence for novel Al tolerance gene(s) in Kenyan germplasm (203B). Need to
genotype mapping population from 203B x Al sensitive parent via GBS to
obtain improved QTL data to assist in cloning of QTL.
• Complete validation of identity of those ZmPSTOL genes that are involved in P
efficiency – expression in transgenic lines and then lab and field evaluation.
• Joint linkage-GWA analysis of 3D root system architecture traits to identify
architecturally complex root traits important for P efficiency . A possible side
product of this may be that this will be a useful resource for genes and/or root
system architecture ideotypes controlling deep rooting for water acquisition
under drought conditions.
• Possible sources of funding: Land these work in maize CRP? Claudia
Guimaraes and Babu Raman of CIMMYT looking for extramural funding for joint
research mining CIMMYT maize germplasm for novel ZmMATE1 alleles. Gates
Foundation is another possibility.