This document discusses the progress made in various integrated breeding projects under Theme 2. It notes that marker-assisted breeding projects for crops like sorghum, rice, chickpea, and cowpea have advanced from concept to execution stages with some populations ready for QTL analysis or near completion of phenotyping and genotyping. Infrastructure improvements for field trials have also been implemented across various African sites. Feedback from a brainstorming session indicated that MABC and MAS are seen as most immediately applicable for breeders' short-term needs, especially for qualitative traits. However, constraints like availability of local genotyping facilities, cost of genotyping, lack of trait mapping information, and need for more training still prevent broader application of markers

1. Theme 2 perspectives
Integrated Breeding

2. Theme 2 has come a long way
since the last GRM
 MARS projects have moved from concept to execution
 Sorghum MARS at first recombination stage
 IRRI rice and chickpea MARS ready for QTL analysis
 Cowpea phenotyping almost completed, genotyping in
progress
 Mexico bean project waiting for SNP genotyping (phenotyping
almost completed)
 Asia DT maize genotyped but more phenotyping needed
 Cassava MARS populations planted in the field for
phenotyping, ready for genotyping
 West Africa rice CI, wheat CI and TL1 bean projects getting
close to phenotyping and genotyping stages

3. Theme 2 has come a long way
since the last GRM
 High throughput marker services ready for business
 Good sets of public SNPs available in all crops (except for
groundnuts)
 Conversion to KASPar platform completed for most crops, to
be completed soon for beans and wheat, additional SNPs
coming for rice
 KBioscience services starting to be used by multiple projects
 Extended breeding lines fingerprint project to be started soon

4. Theme 2 has come a long way
since the last GRM
 Field infrastructure improvement project coming to
fruition
 Weather stations installed at 19 African locations
 New irrigation system being installed at 13 African sites
 Operational or nearly so at 6 sites
 Four more sites to be completed by end 2011
 Engineering design work being started for 3 new sites
 Plot rehabilitation, fencing and other necessary improvements
also implemented as needed
 Goal to have irrigation and other improvements ready at all 10
Phase 1 sites by end of year

5. Feedback from brainstorming
session
 What MB approaches are most useful to meet short-
term NARS breeders needs?
 MABC and MAS seen as most immediately applicable
 A number of programs are already using them (with SSRs)
 Routine use for wheat in India, getting there for rice
 Especially applicable for qualitative traits (pest tolerance, etc.)
 Early use of MABC helps introduce new traits into breeding
programs
 MARS still in exploratory stage
 Seen as potentially very useful for quantitative traits
 Best potential in maize, sorghum
 GWS not seen as having much impact in the short term, could
have good potential for the future

6. What MB approach (MABC, MAS, MARS, GWS) would be
most useful to address your breeding needs?
%
MAS
MABC
MARS
GWS

7. Feedback from brainstorming
session
 What constraints do you still have preventing broad
application of markers in your programs?
 Availability of local facility for genotyping (although not as much
of an issue anymore with KBioscience contracting)
 Cost of genotyping
 Lack of trait mapping information limiting MAS and MABC use
in many crops
 Unvalidated QTLs
 Transferability of markers across populations
 Need to have fine mapping around key traits to eliminate
deleterious linkages
 More training on MAB methodologies still needed
 More training on handling of large amounts of genotyping data