Post on 29-Nov-2014
description
TL 1 Objective 3: Improve common bean productivity for marginal environments in sub-Saharan Africa
Bodo Raatz CIAT
Lisboa, September 2013
• .
Using markers for biotic stress resistance
SNP genotpying: Tm shift assay
A
G
from Wang et al. 2005 °C
resistant
susceptible • Based on SNP-specific primers
• Genotyping by melting point analysis
• No fluorescent primers required
C-A
BCMV: bc-3 candidate gene: eIF4E NADERPOUR et al. MOLECULAR PLANT PATHOLOGY (2010)
primer 1
C
primer 2 A
primer reverse
BCMV: bc-3 Tms marker
resistent
susceptible
no call
all
Storage insects: bruchid resistance
Bruchids (Zabrotes subfasciatus)
PV-ATCT001, Yu et al, 2000
Dissociation CurveAPA gene
R
S
80 84
Common Bacterial Blight (CBB)
MAS with • SU91 on Chr8 (Pedraza et al.
1997) • SAP6 on Chr10 (Miklas et al.
2006)
Bacterial blight: Xanthomonas
CBB resistance QTLs
Marker conversions Chr Position G35346 AFR298 AND696 G10474 G40001 G5686 MD23-24 SEA5 VAX1 Chr01 219,278.00 T A A A A A A A A Chr01 219,650.00 T C C C C C C C C Chr01 219,722.00 T C C C C C C C C Chr01 219,749.00 G A A A A A A A A Chr01 219,950.00 C T T T T T T T T Chr01 219,952.00 T A A A A A A A A Chr01 220,668.00 T A A A A A A A A Chr01 221,020.00 G C C C C C C C C Chr01 252,386.00 C G G G G G G G G Chr01 252,420.00 T A A A A A A A A Chr01 253,519.00 A T T T T T T T T Chr01 253,526.00 T G G G G G G G G Chr01 253,542.00 C T T T T T T T T Chr01 258,082.00 C G G G G G G G G Chr01 264,339.00 C T T T T T T T T Chr01 265,119.00 T G G G G G G G G Chr01 265,168.00 T G G G G G G G G Chr01 265,336.00 A G G G G G G G G Chr01 265,418.00 C G G G G G G G G Chr01 265,713.00 C T T T T T T T T Chr01 265,722.00 C T T T T T T T T Chr01 266,882.00 C A A A A A A A A Chr01 267,398.00 A G G G G G G G G Chr01 267,562.00 C A A A A A A A A Chr01 267,688.00 T C C C C C C C C Chr01 267,727.00 T A A A A A A A A Chr01 268,418.00 C G G G G G G G G Chr01 268,648.00 A C C C C C C C C Chr01 271,111.00 A G G G G G G G G Chr01 271,132.00 T C C C C C C C C Chr01 271,437.00 A G G G G G G G G Chr01 271,644.00 T C C C C C C C C Chr01 272,223.00 G C C C C C C C C Chr01 272,579.00 G A A A A A A A A Chr01 272,645.00 G C C C C C C C C
Jorge et al
SNP sources: • 1500 SNP set
BeanCAP • 9 genotypes
sequenced
Angular Leaf Spot
Marker: Sc267437 Chr 8 G10474
Marker: P50 Chr. 4 G5686
• SNP based on SSR markers confirmed and converted
• Finemapping on Chr 4 – Resistance gene 43.5 – 43.9 Mbp
42.0 42.5 43.0 43.5 44.0 44.5 45
0
2
4
6
8
Chromosome 4 (Mbp)
LOD
scor
e
Beat Keller, 2013
Bean Stem Maggot • QTL mapping underway • 100 additional SNPs genotyped (Daniel Ambachew)
• BSM evaluations in Zimbabwe, Malawi and Ethiopia
tolerant susceptible
Maps for DOR x BAT SER16 x G35346
Drought tolerance and root traits
-1 Yield Root traits
QTL analysis Federico Velasquez
Map for SEA x MD
MARS
• PhD thesis of Fitsum Alemayehu SARI, Ethiopia
• Population of ~200 Lines • Phenotyping drought & irrigated at 4
locations – 2x Palmira, 2x Ethiopia
• Genotyping: – Kbio/LGC ~150 SNP markers – additional 14.000 fluidigmdata points
• Marker Analysis in progress – DNAs sent, extracted from seed
(CAL 143xSAB 620) X SAB 626 (SAB 628xCAL 143) X SAB 659 (SAB 628xCAL 143) X SAB 686
G 12229 x AND 277
CAL143
(ABA 58x AFR298)F1xSAB258 (COS 16 x AFR298)F1 x SAB258
SAB258 ABA58 AFR298 COS16
41 lines 54 lines 30 lines
26 lines 42 lines
F5
F5 F1: CAL 143xSAB 620 F1: SAB 628xCAL 143
F1: ABA 58x AFR298 F1: COS 16 x AFR298 F1 F1 F1
F1 F1
SAB620 SAB626 SAB628 SAB659 SAB686
MARS
Evaluation Evaluation Evaluation Evaluation
Population development
F1 F2
F4
• QTL Analysis • Select markers
F5
MARS
MARS
Evaluation Evaluation Evaluation Evaluation
Population development
F1 F2
F4
• QTL Analysis • Select markers
F5
MARS
• QTL Analysis • Select markers
Genotype
F3
MARS Genotype
evaluate
Select worst lines Select best lines
• QTL Analysis • Select markers
F4 F5
evaluate
F4 F5
F4 F5
evaluate
MARS Conventional selection
Select worst lines Select best lines
F3 F3
2nd MARS crossing
cycle
•Select best lines •Make new crosses
MAGIC
• 8-parental population established • F4:6 Phenotyping started in July • Genotyping: DNA ready to send for GBS
SXB 412 INB 827 ALB 213 SEN 56 SCR 2 MIB 778 SCR 9 INB 841
79 F1 5 F1 38 F1 99 F1
323 F1 272 F1
728 F1 500 selected
499 F2
996 F3 families
926 F4.5 families
926 F4:6 families
MAGIC population in common bean (mesoamerican gene pool)
Genotype individuals
Drought phenotyping
MAGIC • 648 genotypes in current drought trial
Breeding products Relationship between irrigated and rainfed grain yield of 36 common bean genotypes grown under field conditions at CIAT-Colombia (2013)
AFR298
CAL143 CAL96
DAB 231 DAB 233
DAB 236
DAB 244
DAB 251
DAB 252
DAB 256
DAB 258
DAB 267
DAB 277
DAB 295 DAB 344
DAB 353
DAB 366
DAB 374 DAB 380
DAB 384
DAB 396
DAB 398
DAB 402
DAB 441 DAB 489 DAB 494 DAB 514
DAB 520 DAB 525
DAB 528 DAB 534
DAB 541
DAB 545
DAB 549 DAB 555
KATB1
0
200
400
600
800
1000
1200
2000 2500 3000 3500 4000 4500
drou
ght Y
DHA
irrigated YPDA
2013 YDHA
Data management
• Adopting defined file formats
• Adopting barcoding • Adopting use of barcoding for seed storage
organization
• Training of partners to adopt defined file formats
Sheet 1 Sheet 2
Trial data Controlled vocabulary trait dictionary
Metadata • Sowing date • Location • Person in charge
Capacity building • Workshop with 30+ breeders in
Kawanda • 2 workshops at CIAT (n ~20) • Fitsum Alemayehu (phd student,
Ethiopia) visited CIAT for 3 months.
Conclusions • MAS for biotic stress moving toward routine • MAGIC and MARS moving forward • Advanced lines show improved yield under
drought • Data Management moving towards adoption • Capacity building ongoing
Anticipated impact: improved germplasm …
View to the future • Unite TL 1 and TL2 activities
• Technology changes – GBS: for fingerprinting, population genotyping – genomic selection
• Fingerprinting / Forensics – Specific projects need to be defined – Impact studies – software
• Organizational changes – Extend work with partners – Data management -software – Links to
• Soils work, agronomy • Other downstream activities
Thank you for your attention!
SARI Ethiopia SARI SELIAN Tanzania DARS Malawi DR&SS Zimbabwe KARI Kenya CIAT Africa