1. : ALTSORGHUM Project
Practical Application of Markers
Jurandir Magalhaes
Maize and Sorghum
- GCP General Research Meeting, Hyderabad, 21 – 25 September 2011 -

2. Physiological Mechanism Encoded by AltSB
 Al-induced organic acid release
Al-citrate
Citrate
Citrate
Citrate
+Citrate Al3+
Citrate : Al3+
(Non-toxic)
(phytotoxic)
+Citrate Al3++Citrate Al3+
Citrate : Al3+
(Non-toxic)
(phytotoxic)
0.0
1.0
2.0
3.0
4.0
0 50 100 150
RRG
RRGRelativeExpression
Al tolerance (RNRG)
r=0.98
(P<0.001)
0.0
1.0
2.0
3.0
4.0
0 50 100 150
RRG
RRGRelativeExpression
Al tolerance (RNRG)
r=0.98
(P<0.001)
24.6 Kb
AltSB: ORF7
ATG TGA 1kb
8 9
AltSB: ORF7
ATG TGAATG TGA 1kb
8 9
Positonal Cloning/Comparative
Genomics rice x sorghum
AltSB: SbMATE

3. Molecular Breeding for Al Tolerance in Sorghum
Weltzien et al. Sorghum diversity and adaptation to drought in West Africa
Allele mining
 MABC

4. 1.3m
1.5m
1.4m
1.8m
2.0m
2.0m
1.3m
1.5m
1.4m
1.8m
2.0m
2.0m
T A GA A
C G GA A
C G TA A
T A TC G
C G TA G
T G GA G
T A GA AT A GA A
C G GA AC G GA A
C G TA AC G TA A
T A TC GT A TC G
C G TA GC G TA G
T G GA GT G GA G
Association Mapping
Linkage Mapping
Allele MiningMABC
Markers genetically linked to
AltSB
Functional loci or
loci in LD with QTN(s)
Nature Review Genetics
2:1-9 (2001)

5. G10-brazilian lines
G9-Caudatum from Africa
G7-Guinea from Western AfricaG7-Guinea from Western Africa
G6- Guinea from Asia
G5-Guinea from southern Africa
G4-Dura from Asia andAfrica
G3-Caudatum,bicolor from China
G11-Kafir from southern Africa
G8-transplanted sorghum from Chad and Cameron
G1-Guine margaritiferum
G2-USA lines
G10-brazilian lines
G9-Caudatum from Africa
G7-Guinea from Western AfricaG7-Guinea from Western Africa
G6- Guinea from Asia
G5-Guinea from southern Africa
G4-Dura from Asia andAfrica
G3-Caudatum,bicolor from China
G11-Kafir from southern Africa
G8-transplanted sorghum from Chad and Cameron
G1-Guine margaritiferum
G2-USA lines
Association Analysis of AltSB
Fernanda Caniato

6. SbMATE_I2_6083pb
Gene fragment 700pb
C-specific allele 483pb
A-specific allele 240pb
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A-specific allele 240pb
BR007
SC283
SC283
SC283
BR007
BR007
Het.
Het.
Gene fragment 700pb
C-specific allele 483pb
A-specific allele 240pb
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A-specific allele 240pb
BR007
SC283
SC283
SC283
BR007
BR007
Het.
Het.
Gene fragment 700pb
C-specific allele 483pb
A-specific allele 240pb
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A-specific allele 240pb
BR007
SC283
Gene fragment 700pb
C-specific allele 483pb
A-specific allele 240pb
Gene fragment 700pbGene fragment 700pb
C-specific allele 483pbC-specific allele 483pb
A-specific allele 240pbA-specific allele 240pb
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A-specific allele 240pb
BR007
SC283
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A-specific allele 240pb
(Gene Fragment) 700pb
C-specific allele 483pb
A
C
A
C
A-specific allele 240pb
BR007
SC283
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
BR007
SC283
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
BR007
SC283
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
independent amplicon (control) 700pb
C
G
A-specific allele 254pb
C-specific allele 254pb
independent amplicon (control) 700pb
C
G
C
G
A-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
G-specific allele 254pb
C-specific allele 254pb
Gene fragment 700pb
Gene fragment 700pbGene fragment 700pb
G-specific allele 254pbG-specific allele 254pb
C-specific allele 254pbC-specific allele 254pb
Gene fragment 700pbGene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
BR007
SC283
SBMATE_I2_6094pb
independent amplicon (control) 700pb
BR007
SC283 A
G
A-specific allele 361pb
G-specific allele 361pb
Gene fragment 700pb
G-specific allele 361pb
A-specific allele 361pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
independent amplicon (control) 700pb
BR007
SC283 A
G
A-specific allele 361pb
G-specific allele 361pb
independent amplicon (control) 700pb
BR007
SC283 A
G
A-specific allele 361pb
G-specific allele 361pb
BR007
SC283 A
G
A
G
A-specific allele 361pb
G-specific allele 361pb
Gene fragment 700pb
G-specific allele 361pb
A-specific allele 361pb
Gene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
Gene fragment 700pbGene fragment 700pb
G-specific allele 361pbG-specific allele 361pb
A-specific allele 361pbA-specific allele 361pb
Gene fragment 700pbGene fragment 700pb
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SC283
SC283
BR007
BR007
Het.
Het.
SBMATE_I2_5985pb
HETEROZIGOTES
0626050
HETEROZYGOTES
BR007
0626050
Tag Markers for Allele Mining and MABC
ARMS – PCR (Barbara Hufnagel)
Gene fragment 615pb
G-specific allele 496pb
T-specific allele 166pb
independent amplicon (control) 615pb
G-specific allele 496pb
T
G
T-specific allele 166pb
BR007
SC283
SC283
SC283
BR007
BR007
Het.
Het.

7. Q1: guineas WA
Q2: caudatums (durras)
Q3: Embrapa collection
Q4: kafir from SA
Q5: durras, bicolor/caudatums
Q6: guineas SA and Asia
RNRG5d(%)
Subpopulations
Al tolerance: RNRG (%)
> 80%
30% < RNRG < 80%
< 30%
Freq.
0.05
0.15
0.80

8. 0
10000000
20000000
30000000
40000000
50000000
60000000
70000000
80000000
90000000
0 1 2 3 4 5 6 7 8 9 10
Physicalposition(bp) SorghumChromosomes
Xcup010.0
Xtxp789.6
Xgap256 Xgap042
Xtxp20814.0
Xtxp32517.4
Xcup0619.6
Xtxp30225.0
SbAGF0829.3
Xcup7335.0
Xtxp35747.0
gpsb08953.8
Xtxp04365.8
Xtxp14967.8
Xtxp03277.0
Xtxp03792.4
mSbCIR28699.7
Xgap057109.0
Xtxp075116.0
Xtxp229120.0
Xgap036128.0
Xtxp522137.0
Xtxp61139.0
Xtxp319 Xcup62158.0
mSbCIR306176.1
Xtxp248179.6
Xcup53183.0
Xtxp46183.2
1
Xtxp960.0
Xtxp0634.3
Xtxp29719.0
mSbCIR22319.7
Xtxp5022.0
Xtxp30436.8
Xtxp00464.8
mSbCIR23866.3
Xtxp072 Xcup7474.0
Xtxp29892.9
SbAGB0397.7
Xcup63107.0
Xtxp445121.7
Xtxp056124.0
Xgap084140.7
Xtxp179143.0
Xtxp428153.2
Xtxp348157.0
Xtxp429158.7
Xcup26168.0
Xtxp296172.0
Xcup40190.0
Xtxp8193.8
ISEP0310199.5
2
Xtxp4560.0
Xcup112.0
Xcup616.0
Xtxp2666.1
ISEP01079.0
Xtxp49211.1
Xtxp49117.3
Xtxp48929.0
Xtxp21530.0
Xtxp48538.0
Xtxp50047.0
Xtxp46156.0
Xtxp03361.0
Xgap23662.8
Xtxp20568.0
Xtxp3171.1
mSbCIR27676.3
Xtxp12088.0
Xtxp231100.0
Xtxp218110.0
Xtxp114112.0
Xtxp439127.3
Xtxp441128.0
Xtxp446131.5
Xtxp442131.9
Xtxp447134.0
Xtxp038 Xtxp421138.0
Xtxp448138.7
Xtxp449140.0
Xtxp422141.0
Xtxp34147.8
Xtxp427158.0
Xcup14 Xtxp69160.0
Xtxp425160.1
Xtxp426164.2
3
Xtxp5060.0
Xtxp5046.1
Xgap12116.0
gpsb15120.0
Xcup0526.0
Xcup2336.0
mSbCIR32343.0
Xtxp343 Xtxp01273.0
Xgap01083.0
SbAGG0293.8
Xcup7196.0
Xtxp2598.8
Xtxp024107.0
Xtxp41108.0
Xtxp60120.7
Xtxp051128.5
Xtxp97150.0
Xtxp021153.0
Xcup20170.0
4
mSbCIR3293.0
Xtxp06514.4
Xtxp09423.0
mSbCIR24826.0
Xtxp03028.9
Xtxp30335.3
Xtxp22559.4
Xtxp01564.0
Xtxp02375.9
Xtxp26294.1
Xtxp13696.1
5
Xtxp5215.0
Xtxp00631.6
Xgap07248.3
Xcup3670.2
Xtxp14586.7
Xtxp26590.0
gpsb069104.7
Xtxp484116.0
Xtxp95125.7
Xtxp176134.1
Xtxp057141.0
Xtxp17149.3
Xcup37165.0
6
Xtxp0400.0
Xtxp364.0
gpsb14813.4
Xtxp41318.5
Xtxp48131.8
Xtxp15938.3
Xtxp31258.0
Xtxp22765.7
Xgap34272.0
Xtxp27874.1
Xcup5574.8
Xtxp09287.8
mSbCIR24689.8
Xcup7096.3
mSbCIR300101.8
Xcup19109.0
Xtxp295124.0
Xcup52126.2
SbAGB02130.8
Xtxp168132.0
7
Xtxp2730.0
Xtxp04732.1
Xtxp52050.0
mSbCIR24052.0
Xcup4753.4
gpsb06766.8
Xtxp29469.3
Xtxp35473.4
Xtxp01886.8
Xtxp32187.0
Xtxp10597.7
gpsb123100.0
Xgap34111.0
8
Xtxp28930.0
Xtxp35850.0
Xtxp45955.2
Xtxp41270.1
Xtxp28780.0
Xtxp41181.0
Xtxp23085.5
Xtxp06787.7
Xcup02104.0
Xtxp010108.4
Xtxp339135.0
Xgap032150.0
SbAGE03150.8
Xgap206160.0
Xgap015170.0
9
Xcup490.0
Xcup425.0
Xcup1310.0
Xtxp02053.0
Xtxp270 Xcup6755.0
mSbCIR28357.5
Xtxp217 Xtxp130(PepC)58.0
Xgap001*78.3
Xtxp320(phyB)82.5
mSbCIR26288.8
Xcup1693.6
Xcup43103.0
Xtxp141104.0
Xcup07115.2
10
Mbp 65 71 74
Kbp 300 - 400 100 - 200 400 - 500 100 - 200 400 - 500 700 - 800 800 - 900 600 - 700 800 - 900 900 - 1000 100 - 200 300 - 400 400 - 500 0 - 100 200 - 300 300 - 400 500 - 600 100 - 200
Xtxp38 STOP1 isu52 ctg29 S17 - AltSB - S73 - M181 Xcup14 DG1 EM1 - M96I2 M1762 - MBP
Marker loci txp441 txp446 txp442 txp421 txp449 txp422 txp34 txp427 txp425 txp426
txp447 txp448 txp69
66 68 69 72 73
Marker Assisted Backross
1 – Foreground selection
2 – Flanking marker selection
(linkage drag)
3 – Background selection

9. Available Resources
Gene-specific markers (10)
SNP markers: 1578
(Martha Hamblin)
Illumina/KASPar

10. Products and Resources
• Background SNP markers
• Association pipeline for Al tolerance
• Assessment of AltSB on acid soils (grain yield advantage)

11. Embrapa Maize and Sorghum
Jurandir Magalhaes
Robert E. Schaffert
Fernanda Caniato
Barbara Hufnagel
Belkiss França
Janaina Melo
Claudia Guimarães
Vera Alves
Ubiraci Lana
Moi Unversity
Sam Gudu
INRAN
Soumana Souley
ICRISAT – Mali: Eva Weltzien and
Fred Rattunde, Willmar Leiser
ICRISAT – Niamey: Bettina
Haussmann and Tom Hash
Cornell University/USDA-ARS
Leon Kochian (USDA/CU)
Jiping Liu (USDA/CU)
Zhangjun Fei (USDA/CU)
Stephen Kresovich (IGD/CU)
Sharon Mitchell (IGD/CU)
Martha Hamblin (IGD/CU)
IRRI: Sigrid Heuer
Sigrid Heuer (IRRI)
Matthias Wissuwa (JIRCAS)

12. Funding
 The Generation Challenge Program
 The McKnight Foundation CCRP Project
 EMBRAPA
 USDA – NRI Competitive Grants Program
 U.S. National Science Foundation
 USDA-Agricultural Research Service