grm 2011: practical application of markers for sorghum breeding

: ALTSORGHUM Project Practical Application of Markers

Jurandir Magalhaes

Maize and Sorghum

- GCP General Research Meeting, Hyderabad, 21 – 25 September 2011 -

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

RR

GR

ela

tiv

e E

xp

res

sio

n

Al tolerance (RNRG)

r=0.98

(P<0.001)

0.0

1.0

2.0

3.0

4.0

0 50 100 150

RRG

RR

GR

ela

tiv

e E

xp

res

sio

n

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

Molecular Breeding for Al Tolerance in Sorghum

Weltzien et al. Sorghum diversity and adaptation to drought in West Africa

Allele mining MABC

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 Mining MABC

Markers genetically linked to

AltSB

Functional loci or

loci in LD with QTN(s)

Nature Review Genetics

2:1-9 (2001)

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 ChinaG11-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 ChinaG11-Kafir from southern Africa

G8-transplanted sorghum from Chad and Cameron

G1-Guine margaritiferum

G2-USA lines

Association Analysis of AltSB

Fernanda Caniato

SbMATE_I2_6083pb

Gene fragment 700pb

C-specific allele 483pb

A-specific allele 240pb

(Gene Fragment) 700pb


A

CA-specific allele 240pb

BR007

SC283

SC283

SC283

BR007

BR007

Het.

Het.

Gene fragment 700pb





A


BR007

SC283

SC283

SC283

BR007

BR007

Het.

Het.

Gene fragment 700pb





A


BR007

SC283

Gene fragment 700pb



Gene fragment 700pbGene fragment 700pb

C-specific allele 483pbC-specific allele 483pb

A-specific allele 240pbA-specific allele 240pb



A


BR007

SC283



A




A

C

A


BR007

SC283

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.

independent amplicon (control) 700pb

C

GA-specific allele 254pb


Gene fragment 700pb

G-specific allele 254pb


Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.

BR007

SC283


C



Gene fragment 700pb



Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.

BR007

SC283


C



Gene fragment 700pb



Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.


C



Gene fragment 700pb



Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.


C



Gene fragment 700pb



Gene fragment 700pb


C




C




C




C

G

C



Gene fragment 700pb



Gene fragment 700pb


G-specific allele 254pbG-specific allele 254pb

C-specific allele 254pbC-specific allele 254pb


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

GA-specific allele 361pbG-specific allele 361pb

Gene fragment 700pb



Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.


BR007

SC283 A



BR007

SC283 A


BR007

SC283 A

G

A


Gene fragment 700pb



Gene fragment 700pb

SC283

SC283

BR007

BR007

Het.

Het.

SC283

SC283

BR007

BR007

Het.

Het.


G-specific allele 361pbG-specific allele 361pb

A-specific allele 361pbA-specific allele 361pb


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


T-specific allele 166pb



T

GT-specific allele 166pb

BR007

SC283

SC283

SC283

BR007

BR007

Het.

Het.

Q1: guineas WA Q2: caudatums (durras) Q3: Embrapa collection Q4: kafir from SA Q5: durras, bicolor/caudatums Q6: guineas SA and Asia

RN

RG

5d(%

)

Subpopulations

Al tolerance: RNRG (%)

> 80%

30% < RNRG < 80%

< 30%

Freq.

0.05

0.15

0.80

0

10000000

20000000

30000000

40000000

50000000

60000000

70000000

80000000

90000000

0 1 2 3 4 5 6 7 8 9 10

Ph

ysi

cal p

osi

tio

n (b

p)

Sorghum Chromosomes

Xcup010.0Xtxp789.6Xgap256 Xgap042Xtxp208

14.0

Xtxp32517.4Xcup0619.6Xtxp30225.0SbAGF0829.3Xcup7335.0Xtxp35747.0gpsb08953.8Xtxp04365.8Xtxp14967.8Xtxp03277.0

Xtxp03792.4mSbCIR28699.7

Xgap057109.0Xtxp075116.0Xtxp229120.0Xgap036128.0Xtxp522137.0Xtxp61139.0

Xtxp319 Xcup62158.0

mSbCIR306176.1Xtxp248179.6Xcup53183.0Xtxp46183.2

1

Xtxp960.0Xtxp0634.3

Xtxp29719.0mSbCIR22319.7Xtxp5022.0

Xtxp30436.8

Xtxp00464.8mSbCIR23866.3Xtxp072 Xcup7474.0

Xtxp29892.9SbAGB0397.7

Xcup63107.0

Xtxp445121.7Xtxp056124.0

Xgap084140.7Xtxp179143.0Xtxp428153.2Xtxp348157.0Xtxp429158.7Xcup26168.0Xtxp296172.0

Xcup40190.0Xtxp8193.8ISEP0310199.5

2

Xtxp4560.0Xcup112.0Xcup616.0Xtxp2666.1ISEP01079.0Xtxp49211.1Xtxp49117.3Xtxp48929.0Xtxp21530.0Xtxp48538.0Xtxp50047.0Xtxp46156.0Xtxp03361.0Xgap23662.8Xtxp20568.0Xtxp3171.1mSbCIR27676.3Xtxp12088.0Xtxp231100.0Xtxp218110.0Xtxp114112.0Xtxp439127.3Xtxp441128.0Xtxp446131.5Xtxp442131.9Xtxp447134.0Xtxp038 Xtxp421138.0Xtxp448138.7Xtxp449140.0Xtxp422141.0Xtxp34147.8Xtxp427158.0Xcup14 Xtxp69160.0Xtxp425160.1Xtxp426164.2

3

Xtxp5060.0Xtxp5046.1

Xgap12116.0gpsb15120.0Xcup0526.0

Xcup2336.0mSbCIR32343.0

Xtxp343 Xtxp01273.0

Xgap01083.0

SbAGG0293.8Xcup7196.0Xtxp2598.8Xtxp024107.0Xtxp41108.0Xtxp60120.7Xtxp051128.5

Xtxp97150.0Xtxp021153.0

Xcup20170.0

4

mSbCIR3293.0

Xtxp06514.4Xtxp09423.0mSbCIR24826.0Xtxp03028.9Xtxp30335.3

Xtxp22559.4Xtxp01564.0

Xtxp02375.9

Xtxp26294.1Xtxp13696.1

5

Xtxp5215.0

Xtxp00631.6

Xgap07248.3

Xcup3670.2

Xtxp14586.7Xtxp26590.0

gpsb069104.7

Xtxp484116.0

Xtxp95125.7

Xtxp176134.1Xtxp057141.0

Xtxp17149.3

Xcup37165.0

6

Xtxp0400.0Xtxp364.0gpsb14813.4Xtxp41318.5

Xtxp48131.8Xtxp15938.3

Xtxp31258.0Xtxp22765.7Xgap34272.0Xtxp27874.1Xcup5574.8Xtxp09287.8mSbCIR24689.8Xcup7096.3mSbCIR300101.8Xcup19109.0Xtxp295124.0Xcup52126.2SbAGB02130.8Xtxp168132.0

7

Xtxp2730.0

Xtxp04732.1

Xtxp52050.0mSbCIR24052.0Xcup4753.4gpsb06766.8Xtxp29469.3Xtxp35473.4Xtxp01886.8Xtxp32187.0Xtxp10597.7gpsb123100.0Xgap34111.0

8

Xtxp28930.0

Xtxp35850.0Xtxp45955.2

Xtxp41270.1Xtxp28780.0Xtxp41181.0Xtxp23085.5Xtxp06787.7

Xcup02104.0Xtxp010108.4

Xtxp339135.0

Xgap032150.0SbAGE03150.8Xgap206160.0

Xgap015170.0

9

Xcup490.0Xcup425.0Xcup1310.0

Xtxp02053.0Xtxp270 Xcup6755.0mSbCIR28357.5Xtxp217 Xtxp130(PepC)58.0

Xgap001*78.3Xtxp320(phyB)82.5mSbCIR26288.8Xcup1693.6Xcup43103.0Xtxp141104.0

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

Available Resources

Gene-specific markers (10)

SNP markers: 1578 (Martha Hamblin)

Illumina/KASPar

Products and Resources

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

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)

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

grm 2011: practical application of markers for sorghum breeding

Technology