TLI 2012: Bean research progress report
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Transcript of TLI 2012: Bean research progress report
1
TL1 meeting Progress in Objective 3:
Common beans
Bodo Raatz, CIAT
Addis Ababa, May 2012
2
Road map
• Ethiopian program
• SNPs
– QTLs in the making in MAGIC, MARS, association mapping
• Markers in application MAS
• Phenotyping
3
Andean
Gene Pool
Cultivated common
bean:
• Two major gene
pools
• Specific grain
classes
…that define the
structure of breeding
programs
Mesoamerican
Gene Pool
4
Activity 2: SNP assay
• Collaboration with USDA-Beltsville, mediated by Xavier
• 1500 SNPs converted to Kaspar (Kbio)
• SNPs chosen that are polymorphic within gene pools and grain classes
• 94 lines genotyped (Milestone 2)
5
Mesoamerican
Andean
Phaseolus coccineus
Phaseolus acutifolius
Phylogeny analysis …
Activity 2: SNP assay genotypes
ma
rke
rs
6
Activity 5.1: MARS PhD thesis of Fitsum Alemayehu SARI, Ethiopia
Sister lines SABs 626, 628, 659, 686
– Drought
– Improved remobilization?
CAL 143
– Released in 6 countries in southern Africa
– Vegetative vigor
– Tolerant of poor soils
X
• 165 markers selected for genotyping
• Results in analysis
7
Activity 5.1: MARS genotyping
sc00244ln360837_151643_G_T_157sc00244ln360837_80567_T_C_1578sc00334ln300981_254308_G_A_187sc00334ln300981_202658_C_T_187sc00964ln122791_59538_A_C_3065
sc00429ln249479_88921_A_G_2138
sc00477ln232797_55899_C_T_2254
sc00050ln749641_133318_T_C_569
sc00022ln1003704_490507_A_C_32
sc00022ln1003704_88768_G_A_325
sc00003ln2130026_318965_G_A_46sc00003ln2130026_249989_T_G_45sc00003ln2130026_221589_T_C_45sc00618ln186586_8943_T_C_25469sc01409ln79819_3642_A_C_350551sc01409ln79819_56167_T_C_35060
0.41.00.7
10.1
41.8
14.5
18.6
5.9
15.3
0.41.14.00.2
1
sc00831ln140879_35627_G_A_2890
BARC-PV-0005808
sc00458ln240490_238835_A_C_221
sc00025ln963649_165119_T_G_356sc00025ln963649_327459_T_C_357
sc00038ln842375_5033_G_A_47257
sc00038ln842375_820428_T_C_480
sc00027ln946161_647185_A_G_380sc00027ln946161_730836_A_C_381
66.8
13.9
55.1
0.7
11.6
4.1
11.2
0.5
2
sc00377ln276023_97213_T_G_2002
sc00426ln251751_240727_C_T_213
sc00079ln659676_266197_T_C_776sc00880ln134596_94488_T_C_2958sc00134ln519503_497021_C_T_110sc00023ln985577_737723_A_G_342sc00023ln985577_404408_A_G_339
sc00061ln715360_52902_C_T_6499
sc00009ln1640450_1304280_C_T_1
62.3
17.5
3.42.14.02.2
12.7
24.0
3
BARC-PV-0000055sc01018ln115966_70654_C_T_3130sc01018ln115966_84234_C_T_3130sc00518ln214431_82881_A_G_2346sc00518ln214431_38754_C_T_2345sc00112ln569344_270381_C_T_979sc00112ln569344_446130_C_T_981sc00112ln569344_538657_G_A_982sc00835ln140787_95095_C_T_2896sc01131ln102720_84539_A_G_3253sc00283ln338214_136440_C_T_171sc00283ln338214_153572_G_T_171sc00283ln338214_233599_A_C_171sc00283ln338214_239137_G_A_171sc00283ln338214_293493_T_C_171sc01149ln100495_6599_A_G_32715sc01149ln100495_19761_C_T_3271sc01149ln100495_32702_T_C_3271sc00043ln806145_763080_A_G_521sc00043ln806145_731182_A_G_521sc00043ln806145_170363_C_A_516sc00043ln806145_102278_G_A_515sc00043ln806145_27550_A_G_5145
sc02743ln31009_27860_A_G_41677sc00721ln160814_116732_A_G_272sc00736ln157270_32680_T_C_2748sc00036ln871953_816000_T_G_463sc00036ln871953_623598_A_C_461sc00036ln871953_260922_C_A_457sc00716ln161188_139140_T_G_271
sc00018ln1167623_926274_C_T_29sc00018ln1167623_515133_C_A_28sc00018ln1167623_30331_G_T_281sc01035ln113702_42942_G_A_3149sc00175ln461633_78259_G_T_1298sc00175ln461633_42284_G_A_1298sc00914ln129176_38656_G_A_3003
1.41.22.11.00.30.40.40.70.21.90.6
10.10.30.8
56.9
0.83.42.01.62.53.9
17.9
3.56.71.32.60.43.9
4
8
sc00516ln215718_103432_C_T_234
sc00169ln473620_158171_C_T_127
sc00004ln1947458_369015_C_T_68sc00004ln1947458_475808_A_G_69sc00004ln1947458_609051_G_A_70sc00004ln1947458_651581_A_G_71sc00004ln1947458_666119_G_A_71sc00004ln1947458_704961_G_A_71sc00004ln1947458_901631_G_A_73sc00004ln1947458_1019379_A_G_7sc00004ln1947458_1047835_C_A_7sc00004ln1947458_1101740_A_C_7sc00004ln1947458_968323_T_C_74sc00004ln1947458_1211738_C_T_7sc00004ln1947458_1308111_T_C_7sc00004ln1947458_1320715_T_C_7sc00004ln1947458_1733897_T_C_8
43.3
32.4
1.90.31.77.70.60.30.44.7
5
sc01815ln56854_15487_C_T_37774
sc00162ln482802_338752_C_T_123sc00162ln482802_86819_T_G_1236
30.7
6
sc00431ln249067_99164_A_G_2143
sc00014ln1397360_934650_A_G_23sc00502ln219883_127438_T_C_231
sc00067ln694271_486308_T_C_696
sc00052ln745181_210054_A_G_585sc00052ln745181_283027_C_T_586sc00064ln701495_548353_A_G_676sc00583ln198651_1233_G_A_24795
sc00153ln494563_454394_G_A_119sc00158ln489092_253333_G_A_121
sc00262ln351368_101277_A_G_164
BARC-PV-0001413sc00002ln2152649_1120369_C_T_3BARC-PV-0001385sc00002ln2152649_1550949_T_G_3
9.7
3.9
5.4
8.8
6.11.7
9.8
2.7
30.9
50.4
1.50.92.1
7
sc00089ln640327_255418_C_T_841
sc01794ln57480_20276_G_A_37654
sc00035ln877458_767887_C_T_454
sc00187ln435150_76559_G_A_1352
67.2
59.6
11.3
8
Activity 5.1: MARS genotyping
9
QTL / association mapping for drought tolerance
Andean genepool Mesoamerican genepool
CAL143 NATAL
SUGAR
PAN127 R.C.
WONDER
SER8 SEQ11 SEC16 SUG131 SER22 SER16
F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1 F1
F2
F3
F4
F2
F3
F4
F2
F4:6 F4:6
160 plants harvested
400 lines
QTL/Association analysis
10
SNP set: Regenotyping for improved QTL map
BAT 881 x G21212 330 polymorphic SNPs
SER16 X (SER16 X G35346) G35346 = Phaseolus coccineus
400 polymorphic SNPs
Pinto Saltillo X Pinto Villa 170 polymorphic SNPs
11
Cut seeds
DNA extraction from seeds
Amplification Test
BM 185 Tissue Lyser
seeds macerated with
stainless steel beads
DNA
extraction
12
Seed storage to planting
Germination test
In field
Cut seeds germinate in the field
13
Activity 5.2: Advanced backcross
• Five Adv. BC populations BC2-F4
• Most lines badly adapted
• 2012: - few lines in breeding program
- QTL appropach abandoned
SOURCE
SER 16 SER 48
CAL 143 126 78
CAL 96 156 128
CIM 9314-36 39 -
14
Mesoamerican donor SER 16 Andean recurrent parent CAL 96
Activity 5.2: Advanced backcross
15
Activity 5.2: Advanced backcross
16
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
996 F3.5 families
F5:7 families for drought phenotyping
MAGIC population in common bean (mesoamerican gene pool)
Genotype in F5??
Genotype individuals
17
Activity 3: MAS for biotic traits
Storage insects:
Bruchids (Zabrotes
subfasciatus)
18
SSR marker for bruchid resistance
PV-ATCT001 – Arc
Cortesia: H.F. Buendia
•20 crosses
Agarose based marker:
RA
Z4
4
RA
Z105
RA
Z106
G18264
CA
L143
SE
Q1006
SE
Q1027
Bla
nco
19
RI =
lo
g{(
Em
erg
ed a
dults/h
atc
hed e
ggs)
+ 1
} /
DA
E *
100
Yield (Kg/Ha)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29 30 31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
87 88
89
90
91
93
94
95 96
97
98
99
100
102
104
105
106
108
111
112
113
114
115
116
RAZ103
RAZ104 RAZ168
54
55
56
57
117
58 59
60
61 62
63
64
65
66
67
68
70
71
72
73
74
75 76
77
78
125
126 127 128
129
CAL143
KATB9
79 80
81
82
83
84
85
86 119
120
121 122
123 124
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
1000 1200 1400 1600 1800 2000 2200 2400 2600 2800
R
RI
S
positive
heterozygote
negative
No Amplification
PV-ATCT001 marker
Activity 3: MAS for bruchid resistance
20
Activity 3: SNPs for bruchid resistance
BAC wild meso
BAT93 meso
G19833 andean
kb
APA: Arcelin-Phytohemagglutinin-amylase Inhibitor family
BAC: 71F18, Kami et al, 2006
21
Precision introgression
• Bruchid resistance (arcelin gene) originates from mesoamerican pool
• 4 markers easily available between genepools
The perfect marker is four markers
R locus
Positive
marker
Positive
marker
negative
marker
negative
marker
1cM 1cM
22
Activity 3: MAS for biotic traits
BGYMV (bean golden yellow
mosaic virus):
SCAR for bgm-1, but occasional
recombinants (14 crosses)
Recessive bc-3 resistance for BCMNV
(bean common mosaic necrotic virus) (64 crosses)
23
C-A
bc-3 candidate gene: eIF4E NADERPOUR et al. MOLECULAR PLANT PATHOLOGY (2010)
180 bp
820 bp
r r r r r r r r s s
1000 bp
24
Common Bacterial Blight (CBB)
MAS with
• SU91 on Chr8 (Pedraza et al. 1997)
• SCAR’s : BC420 on Chr6 (Yu et al. 1998)
• SAP6 on Chr10 (Miklas et al. 2006) .
Bacterial blight: Xanthomonas
25
BMbS15 0 BMbS13 SUcat01 BMbS12
3
BMbS5 5 SU91 9 SUag01 gVQ
12
BMbS10 13 BMbS4 15
40
BMa27 60
BM151 78 BMb386 83 BMb277 86
PVBR173 94
BMc121 111
PVBR71 141
BMb1319w 167
Xf
0
2
4
6
8
10
12
14
16
18
20
22
24
26
28
30
Xc
Chr 8
Map size : 166.82 cM
BMb1196w
BM212 0
BMd42 21
PV158 38
PV181 47 PV185 51 SAP6 55
BMb96 93 BMc63 102 IAC54 109 BMb302 111 BMb167 113 BMc66 118
0
1
2
3
Xc
Xf
Xc
4
6
8
10
Chr 10
Map size : 117.59 cM
R2 =20%
R2 =49%
BMbS12
A
CBB resistance QTLs
26
• 36 advanced lines characterized (milestone 6)
• Drought trials in
– 2 saison in CIAT (2010, 2011), Palmira, ±drought
– 1 saison in Ethiopia, ±drought
• 3 visual scales for wilting, podfilling and degree of leaf loss analyzed (milestone 7)
Activity 4: Drought tolerant traits
27
Irrigated grain yield (kg ha-1)
1800 2000 2200 2400 2600 2800 3000 3200 3400 3600 3800
Rain
fed
gra
in y
ield
(kg
ha
-1)
200
400
600
800
1000
1200
CAL 143
CAL 96
DAB 295DAB 489
DAB 494DAB 528
DAB 441
DAB 520
DAB 318
DAB 530
DAB 302
DAB 261
DAB 395
DAB 557
DAB 545
DAB 353 DAB 317
DAB 344
DAB 380
DAB 564DAB 493
KATB 1 AFR 298
DAB 432
DAB 525DAB 541
DAB 555
Mean: 798LSD0.05: 383
Mean: 2934LSD0.05: 565
Relationship between irrigated and rainfed grain yield of 36 common bean genotypes grown under field conditions at
CIAT-Colombia
28
Activity 4: Visual scales
Resistance to Wilting
P.a.
29
Adapted from King et al. 2009 Crop Science 49:290-298;
0 = no wilting and 100 = plant death
Wilting score at 41 days after planting
5 10 15 20 25 30 35
Rain
fed
gra
in y
ield
(kg
ha
-1)
200
400
600
800
1000
1200
CAL 143
CAL 96
DAB 295
DAB 489 DAB 494 DAB 528
DAB 441
DAB 504
DAB 532
DAB 520
DAB 318
DAB 530
DAB 302
DAB 261DAB 395
DAB 326
DAB 557DAB 534
DAB 545
DAB 353 DAB 290
DAB 514
DAB 317
DAB 344DAB 380
DAB 555
DAB 564
DAB 493
KATB 1AFR 298
DAB 432
Mean: 798LSD0.05: 383
Mean: 18.9LSD0.05: 8.6
r = -0.36***
Relationship between leaf wilting and rainfed grain yield of 36 common bean genotypes grown under field conditions
at CIAT-Colombia
30
0 = well-filled grain; 10 = more than 50% of grain is not well-filled
Rainfed seed fill score2 3 4 5 6 7
Rain
fed
gra
in y
ield
(kg
ha
-1)
200
400
600
800
1000
1200
CAL 143
CAL 96
DAB 295
DAB 489DAB 494 DAB 528
DAB 441
DAB 504
DAB 520
DAB 318
DAB 530 DAB 302
DAB 261DAB 395
DAB 532DAB 557
DAB 534
DAB 545
DAB 353
DAB 290
DAB 317
DAB 344DAB 380
DAB 555
DAB 564
DAB 493KATB 1AFR 298
DAB 432
DAB 549DAB 525
DAB 286Mean: 798LSD0.05: 383
Mean: 4.78LSD0.05: 2.0
r = -0.47***
Relationship between seed filling and rainfed grain yield of 36 common bean genotypes grown under field conditions
at CIAT-Colombia
31
Conclusions
• SNPs used in QTL and association mapping
• MARS moving forward
– Seed DNA extraction permits flexibility
• MAS for biotic stress in implementation, moving toward routine
• Advanced lines show improved yield
• Visual scale of pod filling useful
32
Thank you for your attention!