Juan David Lobaton - IITAgl2016conf.iita.org/wp-content/uploads/2016/03/...Since 1967 / Science to...
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Since 1967 / Science to cultivate change Juan David Lobaton
Transcript of Juan David Lobaton - IITAgl2016conf.iita.org/wp-content/uploads/2016/03/...Since 1967 / Science to...
Since 1967 / Science to cultivate change
Juan David Lobaton
Juan David Lobaton, Paulo Izquierdo, Juanita Gil, Jorge Duitama, Steve Beebe, Bodo Raatz
Livingstone 2016
Molecular marker development using sequencing data and
GWAS for yield component QTL under drought in a common bean MAGIC
population
Since 1967 / Science to cultivate change
WGS (whole genome sequencing)
• 9 genotypes re-sequenced • ~ 12 x each
Andean Ref G19833
Mesoamerican G10474
Coccineus G35346
Acutifolious G40001
Andean G5686
Since 1967 / Science to cultivate change
SNPs
Ref AFR298 AND696 G5686 MD 23-24 SEA 5 VAX 1 G10474 G35346 G40001 P. Coccineus P. acutifolius
Re-sequencing data for Phaseolus genotypes
Since 1967 / Science to cultivate change
Variation in gene coding regions
Since 1967 / Science to cultivate change
Diversity based on WGS
Mesoamerican
genepool
Andean genepool
P. coccineus
P. acutifolius
Since 1967 / Science to cultivate change
• Schmutz et al 2014 • Song et al 2015 • Paul Gepts • CIAT
CIAT VCF files available at: http://gigwa.southgreen.fr/
Mesoamerican genepool
Andean genepool
Since 1967 / Science to cultivate change
Sequencing depths of various WGS data sets
0
100000000
200000000
300000000
400000000
500000000
600000000
700000000
800000000
900000000
AFR_
298
AND_
696
G104
74
G198
33
G353
46
G353
46_s
en
G400
01_s
en
G568
6
MD_
23-2
4_bo
wtie
2.lo
g
SEA_
5_bo
wtie
2.lo
g
Song
2015
_BAT
_93
Song
2015
_BU
CKSK
IN
Song
2015
_C-2
0
Song
2015
_CAL
_EAR
LY
Song
2015
_CO
RNEL
L_49
-242
Song
2015
_FIE
RO_b
owtie
2.lo
g
Song
2015
_JAL
O_E
EP_5
58
Song
2015
_KAR
DIN
AL
Song
2015
_LAK
ER
Song
2015
_LAR
K
Song
2015
_MAT
TERH
ORN
Song
2015
_MIC
HELI
TE
Song
2015
_RED
_HAW
K
Song
2015
_SIE
RRA
Song
2015
_STA
MPE
DE
Song
2015
_T-3
9
Song
2015
_UC_
WHI
TE
Song
2015
_UI_
906
SRS4
8180
6-Po
ol3
SRS4
8180
7-Po
ol6
SRS4
8180
8-Po
ol2
SRS4
8180
9-Po
ol5
SRS4
8181
0-Po
ol7
SRS4
8181
1-W
ildM
eso
SRS4
8181
2-W
ildAn
dean
SRS4
8181
3-Po
ol4
SRS4
8181
4-Po
ol1
VAX_
1
VAX_
4
VAX_
6
Tota
l rea
ds
Sample
Total Reads
Since 1967 / Science to cultivate change
Diversity stats in P. vulgaris samples
Fst And vs Meso Diversity in Mesos Diversity in Andeans Repetitive regions
Since 1967 / Science to cultivate change
Phg-2 locus: available marker types
Genotype ALSC
hr08
_CT_
5779
8
PF5
MAS
_ALS
10a
Sc26
7437
HRM
G10474 T:T + G:G G:G G:G G4691 T:T + G:G G:G G:G G855 C:C + T:T T:T T:T G18970 C:C + G:G G:G G:G G10909 C:C + G:G G:G G:G G5686 C:C - T:T T:T T:T MAB 300 C:C + T:T T:T T:T SEL 1481 C:C + T:T T:T T:T AND 277 C:C - T:T T:T T:T MEXICO 54 C:C - G:G G:G G:G G5653 C:C - G:G G:G G:G MBC 35 C:C + T:T T:T T:T SEL 1478 C:C - T:T T:T T:T MBC 33 C:C - T:T T:T T:T MBC 39 C:C - T:T T:T T:T NUA 56 C:C - T:T T:T T:T G1805 C:C + T:T T:T T:T G14519 C:C + G:G G:G G:G SEL 1475 C:C - G:T G:T ? SEL 1476 C:C - T:T T:T T:T SEL 1477 C:C - T:T T:T T:T G21242 C:C + ? G:G G:G G23823E C:C + T:T T:T T:T MBC 7 C:C + T:T T:T T:T MBC 26 C:C - T:T T:T T:T MBC 28 C:C - T:T T:T T:T MBC 34 C:C - T:T T:T T:T SPRITE C:C - T:T T:T T:T BAT 93 C:C + T:T T:T T:T XAN 112 C:C + G:G G:T G:G JULES C C + G G G G G G
Since 1967 / Science to cultivate change
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 F5
MAGIC population in common bean (Mesoamerican gene pool)
Genotype individuals
Drought phenotyping
Total 630 samples for GBS
648 F5:6
648 F5:7
Since 1967 / Science to cultivate change
MAGIC population field trial • 648 genotypes in drought trial
• 2013 • 2014
Since 1967 / Science to cultivate change
Genotyping by sequencing (GBS) • ApeKI Cornell protocol • 21k SNPs
• Analysis: MLM tassel
2013
2014
GWAS: days to maturity
GWAS: grain yield
Since 1967 / Science to cultivate change
GWAS: SNPs vs haplotype blocks 8 7 6 5 4 3 2 1 0
8 7 6 5 4 3 2 1 0
Since 1967 / Science to cultivate change
Haplotype GWAS: Days to flowering, chromosome 1
2013 LOCUS HAPLOTYPE NANAL BETA R2 STAT log(p)
1 H56 TGACGC 435 1.816 0.5041 20.98 67.2 2 H56 GTGACC 435 -1.297 0.2857 -13.16 32.8 3 H56 TTGACG 435 -0.6936 0.03827 -4.151 4.4
