Download WHY BEAN? DOMESTICATED BEAN SPECIES P. vulgaris L. in

1/19/2016
Bean Adapt: The Genomics of Adaptation during Crop Expansion in Bean
WHY BEAN?
Phaseolus vulgaris L.
Family: Leguminosae - Genus: Phaseolus
Diploid species (2n = 2x = 22)
Annual and predominantly self-pollinating (autogamous) species
Evolution in a changing environment: the genetic architecture of adaptation
outside centers of domestication of Phaseolus vulgaris and P. coccineus
• The most important food and feed legume for direct consumption
• Crucial protein, vitamin and mineral source for farmers in Latin America and Africa
• Health benefits and human disease prevention (lower risk of obesity, diabetes,
cardiovaskular diseases, and colon, prostate and breast cancer
• Major role in development of sustainable crop systems
• Development of genomic tools and genetic resources for plant breeding
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Vincent Van Gogh - The Potato Eaters 1885
Annibale Carracci, The Bean Eater , 1584-1585
DOMESTICATED BEAN SPECIES
P. vulgaris L. in AMERICA
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P. vulgaris
(common bean)
P. dumosus
P. coccineus
P. acutifolius
P. Lunatus
(runner bean)
(tepary bean)
(lima bean)
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Mesoamerican
gene pool
Independent
domestications
Northern Peru
and Ecuador
Andean
gene pool
Gepts et al. 1986; Gepts & Bliss 1988; Koenig & Gepts 1989; Singh et al. 1991; Rossi et al. 2009; Becerra Velasquez
& Gepts 1994; Freyre et al. 1996; Tohme et al. 1996; Papa & Gepts 2003; Blair et al. 2006; Diaz & Blair 2006; Kwak
et al. 2009; Kwak & Gepts 2009; Bellucci et al. 2014; Schmutz et al. 2014
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P. vulgaris L. in EUROPE
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Distribution of the Mesoamerican and Andean gene pools and their hybrids in Europe and other continents. Pie charts
show the Mesoamerican (blue) and Andean (red) gene-pool frequencies (Bellucci et al., 2014)
The whole genome and the new
era for Phaseolus research
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Figure 5 Genome-wide
association analysis of seed
weight.
(a) A 280-member panel of Mesoamerican
cultivars was grown in 4 locations in the
United States. Phenotypic data were
coupled with 34,799 SNP markers and
analyzed using a mixed-model analysis
that controlled for population structure
and genotype relatedness. (b) A close-up
view of the GWAS results for seed weight
and linkage disequilibrium (r2) around a
1.23-Mb Mesoamerican sweep window
on Pv07. The positions of candidate genes
for domestication are noted by asterisks
above the GWAS display. The candidates
range from Phvul.007G094299 to
Phvul.007G.99700
Rodriguez M,, et al. (2013)
THE PROJECT
Figure 1 Structure of the P. vulgaris genome and synteny with the G. max genome.
(a) Gray
lines connect duplicated genes. (b) Chromosome structure with centromeric and pericentromeric regions in black and gray,
respectively (scale is in Mb). (c) Gene density in sliding windows of 1 Mb at 200-kb intervals. (d) Repeat density in sliding
windows of 1 Mb at 200-kb intervals. (e) Recombination rate based on the genetic and physical mapping of 6,945 SNPs and
SSRs. (f,g) First syntenic region (f) and second G. max syntenic region (g) due to a lineage-specific duplication resulting in two
chromosome segments for every segment in P. vulgaris.
PROJECT AIM
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GbS on 11,500 Accessions
Resequencing 560 genotypes
Transcriptomics and
Metabolomics
Population genomics
Admixture mapping
GWAS
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dissect out the genetic basis and phenotypic consequences of
the adaptation to new environments of the common bean and
the runner bean, through the study of their introduction, from
their respective centers of domestication in the Americas, and
expansion through Europe, as a recent and historically welldefined event of rapid adaptation.
Genes for
adaptation
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Landraces
Landraces
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Most of the PS genes (83%) were fixed in MD, 14.2% presented shared
polymorphism
Molecular diversity in wild P. vulgaris
2.8% fixed in the MW and polymorphic in the MD
DOMESTICATION also increased FUNCTIONAL DIVERSITY
ADMIXTURE MAPPING
Results of Mesoamerican wild bean data (SGLMM) Loci that show significant
environmental effects, as summarised by PCA3, PCA4 and PCA5, are highlighted as red
dots and orange dots.
PCA3
PCA4
4.00
SNP 12
2.00
SNP 36
SNP 127
SNP 66
6.00
SNP 25
-2.00
-3.00
4.00
SNP 75
2.00
SNP 80
SNP 104
SNP 58 SNP 95
0.00
Log Bayes factor
-1.00
SNP 1
8.00
6.00
SNP 126
Log Bayes factor
Log Bayes factor
SNP 65
8.00
SNP 109
0.00
Pop2
10.00
10.00
SNP 71
SNP 64
1.00
Generation Pop1
PCA5
12.00
3.00
Rodriguez et al., (New Phytologist 2015)
4.00
SNP 25
SNP 50 SNP 67
SNP 75
2.00
SNP 13
SNP 42
SNP 46
0.00
-2.00
-4.00
-2.00
-5.00
-4.00
-6.00
-6.00
-7.00
-8.00
0
20
40
60
80
Locus index
100
120
-4.00
-6.00
0
20
40
60
80
Locus index
100
120
0
20
40
60
80
Locus index
100
120
Rodriguez et al., (New Phytologist 2015)
Phaseolus vulgaris
Phaseolus coccineus
Pv_ALL: GbS
Pv_core1: GbS WGS, phenotyping (MLFT)
Pv_ALL: GbS
Pv_core2: GbS WGS, phenotyping (MLFT), molecular phenotyping: Metabolomics and
transcriptomics under tropical short-day vs a temperate long-day environment simulation
Pv_core1: GbS WGS, standard and molecular phenotyping: Metabolomics and
transcriptomics under tropical short-day vs a temperate long-day environment simulation
10.000
500
200
single seed purified accessions
50% from America
50% from Europe
Pv_ALL
Pv_core1
1.500 accessions
60 accessions
50% from America and 50% from Europe
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Largest Genebank collections
Ex-situ resources
P. lunatus
14,434
P. acutifolius
1,366
P. coccineus
5,279
P. dumosus
956
Other species (52)
1,081
Phaseolus vulgaris – total 196 genebanks
Accs
30873
14460
12475
12353
Genebank
COL003
BRA008
BRA003
USA022
8446 DEU146
7216 CHN001
6000 MWI004
5972 RUS001
Phaseolus vulgaris
193,449 accessions
5210 MEX024
4048 HUN003
3514 KEN015
3075 RWA023
Source: http://www.fao.org/views-archive
Centro Internacional de Agricultura Tropical, CIAT, Cali, Colombia
Embrapa Arroz e Feijão, CNPAF, Capivara – Goiânia, Brazil
Embrapa Recursos Genéticos e Biotecnologia, CENARGEN, Brasília / DF, Brazil
Western Regional Plant Introduction Station, USDA-ARS, Washington State
University, W6, Pullman, WA, USA
IPK Gatersleben, Germany
Institute of Crop Science, Chinese Academy of Agricultural Sciences, ICS-CAAS,
Beijing, China
Bunda College of Agriculture, BCA, Lilongwe, Malawi
N.I. Vavilov All-Russian Scientific Research Institute of Plant Industry, VIR, St.
Petersburg, Russia
Instituto de Recursos Genéticos y Productividad, Colegio de Postgraduados,
IREGEP, Montecillo, Texcoco, México
Institute for Agrobotany, RCA, Tápiószele, Hungary
National Genebank of Kenya, Crop Plant Genetic Resources Centre – Muguga,
KARI-NGBK, Muguga, Kenia
Rwanda Agriculture Board, RAB, Kigali, Rwanda
Source: http://www.fao.org/views-archive
WORKFLOW
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78 countries
Collected/obtained between 1942-2014
2317 Accessions with GIS data
IPK Phaseolus collection
Biostatus
Unknown [0]
Wildplant [100]
Landrace [300]
Genet. Stock [400]
Breeding line [410]
Hybrid [412]
Mutant [421]
Cultivar [500]
total
P. coccineus
2
412
1
25
440
P. vulgaris
114
75
5488
251
112
10
8
2440
8498
total
116
75
5900
251
113
10
8
2465
8938
Work Package 1
Data Warehouse
WORK PACKAGES
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data generation
storage – analysis - connectivity
visualisation
•
•
Web Portal
Data
Warehouse
GBIS
IPK Genebank
information system
Interactive haplotype
browser
Comparison to existing
marker data to guide prebreeding and collection
management
interfaces
•
•
•
•
•
•
EURISCO
transPLANT
de.NBI
DivSeek
Digital Seed Bank
GLIS
(Passport, Geo Reference PGR
Management), Online ordering)
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MAIN DELIVERABLES
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Haplotype reconstruction (BeanHapMap)
• An Immortal collection of pure lines in P. vulgaris
• Computed haplotypes from 500 Pv_core1 accessions, and haplotypes for Pv_ALL.
Transcriptomics
• List of genes and phenotypes showing signature of selection for adaptation
10.000
500
Metabolomics
• List of loci significantly associated with traits & environmental variables.
Phenotypes controlled
conditions 200 lines
200
• Improved expression associated genome annotation.
Phenotypes MLFT
• List of strong candidates for validation.
WGS 500 pure lines
• List of validated candidates
GbS 10000 pure lines from landraces (Pv_ALL)
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