Applied Plant Breeding and Cultivar Development
An Evolutionary Approach towards
Bean Conservation – from Wild Bean
to its Genome to the Field
Paul Gepts
Plant Sciences, UC Davis
6o Congreso Brasileiro de Melhoramento de Plantas
1 a 4 de agosto, 2011 – Búzios, RJ
Empiricism in plant breeding and
genetic resources conservation
• Boon or bane of the field?
– Highly successful
•
•
•
•
•
Progress from selection
Different types of inheritance
Different degrees of environmental effects
Combination and correlation of traits
Adoption of new technologies
– “Cannot get no respect”
• “Basic information is lacking”
• “Less precise”
• Response?
– Examples from germplasm conservation: Adoption of wide
range of approaches: How to penetrate the “Black Box”?
Crop Biodiversity Conservation (I)
• Ex situ: gene banks:
– Largest: USA: 500,000
samples; China: 390,
000; Germany:
160,000; Brazil:
150,000 (EMBRAPA
2008 data)
– CGIAR gene banks
– Svalbard seed vault
– Many other gene
banks: 1,750 individual
genebanks worldwide,
about 130 of which
hold more than 10,000
accessions each
Gene Banks around the World:
> 10,000 accessions
State of the World’s Plant Genetic Resources for Food and Agriculture (SOTW2), 2009
Crop Biodiversity Conservation (II)
• In situ:
– Natural vegetation
– Farmers’ fields and backyards
• Complements ex situ
– Subject to evolutionary forces
– Provides a bio-cultural context
• More urgency
– Global environmental change
Outline
How to penetrate the “Black Box”?
– A phylogenetic/genealogical approach to
understanding genetic diversity of a crop species:
• The diversification of common bean (Phaseolus vulgaris)
– A GIS approach the discovery and use of genetic
diversity in gene banks
• Example of Brasilian bean landraces
– A genomic approach to discovery and transfer of
genetic diversity
• Development of PhaseolusGenes: Bean breeder’s toolbox for
marker discovery
• Comparative genomics with model experimental systems
What are beans and why study them?
San Agustín del Pulque, MEX (2004)
 Complement cereals as a source of
nitrogen during cultivation
 Complement cereal and root crops as
a source of protein
 Among the 10 foods that pack the
most anti-oxidants (USDA study, 2004):
Small red, red kidney, pinto beans
Phaseolus beans
 Composition
Plant proteins
Minerals: iron and zinc (~
meats, poultry, and fish)
Dietary fiber
Vitamins: folate (low in diets of
many Americans)
 Reduces breast cancer (Thompson
7
et al. 2008)
How to Penetrate the “Black Box”?
A Phylogenetic/Genealogical Approach to Understanding
Genetic Diversity of a Crop Species: The Diversification of
Common Bean (Phaseolus vulgaris)
Phylogeny/Genealogy of Common Bean
Other Phaseolus
species
Domestication
Dissemination
M
G
D
J
Gene flow
Domesticated landraces
in Mesoamerica
Domesticated outside
Center of origin
Wild Mesoamerican
Feral
or
weedy
Wild
ECD &
N. PER
C
P
NG
Domesticated landraces
in Andes
Wild Andean
Feral or
weedy
Domesticated outside
Center of origin
9
Multiple Sources, Several Years
• Applications to Bean Breeding
Two major geographic gene pools
• Observation: Andean and
Mesoamerican gene pools
– Geographic differentiation
prior to domestication
Gepts & Bliss 1985; Gepts et al. 1986; Singh et al.
1991a,b,c,; Becerra-Velasquez & Gepts 1984; Debouck
et al. 1993; Freyre et al. 1996; Papa & Gepts 2003;
Kwak & Gepts 2009
• Consequence:
– Bean breeding:
Domestications
Mesoamerican
Andean
• 2 breeding pools, Andean
and Mesoamerican
• 7 races
inter-racial crosses within
gene pools
• For inter-gene pool crosses:
Adapt breeding method to
account for wider genetic
distance: e.g., 1 BC
11
Reduction in Levels of Genetic
Diversity
• Observation:
Reduction in genetic
diversity
M13-related RFLPs
0.25
0.2
0.15
Meso
Andean
0.1
– Single domestication in
each gene pool
– Plant breeding
Gepts et al. 1986; Sonnante et al.
1994
0.05
0
Wild
Landraces
US Cultivars
• Consequence:
– Use landraces and wild
germplasm in breeding
– Use other Phaseolus
species
Breeding Strategies to Broaden the
Genetic Diversity of Common Bean
Kelly et al. 1998
13
Results of Gene Flow Studies in Mexico
• Gene flow:
–Introgression: 20-50% of wild individuals
in sympatric populations
–Asymmetric: Three- to four-fold higher in
D  W than in W  D
– Paradox: Self-pollinated species; yet,
measurable effect of outcrossing
–Displacement of alleles in W by alleles of
D, except around genes for domestication in
~ 80 % of the genome
Photo: R. Papa
Papa & Gepts 2003, 2004; Payró
de la Cruz et al. 2004; ZizumboVillareal et al. 2005; Papa et al.
2007
• Implications:
--In situ conservation? Complemented with
ex situ conservation
--Unwanted escape of genes but also
strategy against escape: genetic footprint
Co-evolution between Common Bean
and Pathogens
Colletotrichum lindemuthianum
Interactions
P
h
a
s
e
o
l
u
s
v
u
l
g
a
r
i
s
MEXICO
M
E
X
I
C
O
E
C
U
A
D
O
R
ECUADOR
ARGENTINA
• Observation:
– Parallel geographic
distribution of genetic
diversity between beans and
pathogens: angular leafspot,
anthracnose, rust, BDMV
Guzmán et al. 1995, Geffroy et al. 1999,
2000; Seo et al. 2004
• Consequence:
– Facilitates breeding:
A
R
G
E
N
T
I
N
A
Geffroy et al. 1999
• Identification of resistance
• Broad representation of
pathogen variation
1• The presumed domestication center of Phaseolus
vulgaris in Mesoamerica
PhD thesis Myounghai Kwak (Korea) with Jim Kami
16
Phylogeny/Genealogy of Common Bean
Other Phaseolus
species
1
Domestication
Dissemination
2
M
G
D
J
Gene flow
Domesticated landraces
in Mesoamerica
Domesticated outside
Center of origin
Wild Mesoamerican
Feral
or
weedy
Wild
ECD &
N. PER
C
P
NG
Domesticated landraces
in Andes
Wild Andean
Feral or
weedy
Domesticated outside
Center of origin
17
Relationship between Wild & Domesticated
types in the Mesoamerican Gene Pool
Also, close genetic
relationship based
on phaseolin protein
electrophoresis
(Gepts 1988)
18
Kwak et al. 2009
The Suggested Domestication Center
of Common Bean in Mexico
19
M. Kwak, J. Kami & P. Gepts, Crop Sci., March 2009
Why the Lerma-Santiago Basin?

Climate: Cwa
 Subtropical: t° coldest
month: 5-18 °C
 Subhumid: 4-6 months of
humidity in summer
 Semi-warm: average annual
t°: 18-22 °C

Vegetation:
 Dry deciduous forest to drier
thorn forest
Westernmost putative domestication location,
Mascota-Ameca Basin
21
Domestication Areas within Mesoamerica
22
How to Penetrate the “Black Box”?
A GIS approach the discovery and use of genetic diversity in
gene banks:
Example of Brazilian bean landraces PhD thesis of
Marilia Lobo Burle (EMBRAPA/CENARGEN) with help of M.J.
del Peloso & L.C. Melo (EMBRAPA/CNPAF)
2•
Genetic Diversity in a Secondary Center
of Origin: Brazil
24
Phylogeny/Genealogy of Common Bean
Other Phaseolus
species
1
Domestication
Dissemination
2
M
G
D
J
Gene flow
Domesticated landraces
in Mesoamerica
Domesticated outside
Center of origin
Wild Mesoamerican
Feral
or
weedy
Wild
ECD &
N. PER
2
C
P
NG
Domesticated landraces
in Andes
Wild Andean
Feral or
weedy
Domesticated outside
Center of origin
25
General Approach
• Combined analysis of genetic
diversity:
– Molecular analysis:
• Genetic relationships
• Admixture
– Phenotypic analysis:

• Characterization: morphological
and agronomic traits (UC Davis)
• Agronomic traits: Yield, field
resistance to CBB, rust
(EMBRAPA)
– Geographic information
systems (GIS)
• Climate
• Biomes, etc.

Maps (1:5,000,000):
 Map of climate
 Mean annual temperature
 Mean annual precipitation
 Biomes
 Original vegetation
 Pedology
CIAT: climatic database Latin
America
26
Brazilian Beans
Fradinho Boca Preta
Macaçar pequeño
Rosinha
Mulatinho
Bico de Ouro
Jalo
Carioca
Bolinha Amarelo
Preto
Roxinho
Bolinha Vermelho
27
http://www.unifeijao.com.br/feijao_do_brasil/mapa.htm
Plant Materials & Molecular Markers
• Plant sample:
– 279 landraces
• Collected by Jaime
Fonseca
• 1 per municipality
– 2 control accessions:
• BAT93 (Mesoamerican),
Jalo EEP558 (Andean)
• Marker sample:
– 67 SSRs (Yu et al. 2000;
Gaitan-Solis et al. 2002;
Blair et al. 2003; Grisi et al.
2007)
– 4 SCAR markers
– 2 Seed proteins + 1 growth
habit candidate gene
28
Molecular variation: STRUCTURE
analysis
Jalo EEP558: landrace; BAT93: (Veranic 2 x Tlalnepantla 64) x (Negro Jamapa x GN Tara)29
Molecular variation: NJ tree
analysis
K=3
30
2. Phenotypic diversity
• Field experiments: 281 varieties
• UC Davis
– Morphological traits:
• seed: pattern, color, brilliance, shape,
weight
• leaflet: leaflet shape and length
• flower: color, days to flowering, …
• determinacy, growth habit
• EMBRAPA-CNPAF, Goiânia
– Agronomic traits:
• Yield
• Disease resistance: CBB, Rust
31
•
PCA of Morphological & Agronomic
Traits
First component:
39%
– Flower color,
seed weight,
flower standard
striping, and pod
beak position
• Second
component: 13%
– Growth habit,
determinacy and
number of days
to flowering
Andean
Mesoamerican
Hybrid
32
3. Eco-geographic
variation
• Biome: mainly semideciduous forest,
pine forest
• Only difference
between A and M?
– Altitude: ~ 100m
– Yearly average T°:
23C
– Average rainfall
growing season: 549
mm
33
SUMMARY
• Three-pronged approach to assessing genetic diversity:
genetic, phenotypic, and environmental:
– Reciprocal confirmation of findings
– Generates hypotheses
– Provides a model for large-scale characterization of germplasm
collections
• Availability of geo-referenced germplasm is a must
• Most landraces of Mesoamerican origin; strong separation
with Andean gene pool
• Large “hybrid” group in Mesoamerican gene pool; may
have superior adaptation to poor soil conditions?
• Identification of markers potentially associated with
tolerance to environmental conditions
• Needs further corroboration before being adopted as a
strategy for genetic diversity discovery
34
How to Penetrate the “Black Box”?
A Genomic Approach to Marker & Gene Discovery and Transfer:
Development of PhaseolusGenes, a breeder’s marker toolbox
http://phaseolusgenes.bioinformatics.ucdavis.edu
UCD Bioinformatics: Dawei Lin, Jose Boveda, Monica Britton, Joe Fass,
Nikhil Joshi, Zhi-Wei Lu
UCD Gepts group: James Kami, José Vicente Gomes dos Santos, Shelby Repinski
Adriana Navarro Gómez, Paul Gepts
Overall design of PhaseolusGenes
URL: http://phaseolusgenes.bioinformatics.ucdavis.edu
Genome Browser
Early Applications of PhaseolusGenes: EXAMPLE
Theor Appl Genet 122: 893–903 (2011)
Identifying additional markers
linked to Co-14 and Phg-1 on PV01
• Previous information:
– Phg-1 maps on PV01 & linked to
SH13
– Co-14 linked to Phg-1
– Location of SH13 is ambiguous:
Pv01 or Pv11
• Alternative markers on PV01?
– Check Cmap
– Run markers against Bulked DNA
for R and S progenies
Two New Markers
CV542014
• Linkage
distances:
TGA1.1
– CV542014:
0.7 cM
– TGA1.1: 1.3
cM
Summary
• PhaseolusGenes:
– Includes all known markers established so far
– Used soybean whole-genome sequence as anchor
because of macro- and micro-synteny
– Facilitates marker discovery after initial mapping
– Can also use synteny for candidate gene discovery
• Further work:
– Addition of three whole-genome sequences of bean
– QTLs from beans
Conclusion
• Adoption of different approaches:
– Molecular Markers
– GIS
– Genomics
• Facilitate use of germplasm and reduce the size of
the “Black Box”: Black Box  Grey Box
Crop Science 46:2278–2292 (2006)