evolution in a changing environment: the genetic architecture of adaptation outside centers of...
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Evolution in a changing environment: the genetic architecture of adaptation outside centers of domestication of Phaseolus vulgaris and P. coccineus
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WHY BEAN?
Family: Leguminosae - Genus: Phaseolus
Diploid species (2n = 2x = 22)
Annual and predominantly self-pollinating (autogamous) species
Phaseolus vulgaris L.
• 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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Annibale Carracci, The Bean Eater , 1584-1585
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Vincent Van Gogh - The Potato Eaters 1885
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DOMESTICATED BEAN SPECIES
P. vulgaris (common bean)
P. dumosus P. coccineus (runner bean)
P. Lunatus(lima bean)
P. acutifolius(tepary bean)
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P. vulgaris L. in AMERICA
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
Independent domestications
Mesoamerican gene pool
Northern Peru and Ecuador
Andean gene pool
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THE PROJECT
GbS on 11,500 AccessionsResequencing 560 genotypes
Transcriptomics and Metabolomics
Population genomicsAdmixture mapping
GWAS
Genes for adaptation
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Pv_ALL: GbS
Pv_core1: GbS WGS, phenotyping (MLFT)
Pv_core2: GbS WGS, phenotyping (MLFT), molecular phenotyping: Metabolomics and transcriptomics under tropical short-day vs a temperate long-day environment simulation
10.000
500
200
Phaseolus vulgaris
Single Seed Descent purified accessions 50% from America
50% from Europe
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WORKFLOW
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MAIN DELIVERABLES
• Computed haplotypes from 500 Pv_core1 accessions, and haplotypes for Pv_ALL.
• List of genes and phenotypes showing signature of selection.
• List of loci significantly associated with traits and environmental variables.
• Improved expression associated genome annotation.
• List of strong candidates for validation.
• List of validated candidates.
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Haplotype reconstruction (BeanHapMap)
10.000
500
200
GbS 10000 pure lines from landraces (Pv_ALL)
Phenotypes controlled conditions 200 lines
Metabolomics
Transcriptomics
WGS 500 pure lines
Phenotypes MLFT
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WORK PACKAGES
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