genetic diversity of the guatemalan climbing bean collection · feed the future innovation lab for...
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GENETIC DIVERSITY OF THE GUATEMALAN CLIMBING BEAN COLLECTION
2017 Feed the Future Legume Innovation Lab Grain Legume Research ConferenceOuagadougou, Burkina Faso
August 15th, 2017
María Gabriela Tobar Piñón, Samira Mafi Moghaddam, Rian Lee, Julio Villatoro, Juan M. Osorno and Phillip E. McClean
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Introduction
• The most important pulse crop for human consumption around the world.
• Source of protein and iron.
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Guatemala has the highest rate of chronic malnutrition in Latin America.
Introduction
http://www.feedthechildren.org
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Milpa system and climbing bean collections
• Intercropping array• Maize, climbing bean and
squash.• In situ collection of climbing
beans, n=600 (50 years). • Survey collection, n=500 (MSU
and ICTA, 2015).• Genetic diversity and
development of varieties.
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Middle America– Mesoamerica– Durango– Jalisco
Races• Andean
– Perú– Nueva Granada– Chile
Singh et al. (1991)
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Beebe et al. (2000), using RAPDs, proposed race Guatemala, mostlyGuatemalan climbing beans.
• Blair et al. (2009), usingmicrosatellites, supported raceGuatemala (61 accessions). Also, proposed Durango-Jalisco complex.
Genetic diversity of Middle American gene pool
Blair et al. (2009)
Andean genepool
Middle American genepool
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Analyze the genetic diversity of Guatemalan climbing bean collections using single-nucleotide polymorphism (SNP) markers.
• Correlate the genotypic data with phenotypic traits of economic/agronomic importance, using a genome-wide association study.
Objectives
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Population selection– 369 Guatemalan accessions (old
collection).– 260 Guatemalan accessions (new
collection).– Mesoamerican Diversity Panel (MDP):
• 100 accessions of race Mesoamerica.• 100 accessions of race Durango-Jalisco.
– 12 wild accessions from Guatemala (USDA-GRIN)
Materials and Methods
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Tissue collection• DNA extraction• Genotype by sequencing
– MseI and Taqα1 restriction enzymes.• SNP calling (136,382 SNPs)
– Samtools, BWA mapping, GATK.– Filtering for 0.05 MAF (102,343 SNPs)
• Population structure and genetic diversity analysis– PCA, ML tree (SNPhylo), STRUCTURE, Fst, He, PIC values.
• Genome wide association study (GWAS)– GAPIT, 4 models.
Materials and Methods
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
K2
K3
K4
K5
STRUCTURE analysisGuatemalan collections and Mesoamerican races
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Phylogenetic treeGuatemalan collections and Mesoamerican races
Durango/Jalisco
Mesoamerica
Guatemala (new)
Guatemala (old)
Wilds
0.2 LDGuatemala (Old)
Guatemala (New)
Durango/Jalisco
Mesoamerica
Wilds
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Principal Components AnalysisGuatemalan collections and Mesoamerican races
Guatemala (Old)
Guatemala (New)
Durango/Jalisco
Mesoamerica
Wilds
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Sup-population Ho He PIC %Monomorphic Fst value
Durango/Jalisco 0.4597 0.3437 0.2680 8.17 0.2904
Mesoamerica 0.4569 0.3366 0.2625 8.08 0.3054
Guatemala (old) 0.4755 0.3623 0.2842 3.30 0.1474
Guatemala (new) 0.4892 0.3897 0.3052 0.50 0.1192
Diversity Statistics
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Phylogenetic tree of Guatemalan beans
Guatemalan old collection
Guatemalan new collection
Guatemalan wilds
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
PCA based on regions, new collection
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
PCA based on elevation, new collection
2500-3000 masl
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Association mapping Elevation
Pv02Pv01 Pv03 Pv04 Pv05 Pv11Pv10Pv08 Pv09Pv06 Pv07
Ring Ubox superfamily proteinRibosomal protein
HEN 4
• Flowering process
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
• Guatemalan climbing beans did not group with any of the previously defined races of common bean.
• Race Guatemala represents a new source of genetic diversity.
• Genomic regions were associated with several traits of economic importance.
• Genomic regions were associated with local adaptation in the Guatemalan climbing beans.
Conclusions
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Feed the Future Innovation Lab for Collaborative Research on Grain Legumes
Acknowledgements
• Dr. Phillip McClean• Dr. Juan Osorno• Dr. Samira Mafi• Rian Lee• Julio Villatoro• Carlos Maldonado• Angela Miranda• Dr. Jill Hamilton• Dr. Ali Soltani