ORIGIN AND GENETIC DIVERSITY OF CROATIAN COMMON BEAN LANDRACES
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1 ORIGIN AND GENETIC DIVERSITY OF CROATIAN COMMON BEAN LANDRACES Zlatko Šatović University of Zagreb, Faculty of Agriculture,, Zagreb, Croatia Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv) BioDiv),, Zagreb, Croatia Belgrade, 2018
2 CoE CroP-BioDiv + 5 Member Institutions Host Institution University of Zagreb, Faculty of Agriculture Institute for Agriculture and Tourism Poreč University of Zagreb, Faculty of Science Agricultural Institute Osijek Institute for Adriatic Crops Split University of Osijek, Faculty of Agriculture CoE CroP-BioDiv
3 OPAB13_751 OPM18_1238 OPZ17_551 OPB11_1371 OPN11_1280 OPE11_477 OPX20_440 ** OPAI14_650 ** OPZ10_576 **** OPW5_1383 *** OPK6_887 *** OPM4_490 *** OPAE2_1551 *** OPB11_941 *** RNAH_AluI ** OPK6_818 **** OPC7_1390 **** OPE5_512 ** OPE11_392 ** OPR3_465 ** OPAB13_1903 OPM11_771 OPAE5_674 OPAE2_1173 OBJECTIVES Conservation of PGR Phenotyping Genotyping qtl1 Bioinformatics Dissemination Conservation of Plant Genetic Resources >> increase the benefits Phenotyping >> high-throughput phenotyping (HTP) platforms Genotyping >> next-generation sequencing (NGS) techniques Bioinformatics >> genome-wide association studies (GWAS) Dissemination >> workshops, summer schools
4 MODEL PLANT SPECIES Major Crops Maize Wheat Soybean Traditional Crops Grapevine Olives Promising Crops Brassicas Alliums Common bean Dalmatian pyrethrum Dalmatian sage
5 ORIGIN AND GENETIC DIVERSITY OF CROATIAN COMMON BEAN LANDRACES Zlatko Šatović University of Zagreb, Faculty of Agriculture,, Zagreb, Croatia Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv) BioDiv),, Zagreb, Croatia Belgrade, 2018
6 PLAN (1) Introduction: Common Bean Domestication (2) Materials and Methods (3) Origin and genetic diversity (4) Further research
7 PLAN (1) Introduction: Common Bean Domestication (2) Materials and Methods (3) Origin and genetic diversity (4) Further research
8 ORIGIN / DIVERGENCE Origin of wild common bean: Mesoamerica Divergence: Andean wild bean diverged from Mesoamerican prior to domestication (~100,000 BP)
9 DOMESTICATION Domestication: Independently domesticated in Mesoamerica and the Andes (~8,000 BP) Mesoamerican centre: indeterminate (maize-bean-squash multicrop system) Andean centre: determinate types (no suitable crop: root crops, quinoa)
10 DIVERSIFICATION Domestication: Mesoamerican centre: indeterminate Andean centre: determinate Diversification: Adaptation to new environments and local preferences Andean centre: indeterminate (after maize introduction: ~7,000-6,000 BP) Mesoamerican centre: determinate (determinacy has been selected independently in both centres)
11 INTRODUCTION TION TO EUROPE Introduction to Europe: 16th century Protugal and Spain several introductions Origin (phaseoline type): Mesoamerican 33% Andean 67% Hybrids: up to 33% - Balkans: (A) The proportion of landraces of the Mesoamerican origin tends to increase in eastern and south-eastern Europe (Albania, Bulgaria, Macedonia, Greece) (B) The proportions found in accessions from Bosnia and Herzegovina, Croatia, Serbia and Slovenia were very similar to those found in the Iberian Peninsula and Italy indicating that common bean was introduced mainly from the Mediterranean Basin
12 PLAN (1) Introduction: Common Bean Domestication (2) Materials and Methods (3) Origin and genetic diversity (4) Further research
13 MATERIALS: LANDRACES IN CROATIA - the majority of the common bean production is based on local landraces - grown by small-scale farmers in low input production systems - no plant breeding programme - landraces known by their traditional names different seed coat patterns and colours also found in neighbouring countries (central Europe, western Balkans) 174 accessions >> 10 morphotypes - aim: origin and genetic diversity - goal: association mapping study 'Kukuruzar' 'Tetovac' 'Biser' 'Trešnjevac' 'Puter' 'Dan i noć' 'Zelenčec'
14 METHODS: MOLECULAR ANALYSES (1) Phaseoline type analysis - a DNA marker for phaseolin-type diversity (2) Microsatellite markers (SSRs) - 26 markers / 135 alleles (3) DArTseq SNP genotyping (SNPs) - 6,599 polymorphic SNP markers
15 PLAN (1) Introduction: Common Bean Domestication (2) Materials and Methods (3) Origin and genetic diversity (4) Further research
16 PHASEOLINE TYPE ANALYSIS I (Mesoamerican) 99% (1) Phaseoline type analysis - three types: 1. type I - Mesoamerican ( S ) 2. type II - Andean ( H or C ) 3. type III - Andean ( T ) II III Phaseoline type: I II III (2) Microsatellite markers (SSRs) - genetic distance: D psa - tree: Neighbor-joining method - two well-supported clades (Mesoamerican vs Andean) - subclade (Andean type III) 0.05
17 SSRs I/A (Mesoamerican) II/B 1 III/B 2 Phaseoline type: I II III Genetic cluster: A B 1 B 2 99% 0.05 SSRs K2 K3 (3) Microsatellites - Bayesian modelbased clustering method for inferring population structure - proportions of membership (Q) of each accession in each genetic cluster assuming two (K2) or three clusters (K3) - clusters / phaseoline: A - type I Mesoamerican B 1 - type II Andean B 2 - type III Andean
18 SNPs Schmutz et al. (2014) >> a reference genome for common bean Valdisser et al. (2017) >> characterization of common bean core collection No. of accessions No. of polymorphic markers SNP/Mbp Observed heterozygosity (H O ) Expected heterozygosity (H E ) - Diversity Arrays Technology (DArT) based on genome complexity reduction and SNP detection through hybridization of PCR fragments Valdisser et al. (2017) 188* 5, *91 landraces + 97 cultivars from all over the world This study 174 6,
19 SNPs I/A (Mesoamerican) II/B 1 III/B 2 99% (4) SNPs markers (linkage equilibirum; LE) - Bayesian modelbased clustering method for inferring population structure - same approach as for SSRs - congruent results K2 K3 Phaseoline type: I II III Genetic cluster: A B 1 B
20 I/A (Mesoamerican) 99% K2 K3 K2 K3 II/B 1 III/B 2 Phaseoline type: I II III SSRs SNPs Genetic cluster: A B 1 B
21 TRUE-TYPES TYPES vs OFFTYPES I I/A (Mesoamerican) 99% (1) True-types - phaseolin type matches the cluster membership (SSRs and SNPs) - percentage of cluster membership (Q) higher than 75% II/B 1 III/B 2 Phaseoline type: I II III SSRs (2) Offtypes - putative hybrids (2.1) Non-corresponding no correspondence between phaseolin types and clusters Genetic cluster: A B 1 B
22 OFFTYPES II I/A (Mesoamerican) II/B 1 III/B 2 Phaseoline type: I II III 99% SSRs (2.2) Mixed origin - percentage of cluster membership (Q) lower than 75% based on SSRs or SNPs Genetic cluster: A B 1 B
23 I/A (Mesoamerican) 99% II/B 1 III/B 2 Phaseoline type: I II III SSRs SNPs Genetic cluster: A B 1 B
24 ORIGIN CROATIA PORTUGAL Offtypes 22% I/A 25% Offtypes 32% I/A 15% III/B 2 39% II/B 1 14% III/B 2 21% II/B 1 32% 174 accessions (1 plant/accession) 175 accessions (10 plants/accession) Leitão et al. (2017)
25 GENETIC DIVERSITY (1) SSRs 26 markers H O = (autogamy) II/B1: highest H E (2) SNPs 6,599 markers H O > I/A: highest H E Observed heterozygosity (H O ) Expected heterozygosity (H E ) = gene diversity I/A II/B 1 III/B 2
26 MORPHO-GENETIC GROUPS - from 10 morphotypes to 16 morpho-genetic groups I/A (Mesoamerican) 'Trešnjevac' II/B1 'Trešnjevac' III/B2 'Trešnjevac' DETERMINATE 'Kukuruzar' 'Puter' 'Puter' DETERMINATE 'Tetovac' 'Dan i noć' 'Dan i noć' DETERMINATE 'Biser' DETERMINATE 'Sivi' 'Zelenčec' DETERMINATE
27 MORPHO-GENETIC GROUPS I/A (Mesoamerican) II/B1 III/B2 'Trešnjevac' 'Trešnjevac' 'Trešnjevac' DETERMINATE 'Kukuruzar' 'Puter' 'Puter' DETERMINATE 'Tetovac' 'Dan i noć' 'Dan i noć' DETERMINATE 'Biser' DETERMINATE 'Sivi' 'Zelenčec' DETERMINATE
28 MORPHO-GENETIC GROUPS I/A (Mesoamerican) II/B1 III/B2 'Trešnjevac' 'Trešnjevac' 'Trešnjevac' DETERMINATE 'Kukuruzar' 'Puter' 'Puter' DETERMINATE 'Tetovac' 'Dan i noć' 'Dan i noć' DETERMINATE 'Biser' DETERMINATE 'Sivi' 'Zelenčec' DETERMINATE
29 RELATIONSHIPS AMONG MORPHO-GENETIC GROUPS Microsatellite markers (SSRs) - genetic distance: Cavalli-Sforza chord distances - tree: Neighbor-joining method I/A (Mesoamerican) II/B III/B : 'Trešnjevac' : 'Tetovac' : 'Kukuruzar' DETERMINATE: 'Biser' : 'Sivi' : 'Puter' : 'Maslina' : 'Dan i noć' : 'Trešnjevac' DETERMINATE: 'Trešnjevac' DETERMINATE: 'Zelenčec' DETERMINATE: 'Dan i noć' DETERMINATE: 'Puter' DETERMINATE: 'Bijeli'
30 PLAN (1) Introduction: Common Bean Domestication (2) Materials and Methods (3) Origin and genetic diversity (4) Further research
31 ASSOCIATION MAPPING - goal: Identification of SNP markers linked to the quantitative trait loci (QTL) related to bioactive nutrient contents in common bean 1. PGR: Croatian common bean landraces 2. Phenotyping: The assessment of seed mineral diversity (Mg, Ca, Fe, Zn, K, P) and phytic acid content 3. Genotyping: - SSRs - genetic diversity and structure - SNPs - DArTseq high-density SNP genotyping 3. Bioinformatics: Genome-Wide Association Study (GWAS)
32 ACKNOWLEDGEMENTS Klaudija Carović-Stanko Zlatko Liber Monika Vidak Jerko Gunjača Martina Grdiša Boris Lazarević CoE CroP-BioDiv
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