Mauricio Parra QuijanoFAO consultant International Treaty on Plant Genetic Resources for Nutrition and Agriculture CAPFITOGEN Program Coordinator

http://www.capfitogen.net

ToolsRepresenta & DIV mapas

INTRODUCTION TO

Representa

Evaluates the ecogeographical representativeness of germplasm collections

Genetic representation

A B C

accggtccc accggtcgc accggtctc

A B C

A A A

A B CAAA

A

B

BBB

C BA

Ecogeographic representation

A BBBBBBB CCC

A B C Unique

A BB CC Even

A BBBB CC Proportional

Representativeness based on ELC maps

y

x

Coordinates of passport dataELC map of Cuba (from ELC mapas tool)

Sites with species´ occurrences

1 2 3 4 5 6 7 8 9 10ELC categories

N e

ntrie

s

100

200

300

Genebank set

1 2 3 4 5 6 7 8 9 10ELC categories

N e

ntrie

s

100

200

300External sources set1 2 3 4 5 6 7 8 9 10

ELC categories

% c

ells

25

50

75

Overall distributionCategories of the map

Χ2 test

upperupper midlower midlower

Quartiles

Validation through germplasm evaluation/characterization

-Apparents

-Non-apparents

Adaptive traits:

DIVmapas

Provides maps of phenotypic, genotypic and/or eco-geographical diversity

Measuring the diversity of the collections

Characterization

Morphological

Biochemical / Molecular /ADN

Agronomical / Physiological / Phytopathological Entomological

Eco-geographical

1246

711

883

1247

012

471

1247

212

473

1248

312

484 11

461

1247

812

479

1148

111

868

2302

1186

911

401

1140

511

406

1140

711

408

1183

511

832

1183

311

484

1182

711

828

1154

211

539

1154

012

468

1189

112

465

1149

311

494

1150

811

506

1150

711

496

1149

211

490

1149

1 1148

911

501

1156

311

504

1150

211

503

1154

311

546

1154

712

474

1183

811

534

1153

211

533

1152

911

527

1152

811

535

1156

411

764

1152

411

523

1152

211

521

1152

011

519

1151

711

518

1185

411

841

1184

212

477

1247

512

476

1246

911

473

1147

211

471

1146

911

470

1147

711

474

1147

511

467

1146

8 1151

611

514

1151

512

461

1184

812

480

1154

912

466

1246

212

463

1187

911

875

1187

211

874

1245

512

456

1148

012

448

1146

011

458

1145

912

453

1245

412

458

1245

912

452

1145

511

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211

451

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811

450 1

1454

1145

611

457

1246

411

466

1146

511

462

1146

4 1245

711

857

1185

311

852

1185

011

851

1244

912

450

1245

112

440

1141

211

410

1141

111

413

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412

436

1243

7 1141

612

441

1243

812

439

1141

711

419

1143

111

430

1142

811

427

1142

611

425

1142

411

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1142

111

422

1243

511

432

1143

311

551

1143

811

439 1155

011

437

1143

611

434

1143

512

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1244

311

556

1156

011

557

1155

812

447

1244

412

445

1144

711

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1144

611

440

1144

111

444

1144

211

443

1148

811

482

1228

312

284

1148

511

487

05

1015

Cluster analysis

hclust (*, "average")

Hei

ght

How we have visualized the genetic diversity

-0.2 0.0 0.2 0.4

-0.3

-0.2

-0.1

0.0

0.1

0.2

0.3

PCO for genotypic characterization

PCO 1

PC

O 2

d = 2

1

2

3 4 5 6

7 8 9 10 11 12

13 14

25 26

33 34 35 36 37 38 39 40

41 42 43 44 45 46 47

48 49 50 51 52

54 55 56 57

58 59 60 61 62 63 64

65 66 67

69

74

75

76 77 78

79 80

81 82 83 84 85

86 87 88

89 90 91 92 93 94 95 96 97 98 99

100 101 102 103 104 105 106

107 108

109

113 120

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123 124

125 126 127

128 129 130

131

132 133 134 135

136

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140 141 142 143

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148 149 150

151 152

153 154

157 158 159

160 161 162 163

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170 171

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181 182 183 184

185

186 187 188 189 190

192 193

X

alt

slope

bio_15

bio_12

bio_18

bio_17

bio_1

bio_9

t_sand

t_caco3

t_cec_clay

t_silt

t_ph_h2o

t_ece

Eigenvalues

How we have visualized the genetic diversity

DIVmapas

A different way to visualize the diversity Collecting sites with a minimum level of geo-referencing quality

DIVmapas

Overlapping a grid (N x N km cells)

DIVmapas

Selection of cells that include collecting sites (centroids are points in yellow )

DIVmapas

Detection of neighbouring cells which centroids (green points) falls at X km (radius ) around of the presence cell centroid (yellow points)

DIVmapas

Generation of areas of influence from each centroid Detection of accessions collected within each area of influence

DIVmapas

OTU 89 233 152

89 0

233 10 0

152 15 14 0

OTU VAR1 VAR2 VAR3 VAR4 VAR5

89 233 0.56 13 600 0

233 198 1.43 13 700 0

152 201 0.88 10 600 1

Distance algorithm

Averaged distance = (10+15+14)/3

= 13

Local multivariate analysis

DIVmapas

Same process for all cells that include collecting sites

DIVmapas

Same process for neighbouring cells

DIVmapas

0 0 0 0 1 3 2

1 1 0 1 1 2 1

1 1 0 1 1 0 0

0 0 0 0 0 0 0

Result 1:Number of analyzed accessions by cell

DIVmapas

0 13 8

0 0 0 0 2 0

0 0 0 0

Result 2:Averaged distances assigned to each cell

DIVmapas

Bias in sampling? Correction via "bootstrapping"

12......n

Median = 2

Applied DIVmapas

Ecuadorian collection ofArachis hipogaea L.

Applied DIVmapas

Number of collecting sites per cell

Applied DIVmapas

Averagedeuclidean distance