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

Tools

Representa

Evaluates the ecogeographical representativeness of germplasm collections

Genetic representation

A B C

accggtccc accggtcgc accggtctc

A B C

A A A

A B C

AAA

A

B

B B

B

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 10

ELC categoriesN

en

trie

s

100

200

300

Genebank set

1 2 3 4 5 6 7 8 9 10

ELC categories

N e

ntr

ies

100

200

300

External 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 / PhytopathologicalEntomological

Eco-geographical

12467

11883

12470

12471

12472

12473

12483

12484 11461

12478

12479

11481

11868

2302

11869

11401

11405

11406

11407

11408

11835

11832

11833

11484

11827

11828

11542

11539

11540

12468

11891

12465

11493

11494

11508

11506

11507

11496

11492

11490

11491 11489

11501

11563

11504

11502

11503

11543

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12474

11838

11534

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11535

11564

11764

11524

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11854

11841

11842

12477

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12476

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11473

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11474

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11467

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11516

11514

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12461

11848

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11549

12466

12462

12463

11879

11875

11872

11874

12455

12456

11480

12448

11460

11458

11459

12453

12454

12458

12459

12452

11455

11453

11452

11451

11448

11450 1

1454

11456

11457

12464

11466

11465

11462

11464

12457

11857

11853

11852

11850

11851

12449

12450

12451

12440

11412

11410

11411

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11414

12436

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11416

12441

12438

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11417

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12435

11432

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11551

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11550

11437

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12442

12443

11556

11560

11557

11558

12447

12444

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11447

11445

11446

11440

11441

11444

11442

11443

11488

11482

12283

12284

11485

11487

05

10

15

Cluster analysis

hclust (*, "average")

He

ight

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

121

122

123 124

125 126 127

128 129 130

131

132 133 134 135

136

137

138

139

140 141 142 143

144

145

148 149 150

151 152

153 154

157 158

159

160 161 162 163

164

165 166

167 168

169

170 171

172

173 174

175

176

177

178

179 180

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"

1

2......n

Median = 2

Applied DIVmapas

Ecuadorian collection ofArachis hipogaea L.

Applied DIVmapas

Number of collecting sites per cell

Applied DIVmapas

Averagedeuclidean distance