Overview of RTB Theme 1 –

Unlocking the value and use potential

of genetic resources

Nicolas Roux, Julie Sardos, Mathieu Rouard, Ismail Rabbi, Flor

Rodriguez, Severin Polreich, Bettina Heider, Ranjana Bhattacharjee,

Xavier Perrier, Angelique d’Hont and Luis Augusto Becerra Lopez-Lavalle

RTB Annual Meeting, Lima Peru, 8 December 2015

Research Objectives

• Population structure analysis

• Assessment of genetic diversity

• Gap analysis

• Variety identification and population structure analysis

• Genetic integrity

• In situ versus ex situ

• Genome sequencing

• Bioinformatics

Genome P

Genome A

(Rodriguez et al, in prep)

S. stenotomum

S. goniocalix

S. phureja

Phylogenetic analysis:

wild and cultivated

potatoes

34

41

99

100

100

100

S. bukasovii

S. candolleanum

S. ambosinum

SNP calling 1:

• Tassel 4 GbS Pipeline

• ref. genome:

PGSC_DM_v4.03

• allele freq 0.05-0.95

• <5% missing data in SNP

• <10% missing data in Taxa

• 13,150 SNP

• 260 Taxa

SNP calling 2:

• CIP Pipeline

• ref. genome:

PGSC_DM_v4.03

• allele freq 0.05-0.95

• <5% missing data in SNP

• <10% missing data in Taxa

• 5,241 SNP

• 274 Taxa

Phylogenetic analysis:

• RAxML

• GTR+CAT model

• 1,000 bootstraps

Wild

potatoes

2x cultivated potatoes

Assessment of genetic diversity

384 D. alata germplasm genotyped

with 34 SSR markers

A total of 847 alleles recorded

across 26 SSRs with mean number

of alleles ranging from 10.6

(CIRAD) to 7.5 (IITA)

IITA INRA CIRAD CTCRI

Group 1

Group 2

Group 1

Group 3

Group 3 Group 4

Group 4

Group 5

Group 5

Group 6

Group 7

Arnau et al (2015). SSR-based genetic diversity in

different collection of Dioscorea alata (under

review)

Indicators INR

A

CIRAD CTCRI IITA

N

At

Am

129

217

9.0

83

255

10.6

82

194

8.1

90

181

7.5

Gap analysis

Priorities for gap filling and conservation by country

Potato

• 32 species (43.8%) are High Priority

Species (HPS) and need to be

prioritized for further collecting

• Castañeda-Álvarez et al. 2015 DOI:

10.1371/journal.pone.0122599 potato

Sweetpotato

• 11 out of 14 (79%) species are

High Priority Species (HPS for

further collecting

• Khoury C.K. et al. 2015 doi:

10.3389/fpls.2015.00251

Gap analysis in banana

Gap analysis (cont.)

Manihot genus & putative ancestor of the domesticated form

Eco-geographic signature of the crop’s domestication patterns

K2

K7

Variety identification

Individual ancestry estimates to determine contribution of ancestral clones to new varieties

Hierarchical clustering dendrogram to determine identical clones.

Projection of

identified clones in

3 regions of Ghana

Population structure

analysis

Variety names often do not match

specific genotypes

182 different names recorded for the entire sample collection and here only names that

occurred > 9 times are represented.

I"

II"

III"

IX"

V"

VI"VII"

VIII" X" XI" KOTEE"AMPENKYENE"

TUAKA"

AFIA0KOFIE"

ESIABAYAA"

BOSOMENSIA"

ABENWOHA"

DEBOR"

BANKYE0"KOKOO"

ANKRA"

Determination of genetically unique varieties in 2 Peruvian diversity hotspots

Baseline characterization

223 76 15

Huancavelica (n =658) Apurímac (n=190)

36.2% of total samples

unique

47.9%

of total samples unique

a. Potato landrace samples (658 from Huancavelica and 190 from Apurimac, Peru) were collected and molecularly analyzed in 2013 and 2014. b. Genetic fingerprinting with 12 polymorphic SSR microsatellite was carried out and 115 alleles

identified in total.

c. The number of unique cultivars and pure duplicates within the genetically characterized (sub)populations was determined.

Geospatial coverage of in situ/ex situ diversity

In situ Ex situ

(baseline

data)

(passport data

CIP

Genebank)

No. different

varieties

No. varieties

registered

Dept: Apurimac

Prov: Cotabambas

Distrito: Haquira* 91 8

Dept: Huancavelica

Prov: Huancavelica

and Acobamba

Districts: Yauli and

Paucara

238

15

• Diversity hotspots geo-spatially

underrepresented at CIP’s genebank.

• Genetic analyses accomplished by 61%

in Huancavelica resulted in 238

different varieties.

total number of varieties from the

respective districts maintained ex situ =

15!

• Former studies of de Haan et al. (2010)

indicated high genotypic diversity and

allelic variation that are site specific.

• Comparative analyses of material

maintained in hotspots and kept in CIP’s

gene bank will help to determine

evolutionary dynamics in situ and

improve the genetic and geo-spatial

coverage of the ex situ collection.

Tetraploid

Diploid

Tri-Pentaploid

Highest

richness Endemism

I. Hotspot identification

MACRO MESO MICRO

Indicators

• Endemism

• Richness

• Coexistence wild relatives

• Diversity of cultural and agro-

ecological conditions

II. Richness-Altitude

Indicators

• Number varieties

• Altitude (masl)

IV. Red List

Indicators

• Abundance

• Frequency

Findings:

• Major diversity between 3800-4300 masl.

Timeline comparison indicates that this altitudinal belt

ascended >250 m during the last 50 years.

• On average >60% of observed varieties are grown by

<5% of farm households. diversity is highly

scattered within the communities

• >70% of varieties show a very low abundance and

frequency in farmers fields. repeated measuring

will reveal how threatened they are.

III. Horizontal dynamics

(crop rotation)

Indicators

• Crop rotation

pattern

Women and Conservation - GENDER

• Women play a central role in in situ

conservation of RTB crops, through

utilizing them for nutrition, health

hazards as well as marketing and

exchange of crops and genetic

material.

• Enhancing their livelihood is essential

to establishing a sustainable, long-term

in situ conservation system for locally

adapted landraces and associated crop

wild relatives.

• Important gender dimensions of in situ

management involve seed selection,

farmer food choices and preference

traits (drivers of conservation), child

nutrition, folk taxonomy and medicinal

uses and feminized conservation,

where temporal or permanent male

migration occurs (Andes, West Africa).

Nieves Mamani, 41 years old conservationist farmer

conserving 235 different potato landraces , from the

Community Cariquina Grande, La Paz Department, Bolivia.

(Photo credit: Victor Iriarte )

a wide phenotypic diversity

but little or no genetic diversity with usual

molecular markers

235,425 polymorphic SNPs of 29 African plantains

and ‘plantain-like’

read number: deviation % from plantain consensus

by chromosome, for each accession

interpretation in chromosome rearrangements

Is a high density SNP coverage of the

genome able to reveal genetic

variations within somaclonal

subgroups?

Clonal differentiation

French Plantain False Horn Plantain Horn Plantain

1) Are these variations due to the

accumulation of mutations over time

(vegetatively propagated) ?

2) Are these variants induced by in

vitro culture?

In 2015, complementary analysis

performed on the accessions only ever

in vivo (provided by IITA Onne station)

Nzumoigne

Ihitisim

Obubit

Ihitisim

11

10

9

8

7

6

5

4

3

2

1

Obino

l’Ewai

Ihitisim

Niangafelo

Agbagba

Nzumoigne

Ntanga

Ihitisim - ITC0121 (analysis 2014)

Ihitisim - ITC0121 (analysis 2015)

Ihitisim – Ni1 (analysis 2015) collection in vivo IITA

Ihitisim was introduced at ITC in 1986 from IITA

Variant genome

Control genome

Chromosome 3

Number of Reads between 10 and 450

8931 SNP s

True-to-type Off-type

Technical Guidelines for

the Safe Movement of

Musa Germplasm –

Published in December

2015

BSV workshop, Montpellier, May 2015

Genome reference sequences

Contribution to the production of Musa genome reference sequences for three

additional M. acuminata subspecies : spp. banksii (Banksii), burmannicoides

(Calcutta4) and zebrina (Maia oa)

spp. malaccensis (DH pahang)

Close to 88% of the assembly anchor to chromosome

(D’hont et al. 2012) and an improved version (Martin et al., BMC genomics, accepted).

zebrina banksii

malaccensis

burmannicoides

Deep re-sequencing (BGI), pan genome and LSV analysis in progress

A

A A A

17-19 August 2015, Bioversity Montpellier, France

January 2015, Ithaca

Bioinformatics: Community of practice

Conclusions

• Benefits of whole genome sequencing

• Synergies between crops and centres

• Importance of data sharing

• Interoperability between databases

• Logistical issues

• Legal issues

• Budget cuts

• In some centres, need for more interactions between

GB-CRP and RTB-CRP

THANK YOU

Augusto Becerra Lopez-

Lavalle

Claudia Perea

Clair Hershey

Joe Tohme

and colleagues

Nicolas Roux

Julie Sardos

Rachel Chase

Mathieu Rouard

and colleagues

Angelique D’Hont

Jean Pierre Horry

Xavier Perrier

Frank Christophe Baurens

and colleagues

Dave Ellis

Flor Rodriguez

Severin Polreich

Bettina Heider

Merideth Bonierbale

and colleagues

Ranjana Bhattacharjee

Tessema Gezahegn

Ismail Rabbi

Rony Swennen

and colleagues