Theme 1 Overview - Unlocking the value and use potential of genetic resources

Theme 1 Overview - Unlocking

the value and use potential of

genetic resources Nicolas Roux

RTB Annual Meeting, Entebbe

29 September, 2014

Introduction – Project Overview

Project Title: Enhancing global RTB productivity through

more targeted use of global RTB genetic diversity

3 Components:

1. Genotyping towards conservation and use of RTB genetic

resources for breeding – Nicolas Roux

2. High-throughput/high-density phenotyping for characterization of

RTB genetic resources – Luis Augusto Becerra

3. Breeding applications for exploiting RTB crop evolution and

domestication traits – Luis Augusto Becerra

GENOTYPING BY SEQUENCING (GBS)

Component 1

Genotyping By Sequencing

Banana • 520 accessions by GBS (Cornell) (including Cv, CWR and hybrids)

• 650 accessions by RADseq (BGI)

Cassava • 3,000 cassava Sub-Saharan African clones by GBS (Cornell)

• 300 cassava LAC Landraces by RADseq (BGI) analysed out of the 800 acc.

Potato • 96 accessions by GBS (Cornell) (wild ancestors of diploid cultivars)

• 170 diploid landraces and 187 derived diploid hybrid progenies

• 1,190 tetraploid breeding lines for genome-wide representation of SNPs

Sweet Potato • ~90 F1 plants from a mapping population

Yam • 1,587 accessions by GBS (Cornell) including 810 D. rotundata genotypes +

470 germplasm accessions from the core collection; and 307 breeding lines

selected for key target traits (awaiting results)

Research Topics

• Understanding genetic diversity and population

structure

• Phylogenetic analysis with wild ancestors

• Clonal differentiation

• Gap analysis

• High-density genetic maps

• GWAS: Genome Wide Association Studies

• Bioinformatics

Pattern of heterozygosity and allele sharing

Contribution of wild relatives to cultivated

species

Confirmation on the previous suggestions to

treat D. cayenensis as a subspecies of D.

rotundata.

Understanding genetic diversity: Yam

Understanding genetic diversity:

African cassava

3,000 cassava clones have been

genotyped using GBS

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Admixture analysis detected nine subpopulations

(Rabbi et al, in prep)

Understanding genetic diversity: potato

170 diploid landraces of Groups Phureja, Stenotomum and Goniocalyx, and

187 derived diploid hybrid progenies of III cycles of recurrent selection were

genotyped by GBS

Results: 41,591 and 35,116 SNPs were identified in the diploid landraces and

hybrid progenies, respectively, at an allele frequency greater than 5% and with

more than 90% data

Objective: Application of Genomic Selection

for early prediction of breeding values for

improving yield, micronutrient content and

Vitamin C in a background of high yielding

heterotic hybrids

(Bonierbale et al, in prep)

Phylogenetic analysis: wild potatoes

GBS, 151,601 SNPs

Preliminary results:

• RAxML tree

• Using GTR+GAMMA

• 100 pseudoreplicates

Genome B

Genome P

Genome A

(Rodriguez et al, in prep)

a wide phenotypic diversity

but little or no genetic diversity with usual

molecular markers

Is a high density SNP coverage of the

genome able to reveal genetic variations

within somaclonal subgroups?

235,425 polymorphic SNPs of 29 African plantains

and ‘plantain-like’

• What consequence on gene expression?

• What implications for plantain improvement?

Clonal differentiation: plantain subgroup

(Perrier et al, in prep)

French Plantain False Horn Plantain Horn Plantain

Gap analysis: potato

A) Species richness map B) Prediction of HPS species

presence for gap filling

(De Haan et al, to be submitted to PLOS One)

Gap analysis: banana

Using RADseq to target Musa collecting within a triangular area of Indonesia

(MusaNet)

AAB

BB

ABB

AA/AAA

M. acuminata

(Triangle Banana Exploration Reports , 2014)

High-density genetic map: cassava

Using GBS to rapidly discover

and genotype thousands of SNP

markers in cassava.

These SNPs are used to

develop high-density genetic

maps for genetic studies and

improvement of reference

genomes.

High-density cassava map

with 6756 SNPs

(Rabbi et al. (2013) Virus Research)

150

100

50

0

Chromosome

Loca

tion (

cM

)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

Genetic map

High-density genetic map: banana

Contribution to the production of Musa genome reference sequences

Through genotyping by sequencing of

mapping populations used to assemble the

sequenced fragments (scaffolds) in

chromosomes

1) Contribution to the improvement of the Musa

acuminata reference sequence (Martin et al. in prep)

2) Contribution to the production of the Musa

balbisiana reference sequence (Jin et al. in prep)

Genetic map

Anchoring

on genetic

map

Chromosomes Sequence

scaffolds

GWAS for domestication: banana/plantain

E. Fondi – CARBAP Wild M. acuminata

Calcutta 4

E. Fondi – CARBAP Cultivated AA P. Mas

Selection of

samples

Candidate region detection

Candidate gene predictions

Available for distribution and further studies (Sardos et al. in prep)

Bioinformatics: architecture

Next-Generation Sequencing Eclipse Plug-in (NGSEP)

(Duitama et al, NAR, 2014)

GBS vs RADseq : preliminary comparison

25,000

Filtering

Mapping & calling

Quality

Trimming

1,700,000

Filtering

Mapping & calling

Quality

Trimming

GBS RADseq

Raw data (reads) for Musa accessions (2x)

#SNPs

MAF

Missingness

Bi-allelic

Polymorphic

#SNPs

Bioinformatics: visualization and interoperability

Diversity tree based on GBS

(linked to passport data)

Details of SNPs along the chromosome of

the Musa reference genome

Genes

SNPs

0

0

In the pipeline…

• Characterization of chromosome

structural variation

• Characterization of somatic

mutants, dwarfism

• Genomic Selection for accelerated

breeding

• Common RTB Bioinformatics

Platform

Lessons learned

• Expertise acquired/improved on Next Generation Sequencing

technologies

• Need to develop a data management plan (of Terabytes of raw data

generated)

• Demanding logistics to analyse samples

• Access to new and unknown material (e.g. Japan, Philippines)

• Large datasets are paving the way to many promising research studies

for RTB GR

So what…..?

• Theme 1 research lays the foundation for improved

use of RTB GR in NextGen breeding – Theme 2

• Increased knowledge on domestication, genepool

diversity, clonal diversification, candidates genes

( abiotic and biotic stresses) – Theme 3

• Increased access to characterized material.

Distribution of high quality material – Theme 4

• Diversity in production systems – Theme 5

• Gene discovery related to quality traits – Theme 6

• Collaboration strengthened within and between

RTB centers and new initiated and genetic,

genomics and bioinformatics tools ready to be

shared with National partners – Theme 7

THANK YOU

Augusto Becerra Lopez-Lavalle

Claudia Perea

Clair Hershey

Joe Tohme

and colleagues

Ranjana Bhattacharjee

Tessema, Gezahegn

Ismail Rabbi

Rony Swennen

and colleagues

Julie Sardos

Rachel Chase

Mathieu Rouard

Nicolas Roux

and colleagues

Angelique D’Hont

Jean Pierre Horry

Xavier Perrier

Frank Christophe Baurens

and colleagues

Stef de Haan

Flor Rodriguez

Awais Khan

Merideth Bonierbale

and colleagues

Theme 1 Overview - Unlocking the value and use potential of genetic resources

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Transcript of Theme 1 Overview - Unlocking the value and use potential of genetic resources