theme 1 overview - unlocking the value and use potential of genetic resources
DESCRIPTION
Presentation at the RTB Annual Review and Planning Meeting (29 Sep-3 Oct 2014)TRANSCRIPT
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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tmeb 419
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00
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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