Presentation delivered by Nicolas Roux during the RTB Annual Meeting, 8-10 December 2015, Lima, Peru

1. Theme 2: Application of Genome-Wide
Association Study (GWAS) and
transcriptomics to study Gene-Trait
associations in banana
Sardos J, Rouard M, Hueber Y, Cenci A, Hyma K.E, van den Houwe I,
Hribova E, Courtois B, Zorrilla-Fontanesi Y, Kissel E, Do H, Dubois E,
Nidelet S, Swennen R, Carpentier SC and Roux N
8 December 2015

2. Outline
• Genome wide association studies (GWAS) for
Seedleness
• Application of GWAS to drought ?
• Understand the complex trait of drought

3. GWAS: basic principles and increase
utilization
• Genome-Wide Association Study was first set up for Human
genetics and consists in examining common genetic variants
(e.g. SNPs) in many different individuals to see if any marker
is associated with a trait
• Successfully used in Arabidopsis, rice and other cereals on
various traits
• Prerequisites for successful association: a panmictic (random
sexual mating), unstructured, diploid and infinite
population
• In practice: “infinite” ok for > 100 individuals
• Models have been developed to balance the confounding
effects of the structure
• But random sexual mating in banana is a problem
(polyploidy, 2 genomes, clonal diversification)

4. Selecting a panel for GWAS in banana
• Selection of the panel
• 498 DArT data available for
224 M. acuminata diploids
(wild + edible)
• 106 accessions were selected:
– Avoiding clone mates
– Smoothing the structure
– TTT (when data available)
• 106 accessions were
genotyped with GBS (Cornell)
among which 26 wild and 78
edible
• Bioinformatics filtration pipeline
allowed to predict 5,544 SNPs
0
50
100
150
200
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50
0 0.1
Distribution of dissimilarities between pairs of
accessions

5. Investigate the structure of the panel
Cl. 1 Cl. 2
Wild from SEA
Wild + cv from
New-Guinea
Admixed accessions

6. Performing GWAS on the full panel
K=4

7. Performing GWAS on the Papuan subset
• Unstructured subset composed of
both wild and cultivated accessions
• 5 regions detected

8. GWAS results: 5 genomic regions identified
Linkage disequilibrium

9. 100-200 kb
Explored region
Chr 3
Exploration of the Banana genome

10. Banana Genome Hub
Chr 3
Exploration of the Banana genome
In total, more than 100 genes

11. Comparative genomics
Gene with unknown
function
Gene with known
function
Model species
Homologous genes
Annotation transfer
Rouard M, Guignon V et al. GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Research, 2011,
10.1093/nar/gkq811

12. Seedlessness: parthenocarpy and sterility
• We discovered 2 genes directly involved in female
sterility in Arabidopsis
• Due to the hormonal pathway related to
parthenocarpy, we considered 11 genes linked with
Auxin, Gibberelins and Abscicic Acid
Pollination Seed Aux GA ABA
Cell division Cell expansionFruit Set
X X

13. For more information
Sardos J, Rouard M, Hueber Y, Cenci A, Hyma K.E, van den
Houwe I, Hribova E, Courtois B and Roux N.
A Genome-Wide Association Study on domestication reveals
the potential of a selected panel to detect candidate genes
in a vegetatively propagated crop, banana (Musa spp.).
Plos One. (accepted with modifications)

14. Field trial
• IITA, Arusha, Tanzania • Bimodal rainfall pattern (900-1100 mm/yr)
• Dry seasons (June – Nov & Dec - Feb)
FAO NewLocClim for Arusha,
Tz, 2015

15. Experimental set-up
• Under discussion but ~15 traits to be recorded but
mainly linked to growth and production
• Results of the field trials are expected to be available
at the beginning of 2017
• GWAS could be performed for this specific traits
once the evaluation completed

16. Drought Stress: Leaf temperature
(Taiz and Zeiger, 2002)
Drought
• Transpiration ~ evaporative cooling
• Reduced transpiration: detect by Infrared imaging
Cachaco (ABB) Nakitengwa (AAAh)
Leaf temperature

17. Sequencing,
genome information
in vitro growth
model at
KULeuven
Understanding complex traits:
drought tolerance
Greenhouse growth model at
KULeuven
Field trials in IITA-Tanzania
ITC
Automated phenotyping facility

18. Transcriptomics study
Grande Naine (AAA)Mbwazirume (AAA) Cachaco (ABB)

19. Common response to osmotic
stress in roots
Zorrilla-Fontanesi Y*, Rouard M*, Cenci A, Kissel E, Do H, Dubois E, Nidelet S, Roux N, Swennen R, Carpentier SC Differential root transcriptomics
in a polyploid non-model crop: the importance of respiration during an early stage of osmotic stress. Scientific reports. (under review)
92 genes differentially expressed in the 3 genotypes
Most affected
pathways are
glycolysis and
fermentation
Osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a
higher oxidative respiration, (ii) alternative respiration and (iii) fermentation.

20. conclusions
• 1st GWAS studies in banana
• Publication accepted with modifications
• Collaboration with IITA on other traits (drought)
• Transcriptomics studies ongoing
• 2nd publication (KUL, Bioversity)
• Other studies (Foc TR4)
• Pre-breeding (gene discovery) useful for breeding
• The preliminary results of this complementary
project allowed to path the way for the Discovery
flagship (nextgen cluster)

21. Thank You