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

Outline

• Genome wide association studies (GWAS) for

Seedleness

• Application of GWAS to drought ?

• Understand the complex trait of drought

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)

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

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Distribution of dissimilarities between pairs of accessions

Investigate the structure of the panel

Cl. 1 Cl. 2

Wild from SEA

Wild + cv from New-Guinea

Admixed accessions

Performing GWAS on the full panel

K=4

Performing GWAS on the Papuan subset

• Unstructured subset composed of

both wild and cultivated accessions

• 5 regions detected

GWAS results: 5 genomic regions identified

Linkage disequilibrium

100-200 kb

Explored region

Chr 3

Exploration of the Banana genome

Banana Genome Hub

Chr 3

Exploration of the Banana genome

In total, more than 100 genes

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

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 expansion Fruit Set

X X

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)

Field trial

• IITA, Arusha, Tanzania • Bimodal rainfall pattern (900-1100 mm/yr)

• Dry seasons (June – Nov & Dec - Feb)

FAO NewLocClim for Arusha,

Tz, 2015

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

Drought Stress: Leaf temperature

(Taiz and Zeiger, 2002)

Drought

• Transpiration ~ evaporative cooling

• Reduced transpiration: detect by Infrared imaging

Cachaco (ABB) Nakitengwa (AAAh)

Leaf temperature

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

Transcriptomics study

Grande Naine (AAA) Mbwazirume (AAA) Cachaco (ABB)

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.

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)

Thank You