Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

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ympo

sium

Mar

k W

. Dav

ey

Lab

Frui

t Bre

edin

g &

Bio

tech

nol,

Dep

t. B

iosy

stem

s,

Kath

olie

keU

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itLe

uven

,

BELG

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mar

k.da

vey@

biw

.kul

euve

n.be

Mad

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012

Taiw

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tern

atio

nal B

anan

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ympo

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Mad

avN

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012

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tern

atio

nal B

anan

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ympo

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Mad

avN

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012

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tern

atio

nal B

anan

a S

ympo

sium

Prot

eom

ics o

f phy

topa

thog

enin

tera

ctio

ns

Gen

etic

div

ersi

ty o

f phy

topa

thog

ens

Qua

ntita

tive

gene

tics

and

QTL

s

Alle

lic d

iver

sity

SNP-

chip

s, g

DN

A

RNA

Seq

Bioc

hem

istr

yM

olec

ular

gen

etic

s

Tool

s, d

evel

opm

ent a

nd m

appi

ng,..

Them

es

Proj

ects

Mad

avN

ov 2

012

Taiw

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tern

atio

nal B

anan

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ympo

sium

Mad

avN

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tern

atio

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anan

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Met

zker

2010

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ure

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iew

s G

enet

ics

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NA

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(RN

ASe

q, e

xon

-seq

uenc

ing)

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Am

plic

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geno

mic

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rget

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sequ

enci

ng(r

educ

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repr

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n lib

rari

es, e

tc.,

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)Bi

sulp

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seq

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gene

tics)

CHiP

...

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Ada

pted

Sbo

ner e

t al.

Gen

ome

Bio

logy

2011

12:

125

.

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

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ympo

sium

Mad

avN

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tern

atio

nal B

anan

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A D

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doi

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1038

/nat

ure1

1241

Mad

avN

ov 2

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Taiw

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tern

atio

nal B

anan

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ympo

sium

http

://ge

nom

evol

utio

n.or

g/C

oGe/

http

://w

ww

.one

kp.c

om/

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

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sium

25 g

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Vel

asc

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tech

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Mad

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ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

stud

y st

ruct

ure

of th

e en

tire

geno

me

geno

me

size

, Ca

talo

gue

of th

e no

. of g

enes

pre

sent

and

thei

r lo

catio

n

intr

a-an

d in

ter-

spec

ies

geno

me

vari

atio

n

stud

y of

gen

e fu

nctio

n

deal

s w

ith tr

ansc

ript

ome

and

prot

eom

e,

assi

gns

func

tions

to a

ll ge

nes

iden

tifie

d in

str

uctu

ral g

enom

ics

Gen

erat

ion

of h

igh

dens

ity m

arke

rs (S

NPs

, SSR

s, in

dels.

.)

Acc

eler

ated

map

-bas

ed c

loni

ng o

f gen

es u

nder

lyin

g Q

TLs.

Ex

plor

atio

n an

d ex

ploi

tatio

n of

nat

ural

ly o

ccur

ring

alle

lic

vari

atio

n at

CG

s co

ntro

lling

agr

onom

ic tr

aits

Gen

omic

s

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Musa

Aim

s

Dev

elop

frui

t of

cul

tivar

s with

cont

rast

ing

pro-

vita

min

A c

arot

enoi

dsco

nten

ts

Com

pare

tran

scri

ptom

es o

f cvs

with

diff

eren

t (A

AA

v A

AB)

Iden

tify

tran

scri

pts

frui

t qua

lity?

Iden

tify

in c

andi

date

gene

(CG

) se

quen

cesf

rom

caro

teno

idsb

iosy

nthe

sisi

.eal

lelic

vari

atio

n

Refin

ege

ne p

redi

ctio

nal

gori

thm

s

Obj

ectiv

es

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Frui

t fro

m 6

c

ultiv

ars,

2 x

AA

A, 2

x A

AB,

Ihol

ena,

Fe

iCo

ntra

stin

g pr

o-vi

tam

in A

(pVA

Cs) c

onte

nts

Mea

n fr

uit

(pVA

Cs) c

onte

nts

AA

A

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2x

87x

diffe

renc

e in

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Cs

conc

entr

atio

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AB

AA

BFe

i

Sam

ples

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Cs

Dav

ey e

t al 2

009

Food

Che

m, D

avey

et a

l 200

7, J

Agr

Food

Che

m

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Isol

ate

RNA

from

>3

frui

t of e

ach

of 6

culti

vars

, 2

x A

AA

, 2 x

AA

B, Ih

olen

a, F

ei

100b

p, P

E se

quen

cing

, one

lane

Illum

ina

GA

II

RNA

Seq

Raw

dat

a

‡

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

read

s (1

00 b

p)

v

a

Read

s

over

lap

Map

ping

New

Co

nsen

sus

Sequ

ence

s

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

v

Read

s al

igne

d to

Mus

a re

fere

nce

CDS

sequ

ence

s (3

6,54

2)Id

entif

y w

hich

gen

es e

xpre

ssed

Re

ad d

epth

indi

cate

s ex

pres

sion

leve

lId

entif

y po

lym

orph

ism

s

Map

ping

Mea

n co

vera

ge o

f 110

‡16

0x‡

tran

scri

pts

29 ‡

41%

of

tran

scri

ptom

eex

pres

sed

CDS

Alig

nmen

t

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Ove

rvie

w o

f M

etab

olis

m

Bata

rd fr

uit t

rans

crip

tom

e=

13,4

68 tr

ansc

ript

sTr

ansc

ript

ome

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mbo

urou

kou

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t tra

nscr

ipto

me

= 14

,083

tran

scri

pts

Tran

scri

ptom

e

Ove

rvie

w o

f M

etab

olis

m

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Scat

ter

plot

of n

orm

alis

ed, l

og2-

expr

essi

on le

vels

Glo

bal e

xpre

ssio

n

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Bata

rd v

sM

bour

ouko

u -

4,09

6 (1

1.2%

), >2

-fol

d lo

g2

diff

eren

tially

exp

ress

ed g

enes

>2-f

old

diff

eren

tial

Regu

latio

n

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

RNA

Seq

read

-map

ping

v r

efer

ence

gen

omes

allo

ws

glob

al,

syst

ems

over

view

of

Unl

ike

mic

roar

rays

, of

gen

e m

odel

s th

eref

ore

data

ca

n la

ter

be r

efin

ed a

nd r

eana

lyse

d

Can

be u

sed

to id

entif

y tr

ansc

ript

s/ge

nes/

splic

e va

rian

ts

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

The

maj

ority

of a

gric

ultu

ral t

raits

are

qua

ntita

tive

/po

lyge

nic

i.e. t

he p

heno

type

is th

e re

sults

of e

xpre

ssio

n of

Cr

op

Trai

ts

uant

itativ

e ra

it oc

i (Q

TL) a

re r

egio

ns o

f the

lin

ked

to a

ph

enot

ypic

trai

t (e.

g. y

ield

s, h

eigh

t, e

tc.)

Stat

istic

al te

sts

carr

ied

out t

o de

tect

be

twee

n m

arke

r in

heri

tanc

e in

pro

geny

of a

cro

ss a

nd p

heno

type

.

If si

gnifi

cant

diff

eren

ces

foun

d be

twee

n in

divi

dual

s co

ntai

ning

a

part

icul

ar m

arke

r th

en th

e m

arke

r is

to

a g

enom

ic

regi

on c

ontr

ollin

g th

e tr

ait

QTL

A

naly

ses

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Dav

ey e

t al 2

006,

Pla

nt P

hysi

ol 1

42, p

343

>95%

pro

babi

lity

.

Ken

iset

al 2

009,

Mol

bre

edin

g

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

AsA_Flesh QTL-1 LOD_7.33, 15.1%

totAsA_Flesh QTL-1 LOD_7.15, 22.1%

totAsA_Skin QTL-1 LOD_4.99, 13.7%

AsA_Flesh QTL-1 LOD_6.45, 17.1%

totAsA_Flesh QTL-1 LOD_6.90, 23.9%

totAsA_Skin QTL-1 LOD_3.76, 12.5%

cand

idat

e ge

nes!

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Pro

vide

s a

set o

f gen

ome

wid

e m

arke

rs (S

NP

s/in

dels

)In

crea

ses

mar

ker d

ensi

ty o

n lin

kage

map

sR

efin

e Q

TL re

gion

s (li

mita

tion

is p

opul

atio

n si

ze)

Pro

vide

s ph

ysic

al p

ositi

ons

of C

G s

eque

nces

(QTL

-col

ocat

ion)

Iden

tify

set o

f und

erly

ing

CG

seq

uenc

esS

impl

ify p

ositi

onal

clo

ning

stra

tegi

es/fi

ne m

appi

ng

Mel

lidou

et a

l 201

2, P

lant

Phy

siol

-A

llelic

varia

nts

of p

aral

ogue

sof

VTC

2 ar

e a

maj

or d

eter

min

ant o

f fru

it vi

tam

inC

con

tent

s in

app

le.

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

‡

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Chro

mos

ome

1

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Gen

ome/

RNA

rese

quen

cing

of c

ultiv

ars

and

alig

nmen

t allo

ws

iden

tific

atio

n of

SN

Ps

Com

pari

son

betw

een

culti

vars

allo

ws

iden

tific

atio

n of

gen

e an

d

Ass

ocia

tion

with

fo

r id

entif

icat

ion

of p

ositi

veal

lele

s fo

r th

e tr

ait

Gen

ome-

wid

e as

soci

atio

n st

udie

s-G

WA

S

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Refe

renc

e ge

nom

eis

a d

oubl

edha

ploi

dW

T A-

geno

me

Com

mer

cial

lyin

tere

stin

ggen

omes

are

trip

loid

Wha

tabo

utth

e B-

geno

me?

?

Refe

renc

e A

-gen

ome

gDN

APK

W28

1 M

read

s, 2

9Gb

of n

ucle

otid

es~3

0x g

enom

eco

vera

ge

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

stru

ctur

aldi

ffer

ence

sbet

wee

nA

and

B g

enom

es?

Culti

var r

eseq

uenc

ing

degr

eeof

alle

licva

riat

ion

and

hapl

otyp

es?

(larg

e en

ough

)M

ultip

le p

opul

atio

nsfo

rdiff

eren

t tra

its

Nee

dfo

rpl

atfo

rms

KASP

/SN

P-ch

ips/

GBS

Link

age

Dis

equi

libri

um in

Mus

a?St

atis

tical

met

hods

forG

WA

S

/phy

siol

ogy/

biol

ogy

is n

owth

e bo

ttle

neck

Mad

avN

ov 2

012

Taiw

an In

tern

atio

nal B

anan

a S

ympo

sium

Fran

cis

Am

oako

-And

oh

Ifige

neia

Mel

lidou

Yase

min

Yilm

adiz

irW

anne

s Ke

ulem

ans

Than

ks!