the new zealand institute for plant & food research limited red hot genes in apple david chagné...

The New Zealand Institute for Plant & Food Research Limited

Red Hot Genes in apple

David Chagné

Mapping and markers team, Palmerston North

Lidia Lozano

Apple breeding, Lleida, Spain


Summer in Northern Spain

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Apple skin colour under warm temperature


EU Marie Curie IRSES project (co-funded by MoRST)

Understanding physiology and molecular control of apple red skin coloration under warm conditions

» Whole tree physiology

» Gene expression of anthocyanin regulating genes

» Genetic mapping and QTL for red colour under warm conditions

» Marker-assisted selection for redder apple cultivars

The Red Hot Gene project


‘Scigold’ x T22 (Envy™) population of 200 F1 trees

Phenotyping for skin colour» visual assessment

» colorimetry (Minolta L*a*b)

» anthocyanin content

QTL mapping for red colour

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‘Scigold’ x T22 (Envy™) population of 200 F1 trees

Genetic map construction» 384 SNPs covering the apple genome

» SNPs detected using the apple genome assembly and validated in a ‘Golden Delicious’ x ‘Scarlett’ and ‘Royal Gala’ x ‘Braeburn’ map

» BeadXpress™ (Illumina®) technique

» 94 individuals and both parents genotyped

QTL mapping for red colour


SNP genotyping in the ‘Scigold’ x T22

Only 25 / 384 markers segregating as expected!!!

ProgenySNP Scigold T022 AA AG GG missing total

GD_SNP01140 AA AA 72 22 0 0 94GD_SNP01465 AA GG 23 32 28 11 94GD_SNP02460 AG AA 31 46 17 0 94GD_SNP00664 AG GG 13 49 31 1 94


SNP data is “OK”: other populations were run using the same SNP set and at the same time: no problem

Pollen contamination and seed mishandling

LD mapping for red colour


SNP data is OK: other populations run using the same set and at the same time: no problem

Pollen contamination and seeds mishandling

BUT…

If this population is not a F1 as expected, can we use LD mapping?

Is it a random set of individuals taken from breeding material?

If the set of trees is not very diverse: 384 SNPs could be enough as LD might be conserved across larger physical distance?

Kinship and population structure test to infer relationship between trees

LD mapping for red colour


Kinship analysis

Frequency distribution (Q & G method)

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Coefficient of coancestry

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Pairwise kinship calculated according to Queller and Goodnight 1989

Full sibs (~2-3%)

Unrelated (~50%)


Population structure test

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Using Structure (Pritchard et al.)


Association between markers and colour

LG98.55E-047.6557GD_SNP00766redness / yellownessa/b

LG179.39E-0411.7144GD_SNP00091dark/brightL


LG99.66E-047.513GD_SNP00766yellownessb

LG99.55E-047.5262GD_SNP00766rednessa


LG90.00147.0644GD_SNP00766Anthocyanin

p_MarkerF_MarkerLocusTrait

Significance of F testF test

LG98.55E-047.6557GD_SNP00766redness / yellownessa/b



LG99.66E-047.513GD_SNP00766yellownessb



LG90.00147.0644GD_SNP00766Anthocyanin

p_MarkerF_MarkerLocusTrait

Significance of F testF test

Trait SNP marker F test significance LG


GD_SNP00766 is located <1 Mb from MdMYB10 (LG9)

We showed that MdMYB10 controls flesh, skin and foliage colour in apple

The association we found is not a big surprise (it validates our LD analysis)… however, MdMYB10 is NOT the Red Hot Gene…

Association between markers and colour

Finding the causative mutation

WD40bHLH

MYB

CHS, F3H, DFR, LDOX, 3UPGT

Espley et al 2009


35S:PAP1 (ortholog of MdMYB10) Arabidopsis under temperature control

Candidates for temperature response (microarray)

Rowan et al. New Phytologist (2009)

Red hot candidate genes


Red hot candidate genes (Nelson)


Red hot candidate genes (Lleida)



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Future work

T089

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T089 x Gala 154 F1 indvT089 x Gala Brookfield® 154 F1 indv

New mapping population


Red Hot Gene team

IRTA, Lleida, Spain

Lidia LozanoIgnasi IglesiasJoan Bonani

IASMA, Trento, Italy

Michela TroggioDiego MichelettiRiccardo Velasco

Plant & Food Research

Richard VolzAllan WhiteSatish KumarSusan GardinerAndrew AllanJohn Palmer

FundingFP7 Marie Curie IRSESMoRSTPlant & Food Research


Thank you

Red hot gene


www.plantandfood.com

the new zealand institute for plant & food research limited red hot genes in apple david chagné...

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