1. Discovery of QTLs
in apple by using the
pedigree-based approach (PBA)
T. Letschka, G. Pagliarani, L. Lozano, W. Guerra, M.C.A.M Bink, J. Kruisselbrink,
R. Voorrips, M. Di Guardo, E. Di Pierro, E. Van de Weg
3. YOUR LOGO
Origin of plant material
>1,500 individuals from 7 different countries
>1,200 individuals in 25 families
• phenotyped for 3 consecutive seasons
• at 4 time points each season (HiDRAS)
• >30 different traits from pre- to post-harvest
• genotyped with Illumina 20K SNP array
• data scrutinizing
• consensus map
4. Genotypic dataset
• 7K SNPs in 1,112 haploblocks through Haplotyper
• Marker density: mean interval = 1 cM
6. Already published data
LG 1: Xu et al. 2012 (2 half sib pops) -> M3 gene
LG 6: Xu et al. 2012 (2 half sib pops) -> M2 gene
LG 8: Liebhard et al. 2003 (Fiesta x Discovery)
Kenis et al. 2008 (Telamon x Braeburn)
Kumar et al. 2012 (genomic selection)
LG 16: Maliepaard et al. 1998 (Prima x Fiesta) -> Ma locus
Liebhard et al. 2003 (Fiesta x Discovery)
Kenis et al. 2008 (Telamon x Braeburn)
Xu et al. 2012 (2 half sib pops)
Kumar et al. 2012 (genomic selection)
Khan et al. 2012 (Malic acid transporter gene Ma1 & Ma2)
Bai et al. 2012 (functional SNP marker in Ma1)
Kenis et al. 2008 (Telamon x Braeburn): LG2, LG10, LG13, LG15, LG17
Bai et al. 2012
14. LG 1 – QTL clustering
TA
Brix
Russeting Attractiveness
Firmness
Fruit size
Observation
• QTLs for different traits co-localize on LG 1
• within 5 cM
• immediately downstream of Rvi6 haploblock
Interpretation
• Is it a pleiotropic effect?
• Are the traits correlated with each other?
• Is there a link to Rvi6 resistance? Linkage drag?
15. Results are highly reliable
• thorough scrutinizing of input data (genotyping, mapping, phenotypes...)
• Short linkage groups
• Marker consistency
• Hardly any double recombinants
• Consistency between generations
• No warnings during QTL analysis runs
• Narrow QTL regions that contain known target genes
Conclusion I
16. Conclusion II
• According to FlexQTL, the phenotypic variance in titrable acid is explained in
a multiple QTL model that involves:
5 decisive QTLs + 1 strong QTL + 2 positive QTLs
• The additive effect of these QTLs accounts for 55% of the observed
phenotypic variance
• Most important QTLs on LG 16, LG 8, LG 1.
• Ma1 & Ma2 could be pinpointed within the QTL region on chromosome 16.
• QTLs for various different quality traits cluster on LG 1, in addition to scab
resistance.
17. Outlook
• Move closer to Ma1 gene
• Investigate on ‘pleiotropic effect‘ on LG 1
• Analyse other QTLs related to TA and Brix
• Examine different time points regarding post harvest
• Compare results to sensorial traits
• Extrapolate markers to be used for marker-assisted breeding
18. Acknowledgements
HiDRAS phenotypers
genotyping facility
mappers
Mario Di Guardo (SNP scoring)
Erica Di Pierro (consensus map)
Roeland Voorrips (Haplotyper)
Hans Jansen (integration of newly phenotyped populations)
Johannes Kruisselbrink (Visual FlexQTL)
Giulia Pagliarani
Hélène Muranty, Stijn Vanderzande
Walter Guerra
Marco Bink
Eric van de Weg
