1. 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

2. The New Zealand Institute for Plant & Food Research Limited Summer in Northern Spain

3. The New Zealand Institute for Plant & Food Research Limited Summer in Northern Spain

4. The New Zealand Institute for Plant & Food Research Limited Summer in Northern Spain Apple skin colour under warm temperature

5. The New Zealand Institute for Plant & Food Research Limited 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

6. The New Zealand Institute for Plant & Food Research Limited ‘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 a b L

7. The New Zealand Institute for Plant & Food Research Limited ‘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

8. The New Zealand Institute for Plant & Food Research Limited SNP genotyping in the ‘Scigold’ x T22 Only 25 / 384 markers segregating as expected!!!

9. The New Zealand Institute for Plant & Food Research Limited 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

10. The New Zealand Institute for Plant & Food Research Limited 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

11. The New Zealand Institute for Plant & Food Research Limited Kinship analysis Pairwise kinship calculated according to Queller and Goodnight 1989 Full sibs (~2-3%) Unrelated (~50%)

12. The New Zealand Institute for Plant & Food Research Limited Population structure test Using Structure (Pritchard et al.)

13. The New Zealand Institute for Plant & Food Research Limited Association between markers and colour TraitSNP markerF testsignificanceLG

14. The New Zealand Institute for Plant & Food Research Limited 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 WD40 bHLH MYB CHS, F3H, DFR, LDOX, 3UPGT Espley et al 2009

15. The New Zealand Institute for Plant & Food Research Limited 35S:PAP1 (ortholog of MdMYB10) Arabidopsis under temperature control Candidates for temperature response (microarray) Rowan et al. New Phytologist (2009) Red hot candidate genes

16. The New Zealand Institute for Plant & Food Research Limited Red hot candidate genes (Nelson)

17. The New Zealand Institute for Plant & Food Research Limited Red hot candidate genes (Nelson)

18. The New Zealand Institute for Plant & Food Research Limited Red hot candidate genes (Lleida)

19. The New Zealand Institute for Plant & Food Research Limited Red hot candidate genes

20. The New Zealand Institute for Plant & Food Research Limited Red hot candidate genes qPCR and power cut!

21. The New Zealand Institute for Plant & Food Research Limited Future work T089 X T089 x Gala154 F1 indv T089 x Gala Brookfield® 154 F1 indv New mapping population

22. The New Zealand Institute for Plant & Food Research Limited Red Hot Gene team IRTA, Lleida, Spain Lidia Lozano Ignasi Iglesias Joan Bonani IASMA, Trento, Italy Michela Troggio Diego Micheletti Riccardo Velasco Plant & Food Research Richard Volz Allan White Satish Kumar Susan Gardiner Andrew Allan John Palmer Funding FP7 Marie Curie IRSES MoRST Plant & Food Research

23. The New Zealand Institute for Plant & Food Research Limited Thank you Red hot gene

24. The New Zealand Institute for Plant & Food Research Limited www.plantandfood.com