Post on 11-Jan-2016
description
transcript
Marker-Assisted Breeding for Apple at the
University of Minnesota and Washington State University
Jim Luby, Kate Evans, and Cameron Peace
Outline of Presentation Timeline and Flow of Apple Breeding Program
Developing Useful Markers with the Marker Assisted Breeding Pipeline
Identity Confirmation
Marker-Assisted Parent Selection (MAPS)
Marker-Assisted Seedling Selection (MASS)
Timeline and Flow of
Apple Breeding Program
Target Marker-Assisted Seedling Selection
Target Marker-Assisted Parent Selection
Developing Useful Markers:
Marker Assisted Breeding Pipeline
Genomics Applied in Apple Breeding
Target Traits
Known QTLs
Applications in breeding
MAPS
MASS
Identity Confirmation
Breeding markersDNA te
sting
serv
icesQTL
prior
ities
Cross
ing
sche
mes
Trial
MASS
Simple validation
Allele effects& distributions
Seedli
ng
selec
tion
sche
mes
Traits and Loci Used at UMN and WSU
Md-ACO1 – Texture (storage)
Md-Exp7 – Texture (Scab Resistance)
Md-ACS1 – Texture (storage)
Ma – Acidity, Texture
Md-PG1 – Texture
“A” – Acidity
Traits and Loci Used at UMN and WSU
Rf – Overcolor
“Bl” – Overcolor, blush vs stripe
Overcolor
Traits and Loci Used at UMN and WSU
Md-Exp7, CHVf1 – Scab Resistance (Texture)
Ma – Bitter Pit(Acidity, Texture)“Bp13”
– Bitter Pit
Apple scab resistance
Photo: M. Clark
Traits and Loci Used at UMN and WSU
Md-ACO1 – Texture (storage)
Md-Exp7, CHVf1 – Texture, Scab Resistance
Md-ACS1 – Texture (storage)
Ma – Acidity, Texture, Bitter Pit
Rf – Overcolor
Md-PG1 – Texture
“Bp13” – Bitter Pit
“Bl” – Overcolor
“A” – Acidity
Identity Confirmation
Identity Confirmation• LOTS of opportunities for errors in a breeding program
– mislabeled parent trees– pollen collection– crossing– seed harvest and handling– seedling handling and propagation– labeling
malus• Ancestry errors in pedigrees of selections and cultivars – Identity and ancestry for breeding and
intellectual property purposes
• Parentage of Seedlings – 1% to 5% error rate not unusual in a cross
Marker-Assisted
Parent Selection
Parent Selection at UMN• Potential parents list - based on
• Crossing objectives • Available trees or pollen• Phenotype data• Pedigree• Genotype data and relative breeding value at each
locus of interest
Name Parent1 Parent2Skin color Rf-SSR
Skin color Rf SNPs
Skin color Bl SNPs
Storage abilty
ethylene ACS1
Storage ability
ethylene ACO1
Storage ability
cell wall PG1
Bitterpit 13Bitterpit
16.1Bitterpit
16.2
TA16 Major Acid
locus
TA 08 Modifies effects of
TA16 locus
Crispness at harvest
16
MARKER SSR SNP SNP SCAR SCAR SSR ss475880861 ss475882553 ss475881697 ss475876558 ss475879081 ss475881704Linkage Group LG09 LG09 LG02 LG15 LG10 LG10 LG13 LG16 LG16 LG16 LG08 LG16
CrimsonCrisp PCFW2-134 PRI669-205 RfRf Blbl FF FN na na FN HH HL FN
Honeycrisp Keepsake F_Honeycrisp138140 Rfrf Blbl FN NN 292 hom NN FN FN LL HL NN
PixieCrunch PCFW2-134 PRI669-205 RfRf Blbl FN FN FN FN HL LL FN
Snowsweet Sharon Fireside 138158 Rfrf BlBl FN NN 292298 FF FN FN HL LL FN
MN1628 Frostbite NorthSpy 138 hom RfRf Blbl FN NN 292298 FN na FN LL HL NN
MN1837 MN1627 MN1691 138 hom RfRf BlBl FF NN 298 hom FN FN FN HL HH FN
MN1914 Honeycrisp Zestar 138 hom RfRf BlBl FF NN 289292 FN NN FN HL LL FN
MN1915 Sweet16 Zestar 138 hom RfRf no call FF NN 289292 FF NN NN HL HL FN
MN1937 Empress Zestar 138 hom RfRf Blbl FF FN 289 hom FN NN NN HH LL FF
MN1942 Honeycrisp NY543 138 hom RfRf blbl or Blbl FN FN 292 hom FN FF FF LL HL NN
MN1955 Honeycrisp Monark 138 hom RfRf Blbl NN NN 292 hom (291 hom?)FN FF FF LL HL NN
MN1965 MN1702 Honeycrisp 140168 rfrf blbl FN NN 292 hom (291 hom?)FN FN FN HL HL FN
MN1971 M_MN1971 Honeycrisp 140 hom rf2rf3 Blbl FN NN 292 hom LL NN
MN1980 Honeycrisp Liberty 138 hom RfRf Blbl NN NN 292 hom (291 hom?)FN NN FN LL HH NN
MN1984 Frostbite Honeycrisp 140 hom rf2rf2 Blbl FN NN 292 hom FN 0 FN LL HH NN
MN1988 Honeycrisp Freedom 138 hom RfRf Blbl NN NN 292298 NN NN NN HL LL FN
MN2000 Keepsake Empress 138152 Rfrf Blbl NN NN 298 hom faintFN NN NN HL HL FN
MN2006 Sawa Honeycrisp 138140152 Rfrf BlBl FF NN 292298 FN 0 FN LL LL NN
MN2008 Summerred Zestar 138152 Rfrf FF NN 289298 FF NN na HH
MN2016 Zestar Arlet 138 hom RfRf BlBl FF NN 289298 FN NN NN HH HL FF
MN2033 Honeycrisp Zestar 138 hom RfRf no call FF NN 289292 FN FN FN HL HL FN
MN2042 Honeycrisp Burgundy 138 hom RfRf Blbl FN NN 292298 FN NN NN HL HL FN
MN2046 Honeycrisp Zestar 138 hom RfRf Blbl FF FN 292298 NN NN NN HL HL FN
MN2095 Etter Pink Honeycrisp 140168 rfrf FN NN 289292 HL
MN2099 Etter Pink Honeycrisp 138168 Rfrf FN NN 292298 HL
Parent Selection at UMN• Prospective cross list
• based on favorable phenotype and genotype combinations
• Logistics • final crossing “call” made in field based on flowering
time, tree availability, pollen quality, etc.
Marker-Assisted
Seedling Selection
Seedling Selection: Sample Collection
96 count seedling tray for sample collection
Photo by Kate Evans
Seedling order replicated in 96 well DNA extraction plate
Genetic tests selected for each cross based on goals and parents
Seedling Selection: Culling DecisionsCulling level set for each allele in each genetic test
Seedling Selection: Genotype Data Report
Photo by Kate Evans
• Genotype report color coded
• Maintains order in seedling tray to facilitate culling
• Culling decision for each seedling combines all genetic tests
Seedling Selection: Culling
• Verbal repetition of seedling location and culling instruction to reduce errors
• Usually best with three people
• Culling requires 2-3 person/hours per 1000 seedlings
Summary• Reliable Markers – Developed for 9 loci and 8 target traits in our germplasm– Functional SNP haplotypes and PCR-based markers (SSR,
Indel)
• Identity confirmation – RosBREED SNP markers used to confirm ancestry of ~ 900 parents,
selections, seedlings and ancestors at UMN, WSU and Cornell– PCR-based Markers used on over 20,000 seedlings at WSU and UMN
• Marker-Assisted Parent Selection – Used to design 120 crosses from 2011 through 2013.
• Marker-Assisted Seedling Selection – Over 20,000 seedlings screened in 2011 through 2013– Culling from 25 to 90% depending on cross and markers
Many Thanks!
Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s
National Institute of Food and Agriculture
MSUAmy Iezzoni (PD)
Jim HancockDechun Wang
Cholani Weebadde
WSUCameron Peace
Dorrie MainKate Evans
Karina Gallardo Vicki McCracken
Nnadozie OraguzieFormer WSU
Raymond JussaumeMykel Taylor
CornellSusan BrownKenong Xu
Clemson Ksenija Gasic
Gregory Reighard
Texas A&MDave Byrne
Univ. of CA-DavisTom Gradziel
Carlos Crisosto
Univ. of New Hamp.Tom Davis
Univ. of MinnesotaJim Luby
Chengyan Yue
Oregon State Univ.Alexandra Stone
Plant Research Intl, Netherlands
Eric van de WegMarco Bink
USDA-ARSNahla Bassil
Gennaro FazioChad Finn
Univ. of ArkansasJohn Clark
Questions?