Germplasm Sets and Standardized Phenotyping Protocols for Fruit Quality Traits in Rosbreed

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Germplasm Sets and Standardized Phenotyping Protocols for Fruit Quality Traits in RosBREED

Jim Luby, Breeding Team Leader Outline of Presentation  RosBREED Demonstration Breeding Programs  Standardized Phenotyping Protocols  Reference Germplasm Sets  SNP Detection Panels  Crop Reference Set  Breeding Pedigree Set RosBREED Demonstration Breeding Programs Clemson U WSU Texas A&M UC Davis U Minn U Arkansas

Rosaceae

Cornell U

WSU MSU MSU Phenotyping Affiliates USDA-ARS Driscolls Corvallis Univ of Florida UNH Standardized Phenotyping Protocols Traits and Standardized Phenotyping Protocols • Identify critical fruit quality traits and other important traits

• Develop standardized phenotyping protocols to enable data pooling across locations/institutions

• Protocols available at www.RosBREED.org Apple Standardized Phenotyping Firmness, Crispness – Instrumental, Sensory

Sweetness, Acidity – Intstrumental, Sensory

Color, Appearance, Juiciness, Aroma – Sensory At harvest Cracking, Russet, Sunburn Storage 10w+7d Storage 20w+7d Maturity Fruit size 5 fruit (reps) per evaluation Postharvest disorders Harvest date, Crop, Dropping RosBREED Apple Phenotyping Locations Wenatchee, WA St Paul, MN

Geneva, NY

• One location for all evaluations would reduce variation among instruments and evaluators

• Local evaluations more sustainable and relevant for future efforts at each institution

• Conduct standardized phenotyping of Germplasm Sets at respective sites over multiple (2-3) seasons

• Collate data in PBA format, conduct quality control, archive Reference Germplasm Sets Crop Reference Set Breeding Pedigree Set SNP Detection Panel Crop Reference Sets • Enable efficient validation and utility assessment of M-L-T associations

• Resource for common benefit

• Genotyped genome-wide with SNP markers and phenotyped for fruit quality traits and other high- impact traits.

• ~480 individuals (cultivars, ancestors, founders, breeding lines, selections, and seedlings) that are fruiting in 2010-2012 Breeding Pedigree Sets

• Resource for proprietary benefit of breeding program benefit only • ~100-300 extra plants for each breeding program that, together with the Crop Reference Sets, allow full representation of founders of interest to that program • Information may remain with each breeding program; data-sharing improves power Reference Germplasm Sets • Approach: - Identify important parents among breeding programs - Trace pedigrees to founders and identify available founders and intermediates - Identify progeny available in breeding programs - Use PediMap™ to visualize pedigree relationships - Calculate allele representation of important parent back through available founders and intermediates - Include progeny to adequately represent important parents - Crop Reference Sets will be publicly archived Identify Important Parent, Ancestors, Progreny Example at U of Minn: Zestar!

AE0109

AE0240

AE0215 Tetofsky Available AE0226 Mantet Ancestor AE0229

AE0230 McIntosh AE0241

AE0308 Oriole StateFair

MN1914 YelTransp MN1925

MN2033

MN2041 Available LivelRasp Fireside MN1691 ZestarZestar! MN2044 progeny MN2050

AE_HCxZest

AE0122

Longfield Unavailable MN1937 Ancestor PattenGr Goodland MN1940

MN2016

DuchOlden MN2046

AE0206

F_Goodland AE0207

F_PattenGr AE0219

AE0103

AE0242 Calculate allele representation of important parent back through available ancestors

Available Ancestor Zestar! = 3.4375 Units through ancestors and itself

Tetofsky Mantet 0.25 McIntosh 0.125 0.5 Oriole StateFair YelTransp 0.125 0.25

LivelRasp Fireside MN1691 ZestarZestar! 0.25 0.5 Longfield 0.125 PattenGr Goodland 1.0

DuchOlden 0.25 0.0625 F_Goodland

F_PattenGr

Unavailable Ancestor Include progeny to adequately represent important parents Goal = 12.5 units minimum 1.0 unit through itself 2.4375 Units through ancestors Tetofsky 12 progeny x Mantet McIntosh 0.5

Oriole StateFair AE0206 YelTransp

LivelRasp Fireside MN1691 ZestarZestar!

Longfield PattenGr Goodland AE0242

DuchOlden F_Goodland 25 progeny x F_PattenGr 0.5 18.5 units through 37 progeny

Zestar! allele representation = ~22 units Apple Crop Reference Set

NY59333-006

Empire Blackjon McIntosh 669NJ5 NY70712-53

NY55158-002 NY88 RussianSeedling Delicious AutumnCrisp Jonathan Coop-18 Crandall AurGoldGa NorthSpy Fuji PacQueen MN1708 NY752 PacRose RomBeauty Honeycrisp P14-126 Arlet MN1628 NY03 Monroe NY10 EsopSpitz Nicola Keepsake

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite

Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Silken WSU52 Oriole Lambourne Wealthy Sonya

Fireside Scifresh Jonamac WSU57 BenDavis Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Honeygold NY04 JamesGr BlushiGol AE0206 Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Haralson

NY06 NY11 Linda Cortland WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue

Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Wijcik MN1915

NY543 F2_26829-2-2 MN1942 Suncrisp Topaz MN1955 MN1702 GingerGold Williams MN2034 WSU35 MN1789 Beacon MN1965 Raritan MN2062 Liberty Macoun WSU48 MN1971 Hudson Spartan MN1764 MN1980 NY15 MN2016 MN2036 MN1802 Regent NY65707-19

MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063

Snowsweet WSU34 Prima Mflor821 MN2000 Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042

AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

Cameo MN1899 MN1925 GMAL4327 CornellPop07 NY12 Ambrosia MN1964 MN2033 Elstar GMAL4328 PRI14-126 MN1837 MN2041 MN1888 Kerr CrimsCrisp Sundance MN2044 MN1836 Sawa Tsugaru NY913 MN2050 Dayton NY09 NJ53 WSU7

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 Apple Crop Reference Set:

U of MN ImportantNY59333-006 Parents Empire Blackjon McIntosh 669NJ5 NY70712-53

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite

Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Silken WSU52 Oriole Lambourne Wealthy Sonya

Fireside Scifresh Jonamac WSU57 BenDavis Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Honeygold NY04 JamesGr BlushiGol AE0206 Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Haralson

NY06 NY11 Linda Cortland WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue

Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Wijcik MN1915

MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063

Snowsweet WSU34 Prima Mflor821 MN2000 Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042

AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 Apple Crop Reference Set:

WSU ImportantNY59333-006 Parents Empire Blackjon McIntosh 669NJ5 NY70712-53

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite

Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Silken WSU52 Oriole Lambourne Wealthy Sonya

Fireside Scifresh Jonamac WSU57 BenDavis Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Honeygold NY04 JamesGr BlushiGol AE0206 Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Haralson

NY06 NY11 Linda Cortland WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue

Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Wijcik MN1915

MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063

Snowsweet WSU34 Prima Mflor821 MN2000 Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042

AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 Apple Crop Reference Set:

Cornell ImportantNY59333-006 Parents Empire Blackjon McIntosh 669NJ5 NY70712-53

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite

Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Silken WSU52 Oriole Lambourne Wealthy Sonya

Fireside Scifresh Jonamac WSU57 BenDavis Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Honeygold NY04 JamesGr BlushiGol AE0206 Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Haralson

NY06 NY11 Linda Cortland WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue

Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Wijcik MN1915

MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063

Snowsweet WSU34 Prima Mflor821 MN2000 Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042

AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 Apple Crop Reference Set:

All Programs’ ImportantNY59333-006 Parents Empire Blackjon McIntosh 669NJ5 NY70712-53

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite

Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Silken WSU52 Oriole Lambourne Wealthy Sonya

Fireside Scifresh Jonamac WSU57 BenDavis Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Honeygold NY04 JamesGr BlushiGol AE0206 Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Haralson

NY06 NY11 Linda Cortland WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue

Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Wijcik MN1915

MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063

Snowsweet WSU34 Prima Mflor821 MN2000 Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042

AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 SNP Detection Panel

• Used for genome scans to identify SNPs distributed along genome

• Up to 20 individuals from Crop Reference Set

• Includes Diverse Key Founders or Intermediate Ancestors NY59333-006

Empire Blackjon McIntosh 669NJ5 NY70712-53

NY55158-002 NY88 RussianSeedling Apple SNP Panel Delicious AutumnCrisp Jonathan Coop-18 Crandall AurGoldGa NorthSpy Fuji PacQueen MN1708 NY752 PacRose RomBeauty Honeycrisp P14-126 Arlet MN1628 NY03 Monroe NY10 EsopSpitz Nicola Keepsake

Melrose WSU2 Sweet16 NY02 BC8S-27-43 Frostbite Founders Intermediate Clivia Pinova BC-8S-27-2 Pop_AurxCP Chinook GoldenDel KidsOrRed Gala Zestar

Braeburn Pop_AurxEnt DuchOlden Splendour Sansa

CrippsPink GranSmith Enterprise Cox Pop_AurxArl Sundowner Ancestors Rubin Idared NY08 LadyWill PRI1661-1 Vanda Pop_AurxHC Delicious StateFair PRI1661-2 NY632

YelTransp Wagener MN1691 Empress WSU49

Burgundy Malinda WSU50 Mantet Akane Golden Delicious Silken WSU52 Oriole Lambourne Wealthy Sonya Cripp’s Pink Fireside Scifresh Jonamac WSU57 BenDavis McIntosh Goodland WSU24 VistaBella NY241 WSU37 AE0251 Montgomery WorcPearm Fuji Honeygold NY04 JamesGr BlushiGol AE0206 Jonathan Sunrise NY05

Melba NY07

Coop-17 EarlyCortland WSU30 NY01 CornellPop08 Honeycrisp Haralson

NY06 NY11 Linda Cortland Cox’s Orange Pippin WSU17 WSU46 NY92607-16 Lodi NY247 WSU36 Delorgue Zestar! Hatsuaki Delblush Fiesta NY14 NY66305-289 Jonagold CornellPop13 Rome Beauty Wijcik MN1915

NY543 F2_26829-2-2 MN1942 Suncrisp Topaz Goldrush MN1955 MN1702 GingerGold Williams MN2034 Northern Spy WSU35 MN1789 Beacon MN1965 Raritan MN2062 CrimsonCrisp Liberty Macoun WSU48 MN1971 Hudson Dolgo Spartan MN1764 MN1980 NY15 MN2016 MN2036 MN1802 Regent NY65707-19 Coop-15 MN1984 Pop_EntxArl MN1627 Freedom Monark MN2056 Duchess of Oldenburg RedBaron Jonafree MN2057 Pop_HCxAr PitmPine Goldrush MN2063 F2 2689-2-2 Snowsweet WSU34 Prima Mflor821 MN2000 Wagener Britemac WSU65 GMAL4332 NY13 MN1706 NJ90 MN1937 Frostbite IngMarie CornellPop09 MN1988 MN1940 Winesap Coop-15 Dolgo MN2031

GMAL4329 Fantazja WSU38 WintBanana MN2042 Haralson AE_HCxJonf NY76406-007 Fortune

YellNewtown AE0118 AE0406 CoromandelRed MN1839 Pop_HCxCP MN1760 BeautBath AE0213 Pop_HCxEnt MN1914

MN2046 PixieCrunch Discovery WSU5 Redfree

AE0210 Acknowledgements

This project is supported by the Specialty Crops Research Initiative of USDA’s National Institute of Food and Agriculture Questions?