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 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: WSU ImportantNY59333-006 Parents 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