Strategies for Funding Problem Solving Research on the Alliums. Michael J. Havey USDA-ARS and University of Wisconsin

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1 Strategies for Funding Problem Solving Research on the Alliums Michael J. Havey USDA-ARS and University of Wisconsin

2 USDA-NIFA Specialty Crops Research Initiative (SCRI)

3 USDA Specialty Crops Research Initiative (SCRI) Research in plant breeding, genetics, and genomics to improve specialty crops Identify and address threats from pests and diseases Improve productivity and profitability over the long term Improved mechanization and technologies that delay or inhibit ripening Prevent, detect, monitor, control, and respond to potential food safety hazards

4 USDA Specialty Crops Research Initiative (SCRI) THANKS TO YOU!!! Responding to listening sessions by federal agencies Providing information on specialty crops Continued communications with congressional delegation

5 USDA Specialty Crops Research Initiative (SCRI) Requires stakeholder input into research priorities

6 Survey on Challenges to Sustainable Production of the Alliums (2006)

7 Survey on Challenges to Sustainable Production of the Alliums (2006)

8 Survey on Challenges to Sustainable Production of the Alliums (2006)

9 Survey on Challenges to Sustainable Production of the Alliums (2006) 100+ respondents (>>onion growers) Top Onion Production Problems in NA: Thrips Iris Yellow Spot Virus Bacterial soft rot (Erwinia) Slippery skin (Pseudomonas) Black mold (Aspergillus) Botrytis leaf blight and neck rot Fusarium basal rot Pink root Heat

10 Conference at 2006 NARC to Prioritize Research Foci

11 High IYSV Thrips CMS Fusarium RNAi Flavor Carbohydrates White rot Botrytis neck rot Bacterial rots Yellow Nutsedge Overall Relevance Moderate Flowering Botrytis leaf blight Pink root Black mold Downy mildew Herbicide tolerance Low Simple Moderate Resistant Germplasm and Inheritance Difficult

12 USDA Specialty Crops Research Initiative (SCRI) 2008: Ensuring US onion sustainability: breeding and genomics to control thrips and Iris Yellow Spot Virus (M. Havey, USDA-ARS and University of Wisconsin) 2009: Advancing onion post-harvest handling efficiency and sustainability by multimodel quality sensing, disease control, and waste stream management (C. Li, Univ. of Georgia) 2010: IPM-PIPE and innovative disease diagnostic tools for onion growers (H. Schwartz, Colorado State University)

13 Thrips

14 Iris Yellow Spot Virus Photos: Fred Crowe & Hanu Pappu

15 USDA-SCRI Project: Breeding & Genomics for Control of Thrips and IYSV NARC 2008

16 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers Value-Added Cultivars

17 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms

18 Field Evaluations for Thrips and IYSV Tolerance ( ) Chris Cramer and Howard Schwartz

19 Field Evaluations for Thrips and IYSV Tolerance ( ) Performing better over years and locations PI Chile Calderana PI Spain PI USA San Joaquin PI USA YSS Winegar PI USA YSS

20 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms Complete Crossing and Genetic Evaluations

21 Genetic Validation of Tolerance A Line TC Family Selected Plants S 1 Family Re-evalutions of progenies

22 Foliage Types in Onion Glossy Semi-glossy Waxy

23 Scanning EM of Leaf Surface Glossy Semi-Glossy Waxy

24 White Onion with Waxy Foliage X Inbred B5351 has Semi-Glossy Foliage

25 Tissue Sampling

26 Gas Chromatography (GC) Mass Spec (MS)

27 GC-MS Output Hentriacontanone-16 Waxy Semi-glossy Glossy

28 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers

29 White Onion with Waxy Foliage Inbred B5351 has Semi-Glossy Foliage 5 -TAGAAAATTGCTAACTGTTGCAGCTTGTGGGAACTGTAGTAAGGAATACTGA-3 ^^^^^^^^^^^^^^^^^^^^^^^^^G^^^^^^^^^^^^^^^^^^^^^^^^^^ Single Nucleotide Polymorphisms (SNPs)

30 SNP Mapping in Semi-Glossy Family Isolated DNA from 120 F 2 progenies SNPs genotyped using KASPar platform Map of 324 markers

31 Mapping of Semi-Glossy Foliage Chromosome 5 Chromosome isotig32307_1162 isotig41553_294 isotig39428_415 isotig25097_2357 contig00142_122 isotig26178_547 isotig29989_644 isotig32901_1333 isotig31628_1166 isotig29167_1843 isotig33680_1027 isotig35383_182 isotig32271_1015 isotig28226_139z isotig37670_180 isotig28787_1516 isotig34198_886 isotig38424_376 isotig14741_247 isotig29282_688 isotig31406_1529 isotig34069_110 isotig28803_1689 isotig33059_107 isotig26595_878 isotig28889_2528 isotig28536_1567 isotig19361_480 isotig31727_1490 isotig14721_448 isotig42464_471 isotig33965_554 isotig35535_407 isotig32376_621 isotig29284_408 isotig34113_654 isotig31477_611 isotig25797_639 isotig40014_661 isotig31278_1407z isotig37209_549 Hentriacontanone isotig33031_559 isotig41937_218 isotig39918_357 isotig30655_190z isotig28239_126 contig00293_452z isotig29209_2397 isotig34313_545 isotig28716_113 isotig36042_298z isotig34753_1109 isotig40501_344 isotig26063_406z isotig29101_1894 isotig28488_2757 isotig35010_835 isotig31939_448 isotig30988_471 isotig29530_152 isotig28398_1732 isotig30110_847 isotig28365_1152 isotig34666_385 isotig33898_339z isotig39752_384z isotig26033_1589z isotig34668_1112z isotig42387_377z isotig29157_1006 isotig29331_101 isotig35302_619z isotig38248_370z Waxes

32 Foliage Types and Thrips Avoidance Glossy and semi-glossy are recessive to waxy Specific waxes missing in glossy Less of many waxes in semi-glossy SNPs tag major genes controlling wax quantities

33 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers Value-Added Cultivars

34 Breeding & Genomics for Control of Thrips and IYSV Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers Value-Added Cultivars Contribution to integrated control of thrips/iysv

35 USDA Specialty Crops Research Initiative (SCRI) Requires stakeholder input into research priorities

36 research priorities from 2013 NARC.pdf Overall Relevance High Moderate IYSV Thrips Fusarium Nutritional benefits White rot Pink root Flavor Botrytis neck rot Carbohydrates Bacterial rots Yellow nutsedge Male sterility Flowering Black mold Herbicide tolerance Botrytis leaf blight Downy mildew Stemphylium? Salt tolerance? Water use efficiency? Low Simple Moderate Resistant Germplasm and Inheritance Phenotypic variation known No evidence of beneficial genetic variation, may need transgenic approach Focus of current SCRI grant (Havey et al.) Detection is focus of current SCRI grant (Li et al.) Newly added item from 2012 NARC Difficult