USDA Specialty Crops Research Initiative (SCRI)

USDA Specialty Crops Research Initiative (SCRI)

USDA Specialty Crops Research Initiative (SCRI) THANKS TO YOU!!! Responding to listening sessions by federal agencies Providing information on specialty crops Help with the required 100% non-federal match Continued communications with congressional delegation

USDA Specialty Crops Research Initiative (SCRI) Ensuring US Onion Sustainability: Breeding and Genomics to Control Thrips and Iris Yellow Spot Virus Onion Storage Rot Management (Charlie Li) Onion ipmpipe & Diagnostics (Howard Schwartz)

Ensuring US Onion Sustainability: Breeding and Genomics to Control Thrips and Iris Yellow Spot Virus Project Director: Michael Havey, USDA-ARS and University of Wisconsin Project Co-Directors: Christopher Cramer, New Mexico State University Hanu Pappu, Washington State University Howard Schwartz, Colorado State University Christopher Town, The J. Craig Venter Institute Project Collaborators: Whitney Cranshaw, Colorado State University Jerry Hawkes, New Mexico State University

Onion Translational Genomics

Genomics Relatively cheap sequencing Expressed Regions Large-scale genomic sequencing High through-put analysis of all sequences Identify all putative coding regions in DNA

Onion Translational Genomics

Onion Translational Genomics Prioritize Target Traits Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers Value-Added Cultivars

Onion Translational Genomics Prioritize Target Traits

Allium Disease and Pest Survey

Allium Disease and Pest Survey

Allium Disease and Pest Survey 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

Conference on Onion Translational Genomics http://haveylab.hort.wisc.edu/cap/index.htm

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

Thrips

Iris Yellow Spot Virus Photos: Fred Crowe & Hanu Pappu

Onion Translational Genomics Prioritize Target Traits Identify Desirable Germplasms Understand the Pest Screen the Host

Detection of IYSV Hanu Pappu RT-PCR ELISA

Mechanical Transmission of IYSV Hanu Pappu

Field Evaluations for Thrips and IYSV Tolerance (2009-10) Chris Cramer and Howard Schwartz

Field Day at NMSU in 2010

Promising Entries for Field Tolerance to IYSV/Thrips 2009 & 2010 (** CO and NM): PI 258956 Chile Calderana PI 264320 ** Spain PI 546140 ** USA San Joaquin PI 546188 USA Yellow Sweet Spanish PI 546192 USA Yellow Sweet Spanish NMSU 07-54-1 USA

Onion Translational Genomics Prioritize Target Traits Identify Desirable Germplasms Complete Crossing and Genetic Evaluations

Genetic Validation of Tolerance A Line TC Family Selected Plants S 1 Family

Onion Translational Genomics Prioritize Target Traits Identify Desirable Germplasms Complete Crossing and Genetic Evaluations Develop Robust High-Throughput Genetic Markers

454 Sequencing of cdnas Chris Town and Michael Havey Red DH Yellow OH-1

454 Sequencing of cdnas Chris Town and Michael Havey Red DH Yellow OH-1 5 -TAGAAAAAATTGCTAACTGTTGCAGCTTGTGGGAACTGTAGTAGCAGGAAT-3 5 -TAGAAAAAATTGCTAATTGTTGCAGCTTGTGAGAACTGTAGTAGCAGGAAT-3

New Haploid Mapping Family Red DH x Yellow OH-1 F1 Haploid Extraction by Borut Bohanec

New Haploid Mapping Family Thanks to Kent Welsh

High Through-Put SNP Genotyping Assays: Illumina Kaspar TaqMan

Mapping of Target Traits

Association Mapping of Resistance or Tolerance to Thrips and/or IYSV

Ensuring US Onion Sustainability: Breeding and Genomics to Control Thrips and Iris Yellow Spot Virus Improved detection and inoculation of IYSV Tolerance to thrips and/or IYSV SNP genotyping platform and high-density map of onion Genetic tagging of semi-glossy foliage Delivery of germplasms and technologies

Onion Translational Genomics Useful Traits DNA Sequences Competitive Cultivars