Plant Genetics: TA INTRO Ryan King

Quick bio Native Oregonian: from Southern Oregon/Rogue Valley Worked with nursery crops, hazelnuts, vegetables, and native plants B.S. in Horticulture at Oregon State in 2013 Took Plant Genetics with Dr. Pat Hayes in 2011 Currently M.S. student with Dr. Jim Myers, Vegetable Breeding and Genetics Program– interested in breeding vegetables for organic/low-input systems

NOVIC 2016 season: managed NOVIC organic vegetable variety trials at OSU’s Lewis Brown Research farm and coordinated with several other farms in the Corvallis area for on-farm trials. Crops included: tomatoes, peppers, corn, winter squash, cabbage and turnips.

What am I Doing here? Thesis project: Assessing genetic differences in populations selected in parallel conventional and organic production systems, using carrots and snap beans as model crops OSU focus: snap beans (self-pollinated model crop) University of Wisconsin focus: carrots (cross-pollinated model crop)

(Carrots)

Thesis Project Goals Long term goal: Determine most effective and efficient strategies for breeding vegetable cultivars optimized for organic production systems Supporting objectives: Compare impact of selection for key traits Measure genotype x system (organic vs. conventional) and genotype x location (Oregon and Wisconsin) interactions for key traits, and their heritability in each system Determine genetic correlation between systems and locations Use next-generation sequencing methods to discover changes at genome level from selection in each system

Project TImeline Spring 2015 Crosses made between Hystyle and Provider, OSU5630 and Black Valentine Summer 2015 F1 grown at OSU Vegetable Research Farm Summer 2016 F2 grown in conventional/organic plots at Lewis Brown Winter 2017 F3 grown in winter nursery in California and in OSU greenhouses (backup) Summer 2017 F4 grown in conventional/organic replicated trials at Lewis Brown. Summer 2018 F5 grown in conventional/organic replicated trials in OR and WI

Common Bean Phaseolus vulgaris L. Fabaceae (Leguminosae) Diploid (n = 11) 2n=2x=22 587 Mb (megabase=million base pairs); (Schmutz et al., 2014) Two independent domestications: Mesoamerica and Andes In 2016, ~12,000 acres were grown for processing in Oregon (USDA, NASS) Photo: Jim Myers

Germination/Early Vigor IMPORTANT TRAITS Germination/Early Vigor Yield/Productivity Plant architecture Pod quality Root systems

Germination

Photo: bonnieplants.com Plant architecture Lodging Surface Area Coverage Pod Distribution Branching Flower number Photo: bonnieplants.com

Pod quality Round pod cross section Low fiber Straight and smooth Image from Burpee.com

Root systems Taproot diameter Number/angles of basal and adventitious roots Root nodulation Root rot severity

How WIll We Assess Genetic Differences? Genotyping will be done for F4 (2017) and F5 (2018) using Illumina SNP chip QTL analysis incorporating mixed model effects to estimate allelic effects and variances Linkage maps and QTLs for evaluated traits SNP polymorphism structures and frequencies Populations will be compared to investigate if similar or same QTLs affect selected traits

EXPECted outcomes Estimates of GxE interactions, genetic variances, models for gene action, and heritabilities of key traits Comparison of direct and indirect selection Identification of genomic regions of carrot and bean with shifts in allelic frequency Molecular markers for important traits Advanced breeding lines for carrots and beans developed in organic and conventional environments Info for vegetable seed companies on need to develop independent breeding programs for organic growers

Questions? Come see me for office hours: ALS 4026A; Wednesdays 9-10 am