2012 Annual Report 1a.Objectives (from AD-416): Extension: We will expand close working relationships among breeders, extensionists, and growers of major Alliums in the US to evaluate germplasms for prioritized pest resistances and lay the foundation for the long-term translational genomics of the Allium vegetables. Workshops will be held at regional and national Allium meetings. Research: We will significantly increase the numbers of robust single nucleotide polymorphisms (SNPs) and develop a high through-put genotyping platform for onion. We will tag chromosome regions controlling prioritized disease-resistance traits of onion and transfer these tools to the private sector. 1b.Approach (from AD-416): Develop a detailed genetic map for onion: o Identify simple single nucleotide polymorphisms (SNPs) in onion; o Develop high throughput SNP genotyping platform for onion; Work with extension professionals to empower growers to complete on-farm evaluations for resistances or tolerances to prioritized diseases and pests; Self-pollinate and testcross selected plants and return seed to the extension-grower collaborators for validation of phenotypes; Deliver validated germplasms to private and public sector breeders; Exploit association genetics to tag grower-selected resistances. Develop workshops for public and private-sector researchers, students, and regional grower and consumer groups for onion to illustrate the usefulness of genomics to solve high-priority research goals. 3.Progress Report: Onion germplasm were identified which suffered less damage due to thrips and/or thrips-vectored Iris Yellow Spot Virus (IYSV). Seed was produced from selected plants and re-evaluated in field plots in Colorado and New Mexico. Selected plants tended to have foliage with reduced waxiness and high vigor. Attempts to mechanically transmit IYSV from onion to onion yielded relatively low transmission rates. The diversity among geographically distant isolates of IYSV are underway. Single nucleotide polymorphisms (SNPs) were identified in expressed regions between two inbred populations of onion. A total of 1256 SNPs were genotyped using progenies from a cross of these two inbreds, of which over 500 segregated. A detailed genetic map of onion SNPs is under construction and the genetic basis of leaf waxiness is being studied. This research relates to Objective 1, Determine the genetic basis of and initiate selection for carrot, onion, cucumber, and melon quality attributes influencing human nutrition and health, disease resistances, and yield and quality components, and stress tolerance in cucurbits, and perform field performance and quality trials and Objective 2, Utilize current biotechnology to discover and evaluate genetic variation and to map agriculturally important traits in Allium, Cucurbit, and Daucus germplasm, and to develop genetic and breeding stocks.