2012 Annual Report 1a.Objectives (from AD-416): The objective of this project is to create sunflower breeding lines with higher level of resistances to both Sclerotinia head rot and Sclerotinia stalk rot by exploiting the available molecular technology of marker-assisted selection in combination with the traditional backcross breeding. Sclerotinia has been ranked as the number one disease problem by sunflower growers in the northern Great Plains since it attacks all parts of the plant including the root, stalk, and head, and causes heavy economic losses. Thus, a desirable sunflower hybrid should possess resistance to both head rot and stalk rot to ensure high productivity. During the previous funding cycle, we successfully identified 16 quantitative trait loci (QTL) underlying head rot resistance in segregating population derived from a cross between two USDA-released lines, HA 441 and RHA 439. These include nine QTL for disease incidence and seven QTL for disease severity in 10 linkage groups. We also tentatively mapped six QTL for stalk rot resistance from the recombinant inbred line (RIL) population derived from RHA 280 x RHA 801. Our results, as well as reports from other research groups, indicat that different genetic factors are involved for head rot and stalk rot resistances since the respective QTL are located on different chromosomes. It should be possible to pyramid these favorable QTL into a few elite sunflower breeding lines with the aid of molecular markers. 1b.Approach (from AD-416): We will use marker-assisted backcrossing to pyramid the head rot and stalk rot tolerant QTL into two recently released lines with stalk rot resistance, CONFSCLR2 and RHA 453. It is well documented that most QTL underlying traits of interest are population-specific, so we will use the best lines from our mapping populations as the tolerant donors and monitor QTL recombination with previously-identified markers. First, we will screen for polymorphism of the QTL-linked DNA markers between the donor and the recipient parental lines and identify a group of markers to be used in the project. We will use the alternative backcross and selection strategy designed specifically for this project to ensure success. The initial marker genotyping will be carried out in the BC1F1 generation and the selected lines will then be subjected to an additional cycle of backcrossing before evaluation in multiple-location trials for resistances to head and stalk rot. In 2008, we will. 1)screen for polymorphism between the donor lines (two lines possessing the most favorable QTL as revealed by DNA markers and phenotypic evaluation) and recipient lines (CONFSCLR2 and RHA 453), and select a group of markers to be used for this project;. 2)to develop segregating BC1F1 populations by making crosses between the donor and recipient lines; and. 3)to initiate marker-assisted selection and identify individuals to produce progeny for the first cycle of field evaluation of head rot and stalk rot resistances in the 2009 growing season. This proposal addresses the following research need of the Sclerotinia Initiative Strategic Plan: "PM 1.7.2: Use marker-assisted selection approaches for Sclerotinia resistance in sunflower" and "PM 3.0.3: Develop new DNA markers for QTL identification and marker assisted Selection". 3.Progress Report: Sclerotinia stalk rot and head rot are two different diseases of sunflower, each with quantitatively inherited resistance in sunflower, caused by the same fungal organism. These two diseases are typically the top two disease threats to sunflower. This research was conducted to show proof of concept for marker assisted selection with the limited number of markers already established for Sclerotinia resistance in sunflower and to develop a larger set of high-throughput genetic markers for Sclerotinia resistance. This year, we continued to backcross Sclerotinia head rot QTL into two moderately susceptible sunflower lines with high yield and quality characteristics, RHA 464 and CONFSCL R5. The former line is an oilseed type and the latter a confectionery sunflower type. We are working on converting these markers to SNPs to make this process easier. The larger effort in this project is the development of a broad-based germplasm collection of sunflower with field data on Sclerotinia resistance and high-throughput SNP marker data to perform association mapping. Association mapping is a relatively new approach adapted from human genetic studies that can find markers associated with traits in large, diverse populations. As of this date, we are preparing a manuscript on the results we obtained, which indicates that paralogs of the COI1 gene in sunflower are major QTL for Sclerotinia Stalk rot. The goal of this research is two-fold, develop germplasm with improved genetic resistance to Sclerotinia, and develop tools that can be used to track these genes and efficiently place them in further improved breeding lines of sunflower. This year, we will be releasing lines of sunflower with improved Sclerotinia head rot resistance. We will also be using this association mapping resource in the near future for Sclerotinia head rot resistance and Phomopsis disease resistance.