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United States Department of Agriculture

Agricultural Research Service


Location: Sunflower and Plant Biology Research

2010 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
This was the second year of our Sclerotinia Initiative project, "Pyramiding Sclerotinia head rot and stalk rot resistances into elite sunflower breeding lines with the aid of DNA markers." Conventional breeding of Sclerotinia resistance using new sources is ongoing. We have genetic lines at various stages of testing that contain alleles for Sclerotinia resistance as well as other value-added traits. In our marker assisted backcrossing experiments, we have concentrated on two pedigrees of interest to our customers, one with RHA 464 background and one with CONFSCL R5 background. These were genetic backgrounds that our customers and stakeholders felt were desirable for traits other than Sclerotinia resistance, and needed additional resistance to Sclerotinia. We are interrogating the populations with known TRAP markers associated with major head rot resistance QTL, and will backcross again in summer 2010 with plants predicted to be the most resistant based on marker profile. In doing this work, we will be fulfilling the first objective of the project: to develop breeding populations and lines with the majority of the resistance QTL that are known to be segregating in the population. The postdoctoral researcher is also in the process of validating primer sets to allow sequencing of putative homologues to defense-related genes in Arabidopsis. The targeted genes were associated with Sclerotinia resistance in Arabidopsis in previously published trials. In July 2010, we plan to submit samples from 103 genotypes and 18 gene segments for sequencing. These sequences will then be compared among the genotypes, and SNP markers developed for further analysis of a larger association mapping population of 260 plant introductions. This is called a "candidate gene" approach to association mapping. Recent progress in the sunflower research community has resulted in the development of around 10,000 EST-characterized SNP markers, which we now plan to use on the same association mapping population as a means of conducting a "genome-wide scan" for Sclerotinia stalk rot resistance. Phenotypic evaluation of the 260 plant introductions for stalk rot and subsequent statistical analysis have already been completed. This effort supports the third objective of our project: to complete model formation and analysis in our association mapping population for stalk rot resistance. The ADODR monitors research progress by quarterly meetings with the Cooperator's personnel and by site visits to field plot locations.

4. Accomplishments

Last Modified: 05/25/2017
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