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United States Department of Agriculture

Agricultural Research Service

Research Project: PYRAMIDING SCLEROTINIA HEAD ROT AND STALK ROT RESISTANCES INTO ELITE SUNFLOWER BREEDING LINES WITH THE AID OF DNA MARKERS
2013 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:

We were able to resequence candidate genes for Sclerotinia, largely found from Henrik Stotz’s previous NSI work, in sunflower with good results. Regressing this data set against replicated field data on 260 sunflower lines and plant introductions (PIs) resulted in two COI1 homologs (called HaCOI1-1 and HaCOI1-2) on opposite ends of LG14 in sunflower showing high significance and explaining about 7% of the total genotypic variation for stalk rot reaction. We followed up on this work by also regressing a set of 8700 SNP markers from a separate SNP genotyping initiative on the same lines and PIs, and found an additional set of 22 non-redundant loci that explained most of the genotypic variation. This work is currently in the process of being published, the candidate gene work is in the late review stages in Theoretical and Applied Genetics, and the genome-wide work is in draft currently. These markers are currently being used in our laboratory in a validation experiment in which we are attempting to improve stalk rot resistance of a large random mating population of sunflower. We also anticipate using them as a selection criterion in early generation stages of our other conventional breeding populations.


Last Modified: 10/20/2014
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