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ARS Home » Southeast Area » Raleigh, North Carolina » Plant Science Research » Research » Research Project #424645

Research Project: Genetic Improvement of Small Grains for Biotic and Abiotic Stress Tolerance and Characterization of Pathogen Populations

Location: Plant Science Research

2017 Annual Report


Objectives
1. Identify and develop improved small grain germplasm with resistance to rusts, powdery mildew, Fusarium head blight, necrotrophic pathogens, and freeze tolerance. 1a: Develop wheat germplasm with resistance to stripe rust, leaf rust, stem rust, and powdery mildew. 1b: Develop wheat germplasm with resistance to Fusarium head blight (FHB). 1c: Develop wheat germplasm with resistance to Stagonospora nodorum blight (SNB). 1d: Identify oat, wheat and barley germplasm with tolerance to freezing. 2. Develop improved methods of marker-assisted selection, and apply markers in development of small grains cultivars. 2a: Identify new markers for important traits in eastern winter wheat germplasm. 2b: Evaluate important traits in eastern winter wheat using molecular markers. 2c: Develop new eastern winter wheat germplasm using marker-assisted breeding. 3. Develop new wheat germplasm and cultivars having enhanced end-use characteristics for the eastern U.S. 4. Determine the virulence structure of small grain pathogen populations and evaluate the risk potential of virulence transfer through gene flow. 4a: Determine the virulence frequencies in the wheat powdery mildew pathogen, Blumeria graminis f. sp. tritici, from different regions in the U.S.


Approach
1. Develop wheat germplasm with resistance to stripe rust, leaf rust, stem rust, and powdery mildew. Develop wheat germplasm with resistance to Fusarium head blight (FHB). Develop wheat germplasm with resistance to Stagonospora nodorum blight (SNB). Identify oat, wheat and barley germplasm with tolerance to freezing. 2. Identify new markers for important traits in eastern winter wheat germplasm. Evaluate important traits in eastern winter wheat using molecular markers. 3. Make new crosses, marker-assisted selection for key traits; phenotyping and selection for improved hard wheats lines; introduce resistance to common bunt; grow and select populations under organic and conventional conditions. 4. Obtain infected plant samples from all states; make single-pustuled isolates, and begin phenotyping and genotyping.


Progress Report
The ARS small grains pathology program responded to an unprecedented wheat stunting and root rot epidemic that caused major economic losses to North Carolina wheat production in 2016. Large portions of the state experienced prolonged soil waterlogging in 2016. Severely stunted wheat plants from saturated fields were examined and Pythium consistently was associated with the symptoms observed. Of hundreds of possible Pythium species common in field crop soil, three were consistently identified in wheat roots and crowns: P. irregulare, P. spinosum, and P. vanterpoolii. P. vanterpoolii and P. spinosum have not previously been reported as pathogens in wheat in the USA. These same three species were again found in the majority of wheat samples diagnosed with Pythium in 2017. All tested isolates were sensitive to mefenoxam, a common anti-Pythium chemical. Work is now underway to see if wheat-specific Pythium strains that may also be hosted by soybean and/or corn are an ongoing problem for North Carolina wheat production. Wheat powdery mildew collaborative research led to identification of Pm 58, a new resistance gene from Aegilops tauschii, and novel mildew resistance loci on chromosome 2B through analysis of a large worldwide collection of wheat accessions from the USDA-ARS National Small Grain Collection (NSGC) core set of germplasm. In addition, collaboration helped make Pm21, an effective gene not currently in use in the U.S., available to wheat breeders. Further, a large study of the wheat powdery mildew population revealed that it is different in the Plains hard wheat area and the eastern soft wheat areas. The study confirmed that the hard wheat population remains avirulent to genes long defeated in the soft wheat area, and more sensitive to triazole fungicides. It also demonstrated that five resistance (Pm) genes recently introgressed from wild wheat relatives should be effective throughout both regions. A subset of 653 spring and winter oat lines, consisting of 250 diverse winter oats tested last year, were evaluated for their response to crown freezing using controlled environment growth chambers. All lines were genotyped using both a 6K Illumina Infinium single nucleotide polymorphism (SNP) chip, and via genotyping by sequencing (GBS). Approximately 4000 high quality SNPs with minor allele frequency >0.05, missing data <0.05, and heterozygosity <0.05 were used for association analysis. A total of eight significant markers were detected on chromosomes 5C, 6C, 11A, and either 8A or 14D. Mean comparison of lines based on the number of desirable alleles possessed for these eight markers show an additive improvement on survival and recovery. These markers may be helpful in screening parents and their progeny when breeding for improved freeze tolerance in oats, especially among germplasm from the southeastern United States. Several genotypes that are spring freeze tolerant were identified in previous years' research. In this instance “spring-freeze tolerance” is defined as the ability to produce seed numbers that are not significantly different from plants that have not been frozen. Crosses between spring-freeze tolerant and susceptible parents have been made and are being advanced using a double-haploid technique. This will be the basis for determining genetic factors involved in tolerance of wheat to sudden spring freezes. Infrared (IR) analysis under natural conditions indicated that plants in the field froze from the bottom of the plant to the top even though leaves were 6 to 8 degrees colder than the bottom and the soil was not frozen. This has been observed under laboratory conditions and confirms that freezing in the laboratory can accurately simulate field conditions. Freezing patterns indicated that even though leaves of plants at mid-boot stage (Feekes 40-43) completely froze, only the tips of those leaves died. In addition, while leaves of most plants froze, the heads of most of the plants survived and produced seed. This suggests that barriers may exist that allow the head to remain unfrozen and therefore not be damaged by freezing temperatures. A collaborative effort with University of Innsbruck, Austria, was completed and showed that some plants have anatomical barriers that prevent ice from penetrating into flowers. These barriers allowed the flowers to supercool to about -10C without freezing. Experiments have been initiated to find similar barriers in wheat, rye and oat. It is possible that oat is missing such barriers making it more susceptible to freezing injury than wheat or rye. Work was done to expand and optimize the models used to predict yield and test weight utilizing data from nine years of the Gulf Atlantic Wheat Nursery (GAWN) and three years of the SunWheat Nursery (SUN). At this point, the GAWN-SUN training population is composed of 650 wheat lines with genotyping data (~35,000 SNP/per line) and extensive field data. These nurseries were grown in an average of seven locations per year over the course of nine growing seasons (2008 to 2016). Statistical analysis was done on all of the field data to determine the best locations and years to use as input in genomic selection models targeted to the North Carolina breeding programs. Curation of the field data is important since lines often do not perform consistently across the diverse locations in Texas, Lousiana, Georgia, North Carolina, Arkansas, and Virginia, where the nurseries were grown. We determined that it was valuable to include yield data from most of the Virginia and North Carolina environments while suitability of data from other locations for yield prediction depended on the year. Statistical analyses of field data from six years data (2011-2016) for the Uniform Southern Soft Red Winter Wheat Scab Nursery (USSRWWSN) were done to provide input into the genomic selection models. Based on GS models using the Fusarium Head Blight (FHB) ratings for the 2011-2015 USSSN in combination with the SNPs, we were able to correctly identify 10 of the 11 most FHB resistant lines in the 2016 USSSN for Deoxynivalenol (DON) content of grain. We also identified 9 of the top 11 lines based ratings of Fusarium Damaged Kernels. These results are very promising and further suggests that genomic selection (GS) can be utilized to streamline variety selection and evaluation for FHB resistance. The overall genomic selection effort was greatly expanded for the 2017 growing season. DNA was isolated and SNP data analyzed for a large number of lines that entered the genomic selection program. ARS scientists were able to develop genomic predictions more than 1,000 lines for grain yield, test weight and FHB resistance traits, along with other traits such as resistance to powdery mildew and stripe rust.


Accomplishments
1. Optimization of genomic breeding methods for Southeastern winter wheat. Each year, wheat breeders spend time and money collecting data on performance of thousands of experimental lines in replicated field plots. Genomic selection is a tool that allows plant breeders to utilize these field data in combination with DNA sequence data to improve the efficiency with which they can identify the best performing lines for release as varieties. ARS scientist at Raleigh, North Carolina, worked with wheat breeders in the eastern growing region to combine DNA marker data with nine years of data on grain yield and disease resistance collected from field evaluation of experimental lines in a collaborative nursery. Scientists developed optimized genomic selection models that had high predictive ability. This study demonstrated the value of genomic selection to improve grain yield, test weight, resistance to powdery mildew and resistance to head scab of wheat. This new tool has now been widely adopted by US soft winter wheat breeders.

2. Improved understanding of wheat powdery mildew pathogen. Powdery mildew is one of the most common and damaging diseases in global wheat production. Blumeria graminis f. sp. tritici, the fungus that causes the disease, can rapidly overcome host resistance or fungicides used in management. Thus, it is important to monitor which resistance genes are effective in which regions, and to locate a continuous stream of new resistance genes to replace those that are defeated. ARS researchers at Raleigh, North Carolina, conducted a large study of the U.S. wheat powdery mildew population and learned that it is different in the Plains hard wheat area and the eastern soft wheat areas. The study confirmed that the hard wheat population remains controlled by resistance genes that are long defeated in the soft wheat area, and is also more sensitive to two common triazole fungicides. The study also demonstrated that five resistance genes recently introduced into common wheat from wild wheat relatives should be effective throughout both regions.

3. Monitoring freezing in wheat under natural conditions using infrared thermography. Depending on timing and growth stage of wheat, complete loss of a crop is possible when freeze events occur in the spring. In the last 2 years in some regions of the U.S. a 40 to 60% loss of yield was attributed to unexpected spring freezes. The heat given off by water when it freezes can be visualized with an infrared camera. Using this technology ARS scientist at Raleigh, North Carolina, determined that under laboratory conditions that many wheat tissues remain unfrozen even when temperatures are below freezing and some parts of the plant are frozen. When moving the cameras to the field, we found that plants in the field always froze from the bottom to the top, even though the tops of the leaves were 6 or 8 degrees colder than the bottom. In addition, older leaves always froze before younger leaves, as was also observed in the lab. Additionally, we found that even though many times “leaf-tip burn” is observed after a winter and spring freeze, the tips of leaves never freeze independent of the whole leaf. This suggests that even though an entire leaf freezes, the tips of leaves are less freezing tolerant and die while the rest of the leaf survives. This provides a basis for studying gene expression within the plant to determine differences in freezing tolerance mechanisms within the plant. The field analysis confirmed that laboratory freeze tests accurately duplicate freezing within plants under natural freezing conditions.

4. Identifying barriers to freezing in plants. The major limitation to growing winter cereals, is their susceptibility to stresses encountered during winter, primarily induced by freezing temperatures. An understanding of how plants in general withstand stresses caused by freezing temperatures is crucial to developing better methods for selecting genotypes that can withstand these stresses. Infrared monitoring revealed that flowers of alpine heather remained unfrozen even though stems of the plants had frozen. Using histological techniques developed in our laboratory an ARS scientist at Raleigh, North Carolina determined that the cells leading into the flowers were acting as a barrier to the growth of ice. These techniques are being used to determine if similar barriers exist in wheat and rye, the most freezing tolerant winter cereals. If these kinds of barriers are missing in oat, this may explain its’ low level of freezing tolerance and provide a basis for an effective screening technique to identify oat genotypes with elite freezing mechanisms that could be crossed with adapted cultivars to improve winter hardiness.

5. Identification of sources of resistance to wheat stem rust. Since its finding in 1999, the Ug99 strain of wheat stem rust and its descendents, has caused the world’s wheat improvement scientists to identify and incorporate new genes for resistance, as well as new combinations of widely-deployed resistance genes. ARS scientists in Raleigh, North Carolina, have evaluated about 75,000 U.S.-adapted wheat varieties and breeding lines in Kenya – where the disease is indigenous. The newly identified genes and new combinations of resistance genes in adapted germplasm enables U.S. wheat breeders to develop new varieties having stem rust resistance, before the disease reaches the U.S.


Review Publications
Petersen, S., Lylerly, J.H., McKendry, A.L., Islam, M.S., Brown Guedira, G.L., Dong, Y., Murphy, J.P. 2017. Validation of fusarium head blight resistance QTL in US winter wheat. Crop Science. 57:1-12.