@misc{hudson_mullens_hind_jamann_balint-kurti_2024, title={Natural variation in the pattern-triggered immunity response in plants: Investigations, implications and applications}, volume={25}, ISSN={["1364-3703"]}, url={https://doi.org/10.1111/mpp.13445}, DOI={10.1111/mpp.13445}, abstractNote={Abstract The pattern‐triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe‐derived molecules known as microbe‐ or pathogen‐associated molecular patterns or molecules derived from compromised host cells called damage‐associated molecular patterns. Membrane‐localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced. This review describes what is known about this variation. We discuss how variation in the PTI response can be measured and how this knowledge might be utilized in the control of plant disease and in developing plant varieties with enhanced disease resistance.}, number={3}, journal={MOLECULAR PLANT PATHOLOGY}, author={Hudson, Asher and Mullens, Alexander and Hind, Sarah and Jamann, Tiffany and Balint-Kurti, Peter}, year={2024}, month={Mar} }
 @article{samira_kimball_samayoa_holland_jamann_brown_stacey_balint-kurti_2020, title={Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum}, volume={10}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-77684-w}, DOI={10.1038/s41598-020-77684-w}, abstractNote={Plants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22-an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Samira, Rozalynne and Kimball, Jennifer A. and Samayoa, Luis Fernando and Holland, James B. and Jamann, Tiffany M. and Brown, Patrick J. and Stacey, Gary and Balint-Kurti, Peter J.}, year={2020}, month={Nov} }
 @misc{jamann_balint-kurti_holland_2015, title={QTL Mapping Using High-Throughput Sequencing}, volume={1284}, ISBN={9781493924431 9781493924448}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2444-8_13}, DOI={10.1007/978-1-4939-2444-8_13}, abstractNote={Quantitative trait locus (QTL) mapping in plants dates to the 1980s (Stuber et al. Crop Sci 27: 639–648, 1987; Paterson et al. Nature 335: 721–726, 1988), but earlier studies were often hindered by the expense and time required to identify large numbers of polymorphic genetic markers that differentiated the parental genotypes and then to genotype them on large segregating mapping populations. High-throughput sequencing has provided an efficient means to discover single nucleotide polymorphisms (SNPs) that can then be assayed rapidly on large populations with array-based techniques (Gupta et al. Heredity 101: 5–18, 2008). Alternatively, high-throughput sequencing methods such as restriction site-associated DNA sequencing (RAD-Seq) (Davey et al. Nat Rev Genet 12: 499–510, 2011; Baird et al. PloS ONE 3: e3376, 2008) and genotyping-by-sequencing (GBS) (Elshire et al. PLoS One 6: 2011; Glaubitz et al. PLoS One 9: e90346, 2014) can be used to identify and genotype polymorphic markers directly. Linkage disequilibrium (LD) between markers and causal variants is needed to detect QTL. The earliest QTL mapping methods used backcross and F2 generations of crosses between inbred lines, which have high levels of linkage disequilibrium (dependent entirely on the recombination frequency between chromosomal positions), to ensure that QTL would have sufficiently high linkage disequilibrium with one or more markers on sparse genetic linkage maps. The downside of this approach is that resolution of QTL positions is poor. The sequencing technology revolution, by facilitating genotyping of vastly more markers than was previously feasible, has allowed researchers to map QTL in situations of lower linkage disequilibrium, and consequently, at higher resolution. We provide a review of methods to identify QTL with higher precision than was previously possible. We discuss modifications of the traditional biparental mapping population that provide higher resolution of QTL positions, QTL fine-mapping procedures, and genome-wide association studies, all of which are greatly facilitated by high-throughput sequencing methods. Each of these procedures has many variants, and consequently many details to consider; we focus our chapter on the consequences of practical decisions that researchers make when designing QTL mapping studies and when analyzing the resulting data. The ultimate goal of many of these studies is to resolve a QTL to its causal sequence variation.}, journal={Methods in Molecular Biology}, publisher={Springer New York}, author={Jamann, Tiffany M. and Balint-Kurti, Peter J. and Holland, James B.}, year={2015}, pages={257–285} }