@article{chen_zhao_tabor_nian_phillips_wolters_yang_balint‐kurti_2023, title={A leucine‐rich repeat receptor kinase gene confers quantitative susceptibility to maize southern leaf blight}, volume={238}, ISSN={0028-646X 1469-8137}, url={http://dx.doi.org/10.1111/nph.18781}, DOI={10.1111/nph.18781}, abstractNote={Southern leaf blight (SLB), caused by the necrotrophic fungal pathogen Cochliobolus heterostrophus (anamorph Bipolaris maydis), is a major foliar disease which causes significant yield losses in maize worldwide. A major quantitative trait locus, qSLB3.04 , conferring recessive resistance to SLB was previously mapped on maize chromosome 3. Using a combination of map-based cloning, association analysis, ethyl methanesulfonate (EMS) and transposon mutagenesis and CRISPR-Cas9 editing, we demonstrate that a leucine-rich repeat receptor-like kinase gene which we have called ChSK1 (Cochliobolus heterostrophus Susceptibility Kinase 1) at qSLB3.04 causes increased susceptibility to SLB. Genes of this type have generally been associated with the defense response. We present evidence that ChSK1 may be associated with suppression of the basal immune response. These findings contribute to our understanding of plant disease susceptibility genes and the potential to use them for engineering durable disease resistance.}, number={3}, journal={New Phytologist}, publisher={Wiley}, author={Chen, Chuan and Zhao, Yaqi and Tabor, Girma and Nian, Huiqin and Phillips, Joanie and Wolters, Petra and Yang, Qin and Balint‐Kurti, Peter}, year={2023}, month={Feb}, pages={1182–1197} }
 @article{neelakandan_kabahuma_yang_lopez_wisser_balint-kurti_lauter_2023, title={Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104}, volume={7}, ISSN={["2160-1836"]}, DOI={10.1093/g3journal/jkad166}, abstractNote={In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error prone repair pathways of non-homologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize, with respect to insertion site features, the genomic distribution of T-DNA incorporation, and mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique which can be adapted to any species of interest.}, journal={G3-GENES GENOMES GENETICS}, author={Neelakandan, Anjanasree K. and Kabahuma, Mercy and Yang, Qin and Lopez, Miriam and Wisser, Randall J. and Balint-Kurti, Peter and Lauter, Nick}, year={2023}, month={Jul} }
 @article{gentzel_park_bellizzi_xiao_gadhave_murphree_yang_lamantia_redinbaugh_balint-kurti_et al._2020, title={A CRISPR/dCas9 toolkit for functional analysis of maize genes}, volume={16}, ISSN={1746-4811}, url={http://dx.doi.org/10.1186/s13007-020-00675-5}, DOI={10.1186/s13007-020-00675-5}, abstractNote={The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9).In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression.We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.}, number={1}, journal={Plant Methods}, publisher={Springer Science and Business Media LLC}, author={Gentzel, Irene N. and Park, Chan Ho and Bellizzi, Maria and Xiao, Guiqing and Gadhave, Kiran R. and Murphree, Colin and Yang, Qin and LaMantia, Jonathan and Redinbaugh, Margaret G. and Balint-Kurti, Peter and et al.}, year={2020}, month={Oct} }
 @article{morales_repka_swarts_stafstrom_he_sermons_yang_lopez‐zuniga_rucker_thomason_et al._2020, title={Genotypic and phenotypic characterization of a large, diverse population of maize near‐isogenic lines}, volume={103}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1111/tpj.14787}, DOI={10.1111/tpj.14787}, abstractNote={Genome wide association studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect, and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1,270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height, and resistance to three foliar diseases and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4-0.8) was relatively high. The 896 genotyped nNILs contain 2,638 introgressions, which span the entire genome with substantial overlap within and among allele donors. Genome wide association with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize nested association mapping population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions and could readily be used for future fine mapping studies.}, number={3}, journal={The Plant Journal}, publisher={Wiley}, author={Morales, Laura and Repka, A. C. and Swarts, Kelly L. and Stafstrom, William C. and He, Yijian and Sermons, Shannon M. and Yang, Qin and Lopez‐Zuniga, Luis O. and Rucker, Elizabeth and Thomason, Wade E. and et al.}, year={2020}, month={May}, pages={1246–1255} }
 @article{xiaodong_olukolu_yang_balint-kurti_2018, title={Identification of a locus in maize controlling response to a host-selective toxin derived from Cochliobolus heterostrophus, causal agent of southern leaf blight}, volume={131}, ISSN={0040-5752 1432-2242}, url={http://dx.doi.org/10.1007/s00122-018-3175-6}, DOI={10.1007/s00122-018-3175-6}, abstractNote={A host-selective, proteinaceous maize toxin was identified from the culture filtrate of the maize pathogen Cochliobolus heterostrophus. A dominant gene for toxin susceptibility was identified on maize chromosome 4. A toxic activity was identified from the culture filtrate (CF) of the fungus Cochliobolus heterostrophus, causal agent of the maize disease southern leaf blight (SLB) with differential toxicity on maize lines. Two independent mapping populations; a 113-line recombinant inbred line population and a 258-line association population, were used to map loci associated with sensitivity to the CF at the seedling stage. A major QTL on chromosome 4 was identified at the same locus using both populations. Mapping in the association population defined a 400 kb region that contained the sensitivity locus. By comparing CF-sensitivity of the parents of the RIL population with that of the F 1  progeny, we determined that the sensitivity allele was dominant. No relationship was observed between CF-sensitivity in seedlings and SLB susceptibility in mature plants; however, a significant correlation (- 0.58) was observed between SLB susceptibility and CF-sensitivity in seedlings. The activity of the CF was light-dependent and was sensitive to pronase, indicating that the toxin was proteinaceous.}, number={12}, journal={Theoretical and Applied Genetics}, publisher={Springer Science and Business Media LLC}, author={Xiaodong, Xie and Olukolu, Bode and Yang, Qin and Balint-Kurti, Peter}, year={2018}, month={Sep}, pages={2601–2612} }
 @article{minker_biedrzycki_kolagunda_rhein_perina_jacobs_moore_jamann_yang_nelson_et al._2018, title={Semiautomated Confocal Imaging of Fungal Pathogenesis on Plants: Microscopic Analysis of Macroscopic Specimens}, volume={81}, ISSN={["1097-0029"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84977595779&partnerID=MN8TOARS}, DOI={10.1002/jemt.22709}, abstractNote={ABSTRACT}, number={2}, journal={MICROSCOPY RESEARCH AND TECHNIQUE}, author={Minker, Katharine R. and Biedrzycki, Meredith L. and Kolagunda, Abhishek and Rhein, Stephen and Perina, Fabiano J. and Jacobs, Samuel S. and Moore, Michael and Jamann, Tiffany M. and Yang, Qin and Nelson, Rebecca and et al.}, year={2018}, month={Feb}, pages={141–152} }
 @article{zhang_yang_rucker_thomason_balint-kurti_2017, title={Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z-mays ssp parviglumis)}, volume={130}, ISSN={["1432-2242"]}, url={https://doi.org/10.1007/s00122-017-2888-2}, DOI={10.1007/s00122-017-2888-2}, abstractNote={In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes. In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.}, number={6}, journal={THEORETICAL AND APPLIED GENETICS}, publisher={Springer Science and Business Media LLC}, author={Zhang, Xinye and Yang, Qin and Rucker, Elizabeth and Thomason, Wade and Balint-Kurti, Peter}, year={2017}, month={Jun}, pages={1285–1295} }
 @article{yang_balint-kurti_xu_2017, title={Quantitative Disease Resistance: Dissection and Adoption in Maize}, volume={10}, ISSN={1674-2052}, url={http://dx.doi.org/10.1016/j.molp.2017.02.004}, DOI={10.1016/j.molp.2017.02.004}, abstractNote={Maize is the world’s most produced crop, providing food, feed, and biofuel. Maize production is constantly threatened by the presence of devastating pathogens worldwide. Characterization of the genetic components underlying disease resistance is a major research area in maize which is highly relevant for resistance breeding programs. Quantitative disease resistance (QDR) is the type of resistance most widely used by maize breeders. The past decade has witnessed significant progress in fine-mapping and cloning of genes controlling QDR. The molecular mechanisms underlying QDR remain poorly understood and exploited. In this review we discuss recent advances in maize QDR research and strategy for resistance breeding.}, number={3}, journal={Molecular Plant}, publisher={Elsevier BV}, author={Yang, Qin and Balint-Kurti, Peter and Xu, Mingliang}, year={2017}, month={Mar}, pages={402–413} }
 @article{bian_yang_balint-kurti_wisser_holland_2014, title={Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population}, volume={15}, ISSN={["1471-2164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84924290940&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-15-1068}, abstractNote={A previous study reported a comprehensive quantitative trait locus (QTL) and genome wide association study (GWAS) of southern leaf blight (SLB) resistance in the maize Nested Association Mapping (NAM) panel. Since that time, the genomic resources available for such analyses have improved substantially. An updated NAM genetic linkage map has a nearly six-fold greater marker density than the previous map and the combined SNPs and read-depth variants (RDVs) from maize HapMaps 1 and 2 provided 28.5 M genomic variants for association analysis, 17 fold more than HapMap 1. In addition, phenotypic values of the NAM RILs were re-estimated to account for environment-specific flowering time covariates and a small proportion of lines were dropped due to genotypic data quality problems. Comparisons of original and updated QTL and GWAS results confound the effects of linkage map density, GWAS marker density, population sample size, and phenotype estimates. Therefore, we evaluated the effects of changing each of these parameters individually and in combination to determine their relative impact on marker-trait associations in original and updated analyses.Of the four parameters varied, map density caused the largest changes in QTL and GWAS results. The updated QTL model had better cross-validation prediction accuracy than the previous model. Whereas joint linkage QTL positions were relatively stable to input changes, the residual values derived from those QTL models (used as inputs to GWAS) were more sensitive, resulting in substantial differences between GWAS results. The updated NAM GWAS identified several candidate genes consistent with previous QTL fine-mapping results.The highly polygenic nature of resistance to SLB complicates the identification of causal genes. Joint linkage QTL are relatively stable to perturbations of data inputs, but their resolution is generally on the order of tens or more Mbp. GWAS associations have higher resolution, but lower power due to stringent thresholds designed to minimize false positive associations, resulting in variability of detection across studies. The updated higher density linkage map improves QTL estimation and, along with a much denser SNP HapMap, greatly increases the likelihood of detecting SNPs in linkage with causal variants. We recommend use of the updated genetic resources and results but emphasize the limited repeatability of small-effect associations.}, number={1}, journal={BMC GENOMICS}, publisher={Springer Science \mathplus Business Media}, author={Bian, Yang and Yang, Qin and Balint-Kurti, Peter J. and Wisser, Randall J. and Holland, James B.}, year={2014}, month={Dec} }