Walia Lab

University of Nebraska Lincoln

    2020

  • Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H. BMC Genomics. 2020
  • Leveraging genome-enabled growth models to study shoot growth responses to water deficit in rice (Oryza sativa). Campbell MT, Grondin A, Walia H, Morota G. Journal of Experimental Botany. 2020
  • The Lateral Root Density gene regulates root growth during water stress in wheat. Placido DF, Sandhu J, Sato SJ, Nersesian N, Quach T, Clemente TE, Staswick P, Walia H. Plant Biotechnology Journal. 2020
  • Variance heterogeneity genome‐wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions. Hussain W, Campbell MT, Diego J, Walia H, Morota G. BMC Genomics. 2020
  • Multi-trait random regression models increase genomic prediction accuracy for a temporal physiological trait derived from high-throughput phenotyping. Baba T, Momen M, Campbell MT, Walia H, Morota G. PLOS One. 2020
  • Divergent phenotypic response of rice accessions to transient heat stress during early seed development. Paul P, Dhatt BK, Sandhu J, Hussain W, Irvin L, Morota G, Staswick P, Walia H. Plant Direct. 2020
  • MADS78 and MADS79 are essential regulators of early seed development in rice. Paul P, Dhatt BK, Miller M, Folsom JJ, Wang Z, Krassovskaya I, Liu K, Sandhu J, Yu H, Zhang C, Obata T, Staswick P, Walia H. Plant Physiology. 2020
  • High night temperature induced changes in grain starch metabolism alters starch, protein, and lipid accumulation in winter wheat. Impa SM, Vennapusa AR, Bheemanahalli R, Sabela D, Boyle D, Walia H, Jagadish SVK. Plant Cell and Environment. 2020
  • 2019

  • PI-Plat: A high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits. Sandhu J, Zhu F, Paul P, Gao T, Dhatt BK, Ge Y, Staswick P, Yu H, Walia H. Plant Methods. 2019
  • Metabolic Dynamics of Developing Rice Seeds Under High Night-Time Temperature Stress. Dhatt BK, Abshire N, Paul P, Hasanthika K, Sandhu J, Zhang Q, Obata T, Walia H. Frontiers of Plant Science. 2019
  • Plant Event Detection from Time-Varying Point Clouds. Gao T, Sun J, Zhu F, Doku H, Pan Y, Walia H, Yu H. IEEE International Conference on Big Data. 2019
  • Interactive Visualization of Time-Varying Hyperspectral Plant Images for High-Throughput Phenotyping. Zhu F, Pan Y, Gao T, Walia H, Yu H. IEEE International Conference on Big Data. 2019
  • Utilizing trait networks and structural equation models as tools to interpret multi-trait genome-wide association studies. Momen M, Campbell MT, Walia H, Morota G. Plant Methods. 2019
  • Predicting Longitudinal Traits Derived from High-Throughput Phenomics in Contrasting Environments Using Genomic Legendre polynomials and B-splines. Momen M, Campbell MT, Walia H, Morota G. G3: Genes, Genomes, Genetics. 2019
  • Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. Du Q, Campbell MT, Yu H, Liu K, Walia H, Zhang Q, Zhang C. Plant Direct. 2019
  • Leveraging breeding values obtained from random regression models for genetic inference of longitudinal traits. Campbell MT, Walia H, Morota G. The Plant Genome. 2019
  • Genomic Bayesian confirmatory factor analysis and Bayesian network to characterize a wide spectrum of rice phenotypes. Yu H, Campbell MT, Zhang Q, Walia H, Morota G. G3: Genes, Genomes, Genetics. 2019
  • Gene Expression analysis associated with salt stress in a reciprocally crossed rice population. Razzaque S, Elias SM, Haque T, Biswas S, Jewel GMNA, Rahman S, Weng X, Ismail AM, Walia H, Juenger TE, Seraj ZI. Scientific Reports. 2019
  • 2018

  • Utilizing random regression models for genomic prediction of a longitudinal trait derived from high-throughput phenotyping. Campbell MT, Walia H, Morota G. Plant Direct. 2018
  • 3D Reconstruction of Plant Leaves for High-Throughput Phenotyping. Zhu F, Thapa S, Gao T, Ge Y, Walia H, Yu H IEEE Big Data Conference. 2018
  • Transient Heat Stress During Early Seed Development Primes Germination and Seedling Establishment in Rice. Begcy K, Sandhu J, Walia H. Frontiers in Plant Science. 2018
  • ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies. Hussain W, Campbell MT, Walia H, Morota G. Plant Direct. 2018
  • 2017-

  • A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa). Campbell MT, Du Q, Liu K, Brien CJ, Berger B, Zhang C, Walia H. Plant Genome. 2017
  • Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. Campbell MT, Bandillo N, Al Shiblawi FRA, Sharma S, Liu K, Du Q, Schmitz AJ, Zhang C, Véry AA, Lorenz AJ, Walia H. PLoS Genetics. 2017
  • Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice. Razzaque S, Haque T, Elias SM, Rahman MS, Biswas S, Schwartz S, Ismail AM, Walia H, Juenger TE, Seraj ZI. Scientific Reports. 2017
  • Image Harvest: an open-source platform for high-throughput plant image processing and analysis. Knecht AC, Campbell MT, Caprez A, Swanson DR, Walia H. J Exp Bot. 2016
  • Heat stress yields a unique MADS box transcription factor in determining seed size and thermal sensitivity. Chen C, Begcy K, Liu K, Folsom JJ, Wang Z, Zhang C, Walia H. Plant Physiology. 2016
  • Schmitz AJ, Begcy K, Sarath G, Walia H. Rice Ovate Family Protein 2 (OFP2) alters hormonal homeostasis and vasculature development. Plant Science. 2015
  • Begcy K, Walia H. Drought stress delays endosperm development and misregulates genes associated with cytoskeleton organization and grain quality proteins in developing wheat seeds. Plant Sciemce. 2015
  • Campbell MT, Proctor CA, Dou Y, Schmitz AJ, Phansak P, Kruger GR, Zhang C, Walia H. Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize. 2015, Plos One.
  • Campbell MT, Knecht AC, Berger B, Brien CJ, Wang D, Walia H. Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice. 2015, Plant Physiology.
  • Folsom, J.J., Begcy, K., Xiaojuan, H., Wang, D., Walia H., Rice FIE1 regulates seed size under heat stress by controlling early endosperm development. 2014, Plant Physiology
  • Placido D. F., Campbell M. T., Jin J., Cui X., Kruger G. R., Baenziger P. S., Walia H., Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat (Triticum aestivum). 2013, Plant Physiology
  • Schmitz A., Jin J., Jikamaru Y., Ronald P., Walia H., SUB1A-mediated submergence tolerance response in rice involves differential regulation of the brassinosteroid pathway. 2013, New Phytologist
  • Seo Y.S., Chern M., Bartley L.E., Han M., Jung K.H., Lee I., Walia H., Richter T., Xu X., Cao P., Bai W., Ramanan R., Amonpant F., Arul L., Canlas P.E., Ruan R., Park C.J., Chen X., Hwang S., Jeon J.S., Ronald P.C.,Towards establishment of a rice stress response interactome. 2011, PLoS Genetics
  • Peleg Z., Reguera M., Walia H., Blumwald E., Cytokinin mediated source-sink modifications improve drought tolerance and increase grain yield in rice under water stress. 2011, Plant Biotechnology Journal 9(7):747-58
  • Rivero R.M., Gimeno J., Van Deynze A., Walia H., Blumwald E., Enhanced cytokinin synthesis in tobacco plants expressing SARK::IPT prevents the degradation of photosynthetic protein complexes during drought. 2010, Plant and Cell Physiology 51(11):1929-41
  • Cotsaftis O., Plett D., Johnson A.T., Walia H., Wilson C., Ismail A.M., Close T.J., Tester M., Baumann U., Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. 2010, Molecular Plant
  • Laurent J., Vogel C., Kwon T., Craig S.A., Boutz D.R., Huse H.K., Nozue K., Walia H., Whiteley M., Ronald P.C., Marcotte E.M., Protein abundances are more conserved than mRNA abundances across diverse taxa. 2010, Proteomics
  • Jung, K.H., Seo, Y.S., Walia, H., Cao, P., Fukao, T., Canlas, P., Amonpant, F., Bailey-Serres, J., Ronald, P.C., The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcriptional factor. 2010, Plant Physiology 152(3):1674-92
  • Walia, H., Wilson, C., Ismail, A., Close, T.J., Cui, X., Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. 2009, BMC Genomics 10:398
  • Walia, H., Josefsson, C., Dilkes, B., Kirkbride, R., Harada, J., Comai, L., Dosage-dependent deregulation of an AGAMOUS-LIKE GENES cluster contributes to interspecific incompatibility. 2009, Current Biology 19(13):1128-1132
  • Kim, S.-H., Bhat P.R., Cui, X., Walia, H., Xu, J., Wanamaker, S., Ismail, A., Wilson, C., Close, T.J., Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. 2009, BMC Plant Biology 9(1):65
  • Walia, H., Wilson, C., Condamine, P., Ismail, A., Zeng, L., Xu, J., Cui, X., Close, T.J., Array-Based Genotyping and Expression Analysis of Barley cv. Maythorpe and Golden Promise. 2007, BMC Genomics 8:84
  • Walia, H., Wilson, C., Liu, X., Ismail, A., Close, T.J., Transcriptional profiling of rice under salinity stress during panicle initiation stage. 2007, Plant Molecular Biology, 63(5): 609-623
  • Walia, H., Wilson, C., Condamine, P., Liu, X., Close, T.J., Role of jasmonic acid in improving salinity tolerance of barley revealed by physiological and large scale gene expression studies. 2007, Plant, Cell and Environment 30(4): 410-421
  • Walia, H., Wilson, C., Wahid, A., Cui, X., Wanamaker, S., Close, T.J., Expression profiling of barley (Hordeum vulgare L.) under salinity stress. 2006, Functional and Integrative Genomics 6: 143-153
  • Walia, H., Wilson, C., Condamine, P., Liu, X., Ismail, A., Zeng, L., Wanamaker, S. I., Mandal, J., Cui, X., Xu, J., Close, T.J., Comparative transcriptional profiling of two contrasting rice (Oryza sativa L.) genotypes under salinity stress during vegetative growth stage. 2005, Plant Physiology 139: 822-835
  • Rostoks, N., Mudie, S., Cardle, L., Russell, J., Ramsay, L., Svensson J.T., Wanamaker S., Walia H., Rodriguez E., Hedley P., Liu H., Close T.J., Marshall D., Waugh R., SNP-based barley integrated linkage map developed from genes responsive to abiotic stress identifies regions of conserved synteny in barley and rice. 2005, Mol Genet Genomics 274(5): 515-527