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| 1 | Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death显示文摘The maize (Zea mays) spikelet consists of two florets, each of which contains three developmentally synchronized anthers. Morpho-logically, the anthers in the upper and lower florets proceed through apparently similar developmental programs. To test for global differences in gene expression and to identify genes that are coordinately regulated during maize anther development, RNA samples isolated from upper and lower floret anthers at six developmental stages were hybridized to cDNA microarrays. Approximately 9% of the tested genes exhibited statistically significant differences in expression between anthers in the upper and lower florets. This finding indicates that several basic biological processes are differentially regulated between upper and lower floret anthers, including metabolism, protein synthesis and signal transduction. Genes that are coordinately regulated across anther development were identified via cluster analysis. Analysis of these results identified stagespecific, early in development, late in development and biphasic expression profiles. Quantita-tive RT-PCR analysis revealed that four genes whose homologs in other plant species are involved in programmed cell death are upregulated just prior to the time the tapetum begins to visibly degenerate (i.e., the mid-microspore stage). This finding supports the hypothesis that developmentally normal tapetal degeneration occurs via programmed cell death. | David S. Skibbe Xiujuan Wang Lisa A. Borsuk Daniel A. Ashlock Dan Nettleton Patrick S. Schnable | 2008 | Journal of Genetics and Genomics2008，35，10： | 2 |
| 2 | Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium显示文摘 | Yanfang Wang Long Qu Jolita J. Uthe Shawn M.D. Bearson Daniel Kuhar Joan K. Lunney Oliver P. Couture Dan Nettleton Jack C.M. Dekkers Christopher K. Tuggle | 2007 | Genomics2007，，1： | 1 |
| 3 | Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture显示文摘 | Ping Che Sonia Lall Dan Nettleton | 2006 | Plant Physiology2006，141，： | 1 |
| 4 | KAT4IA:K-Means Assisted Training for Image Analysis of Field-Grown Plant Phenotypes显示文摘High-throughput phenotyping enables the efficient collection of plant trait data at scale.One example involves using imaging systems over key phases of a crop growing season.Although the resulting images provide rich data for statistical analyses of plant phenotypes,image processing for trait extraction is required as a prerequisite.Current methods for trait extraction are mainly based on supervised learning with human labeled data or semisupervised learning with a mixture of human labeled data and unsupervised data.Unfortunately,preparing a sufficiently large training data is both time and labor-intensive.We describe a self-supervised pipeline(KAT4IA)that uses K-means clustering on greenhouse images to construct training data for extracting and analyzing plant traits from an image-based field phenotyping system.The KAT4IA pipeline includes these main steps:self-supervised training set construction,plant segmentation from images of field-grown plants,automatic separation of target plants,calculation of plant traits,and functional curve fitting of the extracted traits.To deal with the challenge of separating target plants from noisy backgrounds in field images,we describe a novel approach using row-cuts and column-cuts on images segmented by transform domain neural network learning,which utilizes plant pixels identified from greenhouse images to train a segmentation model for field images.This approach is efficient and does not require human intervention.Our results show that KAT4IA is able to accurately extract plant pixels and estimate plant heights. | Xingche Guo Yumou Qiu Dan Nettleton Cheng-Ting Yeh Zihao Zheng Stefan Hey Patrick SSchnable | 2021 | Plant Phenomics2021，3，1： | 0 |
| 5 | Flor Revisited(Again):eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley显示文摘Genes encoding early signaling events in pathogen defense often are identif ied only by their phenotype.Such genes involved in barley-powdery mildew interactions include Mla,specifying race-specif ic resistance;Rar1(Required for Mla12-specif ied resistance1),and Rom1(Restoration of Mla-specif ied resistance1).The HSP90-SGT1-RAR1 complex appears to function as chaperone in MLA-specified resistance,however,much remains to be discovered regarding the precise signaling underlying plant immunity.Genetic analyses of fast-neutron mutants derived from CI 16151(Mla6)uncovered a novel locus,designated Rar3(Required for Mla6-specified resistance3).Rar3 segregates independent of Mla6 and Rar1,and rar3 mutants are susceptible to Blumeria graminis f.sp.hordei(Bgh)isolate 5874(AVR a6),whereas,wild-type progenitor plants are resistant.Comparative expression analyses of the rar3 mutant vs.its wild-type progenitor were conducted via Barley1 GeneChip and GAIIx paired-end RNA-Seq.Whereas Rar1 affects transcription of relatively few genes;Rar3 appears to inf luence thousands,notably in genes controlling ATP binding,catalytic activity,transcription,and phosphorylation;possibly membrane bound or in the nucleus.eQTL analysis of a segregating doubled haploid population identified over two-thousand genes as being regulated by Mla(q value/FDR=0.00001),a subset of which are signif icant in Rar3 interactions.The intersection of datasets derived from mla-loss-of-function mutants,Mla-associated eQTL,and rar3-mediated transcriptome reprogramming are narrowing the focus on essential genes required for Mla-specified immunity. | Roger Wise Priyanka Surana Greg Fuerst Ruo Xu Divya Mistry Julie Dickerson Dan Nettleton | 2014 | Journal of Integrative Agriculture2014，13，2： | 0 |
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