Browsing by Author "Whetten, Ross W."

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    Studying the Functional Genomics of Stress Responses in Loblolly Pine With the Expresso Microarray Experiment Management System
    Heath, Lenwood S.; Ramakrishnan, Naren; Sederoff, Ronald R.; Whetten, Ross W.; Chevone, Boris I.; Struble, Craig A.; Jouenne, Vincent Y.; Chen, Dawei; van Zyl, Leonel; Grene, Ruth (Hindawi, 2002-01-01)
    Conception, design, and implementation of cDNA microarray experiments present avariety of bioinformatics challenges for biologists and computational scientists. The multiplestages of data acquisition and analysis have motivated the design of Expresso, asystem for microarray experiment management. Salient aspects of Expresso includesupport for clone replication and randomized placement; automatic gridding, extraction ofexpression data from each spot, and quality monitoring; flexible methods of combiningdata from individual spots into information about clones and functional categories; and theuse of inductive logic programming for higher-level data analysis and mining. Thedevelopment of Expresso is occurring in parallel with several generations of microarrayexperiments aimed at elucidating genomic responses to drought stress in loblolly pineseedlings. The current experimental design incorporates 384 pine cDNAs replicated andrandomly placed in two specific microarray layouts. We describe the design of Expresso aswell as results of analysis with Expresso that suggest the importance of molecularchaperones and membrane transport proteins in mechanisms conferring successfuladaptation to long-term drought stress.
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    Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome
    Caballero, Madison; Lauer, Edwin; Bennett, Jeremy; Zaman, Sumaira; McEvoy, Susan; Acosta, Juan; Jackson, Colin; Townsend, Laura; Eckert, Andrew; Whetten, Ross W.; Loopstra, Carol; Holliday, Jason A.; Mandal, Mihir; Wegrzyn, Jill L.; Isik, Fikret (2021-06)
    Premise An informatics approach was used for the construction of an Axiom genotyping array from heterogeneous, high-throughput sequence data to assess the complex genome of loblolly pine (Pinus taeda). Methods High-throughput sequence data, sourced from exome capture and whole genome reduced-representation approaches from 2698 trees across five sequence populations, were analyzed with the improved genome assembly and annotation for the loblolly pine. A variant detection, filtering, and probe design pipeline was developed to detect true variants across and within populations. From 8.27 million variants, a total of 642,275 were evaluated and 423,695 of those were screened across a range-wide population. Results The final informatics and screening approach delivered an Axiom array representing 46,439 high-confidence variants to the forest tree breeding and genetics community. Based on the annotated reference genome, 34% were located in or directly upstream or downstream of genic regions. Discussion The Pita50K array represents a genome-wide resource developed from sequence data for an economically important conifer, loblolly pine. It uniquely integrates independent projects that assessed trees sampled across the native range. The challenges associated with the large and repetitive genome are addressed in the development of this resource.