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Caballero M, Lauer E, Bennett J, et al. Toward genomic selection in . Appl Plant Sci. 2021;9(6):e11439doi: 10.1002/aps3.11439.
Caballero, M., Lauer, E., Bennett, J., Zaman, S., McEvoy, S., Acosta, J., Jackson, C., Townsend, L., Eckert, A., Whetten, R. W., Loopstra, C., Holliday, J., Mandal, M., Wegrzyn, J. L., & Isik, F. (2021). Toward genomic selection in . Applications in plant sciences, 9(6), e11439. https://doi.org/10.1002/aps3.11439
Caballero, Madison, et al. "Toward genomic selection in ." Applications in plant sciences vol. 9,6 (2021): e11439. doi: https://doi.org/10.1002/aps3.11439
Caballero M, Lauer E, Bennett J, Zaman S, McEvoy S, Acosta J, Jackson C, Townsend L, Eckert A, Whetten RW, Loopstra C, Holliday J, Mandal M, Wegrzyn JL, Isik F. Toward genomic selection in . Appl Plant Sci. 2021 Jul 02;9(6):e11439. doi: 10.1002/aps3.11439. eCollection 2021 Jun. PMID: 34268018; PMCID: PMC8272584.
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Appl Plant Sci. 2021 Jul 02;9(6):e11439. doi: 10.1002/aps3.11439. eCollection 2021 Jun.

Toward genomic selection in .

Applications in plant sciences

Madison Caballero, Edwin Lauer, Jeremy Bennett, Sumaira Zaman, Susan McEvoy, Juan Acosta, Colin Jackson, Laura Townsend, Andrew Eckert, Ross W Whetten, Carol Loopstra, Jason Holliday, Mihir Mandal, Jill L Wegrzyn, Fikret Isik

Affiliations

  1. Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut 06269 USA.
  2. Department of Forestry and Environmental Resources North Carolina State University Raleigh North Carolina 27695 USA.
  3. Department of Biology Virginia Commonwealth University Richmond Virginia 23284 USA.
  4. Department of Ecology and Conservation Biology Texas A&M University College Station Texas 77843 USA.
  5. Department of Forest Resources and Environmental Conservation Virginia Polytechnic Institute and State University Blacksburg Virginia 24061 USA.
  6. Department of Biology Claflin University Orangeburg South Carolina 29115 USA.

PMID: 34268018 PMCID: PMC8272584 DOI: 10.1002/aps3.11439

Abstract

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 (

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.

© 2021 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.

Keywords: Pinus taeda; exome capture; genomic selection; genotype array; genotyping‐by‐sequencing (GBS); loblolly pine; variant detection

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