Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. 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. Applications in Plant Sciences, 9(6):e11439, 2021. _eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.11439![Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 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.
@article{caballero_toward_2021,
title = {Toward genomic selection in {Pinus} taeda: {Integrating} resources to support array design in a complex conifer genome},
volume = {9},
copyright = {© 2021 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America},
issn = {2168-0450},
shorttitle = {Toward genomic selection in {Pinus} taeda},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11439},
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 (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.},
language = {en},
number = {6},
urldate = {2026-01-16},
journal = {Applications in Plant Sciences},
author = {Caballero, Madison and Lauer, Edwin and Bennett, Jeremy and Zaman, Sumaira and McEvoy, Susan and Acosta, Juan and Jackson, Colin and Townsend, Laura and Eckert, Andrew and Whetten, Ross W. and Loopstra, Carol and Holliday, Jason and Mandal, Mihir and Wegrzyn, Jill L. and Isik, Fikret},
year = {2021},
note = {\_eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.11439},
keywords = {Pinus taeda, exome capture, genomic selection, genotype array, genotyping-by-sequencing (GBS), loblolly pine, variant detection},
pages = {e11439},
}
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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. 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Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America},\n\tissn = {2168-0450},\n\tshorttitle = {Toward genomic selection in {Pinus} taeda},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11439},\n\tdoi = {10.1002/aps3.11439},\n\tabstract = {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. 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