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3 results on '"Holliday, Jason A."'

1. Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome

Author

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, Mandal, Mihir, Wegrzyn, Jill L, and Isik, Fikret

Subjects
Agricultural, Veterinary and Food Sciences, Crop and Pasture Production, Human Genome, Genetics, Biotechnology, exome capture, genomic selection, genotype array, genotyping-by-sequencing, loblolly pine, Pinus taeda, variant detection, genotyping‐by‐sequencing, Crop and pasture production
Abstract

PremiseAn 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).MethodsHigh-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.ResultsThe 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.DiscussionThe 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.

Published
2021

2. Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

Author

Guerra, Fernando P, Suren, Haktan, Holliday, Jason, Richards, James H, Fiehn, Oliver, Famula, Randi, Stanton, Brian J, Shuren, Richard, Sykes, Robert, Davis, Mark F, and Neale, David B

Subjects
Populus, Plant Leaves, Carbon, Nitrogen, Lignin, Genetic Markers, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Genome, Plant, Wood, California, Metabolic Networks and Pathways, Genome-Wide Association Study, Metabolome, Whole Exome Sequencing, Cellulose, GWAS, Growth, Sequence capture, Stable isotopes, Wood metabolome, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Genome, Plant, Human Genome, Genetics, Biological Sciences, Medical and Health Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value

Published
2019

3. Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa.

Author

Guerra, Fernando P, Suren, Haktan, Holliday, Jason, Richards, James H, Fiehn, Oliver, Famula, Randi, Stanton, Brian J, Shuren, Richard, Sykes, Robert, Davis, Mark F, and Neale, David B

Subjects
Populus, Plant Leaves, Carbon, Nitrogen, Lignin, Genetic Markers, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Genome, Plant, Wood, California, Metabolic Networks and Pathways, Genome-Wide Association Study, Metabolome, Whole Exome Sequencing, Cellulose, GWAS, Growth, Sequence capture, Stable isotopes, Wood metabolome, Exome Sequencing, Human Genome, Genetics, Affordable and Clean Energy, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundPopulus trichocarpa is an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461 P. trichocarpa clones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value

Published
2019

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