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Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits.
Chhetri, Hari B; Macaya-Sanz, David; Kainer, David; Biswal, Ajaya K; Evans, Luke M; Chen, Jin-Gui; Collins, Cassandra; Hunt, Kimberly; Mohanty, Sushree S; Rosenstiel, Todd; Ryno, David; Winkeler, Kim; Yang, Xiaohan; Jacobson, Daniel; Mohnen, Debra; Muchero, Wellington; Strauss, Steven H; Tschaplinski, Timothy J; Tuskan, Gerald A; DiFazio, Stephen P.
Afiliación
  • Chhetri HB; Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.
  • Macaya-Sanz D; Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.
  • Kainer D; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Biswal AK; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
  • Evans LM; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
  • Chen JG; Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.
  • Collins C; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Hunt K; ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.
  • Mohanty SS; ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.
  • Rosenstiel T; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
  • Ryno D; Department of Biology, Portland State University, Portland, OR, 97207, USA.
  • Winkeler K; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
  • Yang X; ArborGen, Inc., 2011 Broadbank Ct., Ridgeville, SC, 29472, USA.
  • Jacobson D; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Mohnen D; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Muchero W; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
  • Strauss SH; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
  • Tschaplinski TJ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
  • Tuskan GA; Department of Forest Ecosystems & Society, Oregon State University, Corvallis, OR, 97331, USA.
  • DiFazio SP; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
New Phytol ; 223(1): 293-309, 2019 07.
Article en En | MEDLINE | ID: mdl-30843213
Genome-wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)-phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole-genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad-sense heritability (H2 ) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single-trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co-expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single-trait association, potentially revealing pleiotropic effects of individual genes. This approach can be particularly useful for challenging physiological traits such as water-use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co-expression and co-methylation data.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Carácter Cuantitativo Heredable / Polimorfismo de Nucleótido Simple / Populus / Estudio de Asociación del Genoma Completo Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: New Phytol Asunto de la revista: BOTANICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Carácter Cuantitativo Heredable / Polimorfismo de Nucleótido Simple / Populus / Estudio de Asociación del Genoma Completo Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: New Phytol Asunto de la revista: BOTANICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido