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Improving lodgepole pine genomic evaluation using spatial correlation structure and SNP selection with single-step GBLUP.
Cappa, Eduardo P; Ratcliffe, Blaise; Chen, Charles; Thomas, Barb R; Liu, Yang; Klutsch, Jennifer; Wei, Xiaojing; Azcona, Jaime Sebastian; Benowicz, Andy; Sadoway, Shane; Erbilgin, Nadir; El-Kassaby, Yousry A.
Afiliação
  • Cappa EP; Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, De Los Reseros y Dr. Nicolás Repetto s/n, 1686, Hurlingham, Buenos Aires, Argentina. cappa.eduardo@inta.gob.ar.
  • Ratcliffe B; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. cappa.eduardo@inta.gob.ar.
  • Chen C; Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
  • Thomas BR; Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
  • Liu Y; Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB, T6G 2E3, Canada.
  • Klutsch J; Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
  • Wei X; Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB, T6G 2E3, Canada.
  • Azcona JS; Department of Forestry, New Mexico Highlands University, Las Vegas, NM, 87701, USA.
  • Benowicz A; Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB, T6G 2E3, Canada.
  • Sadoway S; Department of Renewable Resources, University of Alberta, 442 Earth Sciences Bldg., Edmonton, AB, T6G 2E3, Canada.
  • Erbilgin N; Forest Stewardship and Trade Branch, Alberta Agriculture and Forestry, Edmonton, AB, T6H 5T6, Canada.
  • El-Kassaby YA; Blue Ridge Lumber Inc., West Fraser Mills Ltd, Unnamed Road, Blue Ridge, AB, T0E 0B0, Canada.
Heredity (Edinb) ; 128(4): 209-224, 2022 04.
Article em En | MEDLINE | ID: mdl-35181761
ABSTRACT
Modeling environmental spatial heterogeneity can improve the efficiency of forest tree genomic evaluation. Furthermore, genotyping costs can be lowered by reducing the number of markers needed. We investigated the impact on variance components, breeding value accuracy, and bias of two phenotypic data adjustments (experimental design and autoregressive spatial models), and a relationship matrix calculated from a subset of markers selected for their ability to infer ancestry. Using a multiple-trait multiple-site single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) approach, four scenarios (2 phenotype adjustments × 2 marker sets) were applied to diameter at breast height (DBH), height (HT), and resistance to western gall rust (WGR) in four open-pollinated progeny trials of lodgepole pine, with 1490 (out of 11,188) trees genotyped with 25,099 SNPs. As a control, we fitted the conventional ABLUP model using pedigree information. The highest heritability estimates were achieved for the ABLUP followed closely by the ssGBLUP with the full marker set and using the spatial phenotype adjustments. The highest predictive ability was obtained by using a reduced marker subset (8000 SNPs) when either the spatial (DBH 0.429, and WGR 0.513) or design (HT 0.467) phenotype corrections were used. No significant difference was detected in prediction bias among the six fitted models, and all values were close to 1 (0.918-1.014). Results demonstrated that selecting informative markers, such as those capturing ancestry, can improve the predictive ability. The use of spatial correlation structure increased traits' heritability and reduced prediction bias, while increases in predictive ability were trait-dependent.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Polimorfismo de Nucleotídeo Único / Pinus Tipo de estudo: Prognostic_studies Idioma: En Revista: Heredity (Edinb) Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Argentina

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Polimorfismo de Nucleotídeo Único / Pinus Tipo de estudo: Prognostic_studies Idioma: En Revista: Heredity (Edinb) Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Argentina