The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Jeremy T Brawner; S K Dillon; David J Lee; Roger Meder; M J Dieters; S G Southerton

doi:10.1007/s11295-012-0530-7

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The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Journal article

Peer reviewed

The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Jeremy T Brawner, S K Dillon, David J Lee, Roger Meder, M J Dieters and S G Southerton

Tree Genetics & Genomes, Vol.8(6), pp.1423-1435

2012

DOI: https://doi.org/10.1007/s11295-012-0530-7

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Abstract

genetic correlation

tests of association

single nucleotide polymorphism (SNP)

Corymbia

Open-pollinated progeny of Corymbia citriodora established in replicated field trials were assessed for stem diameter, wood density, and pulp yield prior to genotyping single nucleotide polymorphisms (SNP) and testing the significance of associations between markers and assessment traits. Multiple individuals within each family were genotyped and phenotyped, which facilitated a comparison of standard association testing methods and an alternative method developed to relate markers to additive genetic effects. Narrow-sense heritability estimates indicated there was significant additive genetic variance within this population for assessment traits (bh 2 ¼ 0:28 to 0:44) and genetic correlations between the three traits were negligible to moderate (rG00.08 to 0.50). The significance of association tests (p values) were compared for four different analyses based on two different approaches: (1) two software packages were used to fit standard univariate mixed models that include SNP-fixed effects, (2) bivariate and multivariate mixed models including each SNP as an additional selection trait were used. Within either the univariate or multivariate approach, correlations between the tests of significance approached +1; however, correspondence between the two approaches was less strong, although between-approach correlations remained significantly positive. Similar SNP markers would be selected using multivariate analyses and standard marker-trait association methods, where the former facilitates integration into the existing genetic analysis systems of applied breeding programs and may be used with either single markers or indices of markers created with genomic selection processes.

Details

Title: The use of genetic correlations to evaluate associations between SNP markers and quantitative traits
Authors: Jeremy T Brawner (Author) - CSIRO Plant Industry
S K Dillon (Author) - CSIRO Plant Industry
David J Lee (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Roger Meder (Author) - CSIRO Plant Industry
M J Dieters (Author) - University of Queensland
S G Southerton (Author) - CSIRO Plant Industry
Publication details: Tree Genetics & Genomes, Vol.8(6), pp.1423-1435
Publisher: Springer
DOI: 10.1007/s11295-012-0530-7
ISSN: 1614-2942
Organisation Unit: Tropical Forests & People Research Centre; University of the Sunshine Coast, Queensland; Forest Industries Research Centre; Forest Research Institute
Language: English
Record Identifier: 99450220302621
Output Type: Journal article

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Collaboration types: Domestic collaboration
Web Of Science research areas: Forestry; Genetics & Heredity; Horticulture

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