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

Brawner, J. T. and Dillon, S. K. and Lee, D. J. and Meder, A. R. and Dieters, M. J. and Southerton, SimonG (2012) The use of genetic correlations to evaluate associations between SNP markers and quantitative traits. Tree Genetics & Genomes, 8 (6). pp. 1423-1435. ISSN 1614-2942

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Article Link(s): http://dx.doi.org/10.1007/s11295-012-0530-7

Abstract

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 ( h ˆ 2 =0.28to0.44 ) and genetic correlations between the three traits were negligible to moderate (r G = 0.08 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.

Item Type:Article
Business groups:Horticulture and Forestry Science
Additional Information:Tree Genetics & Genomes
Keywords:Genetic correlation Tests of association Single nucleotide polymorphism (SNP) Corymbia
Subjects:Forestry > Research. Experimentation
Science > Botany > Genetics
Deposited On:10 Apr 2014 02:45
Last Modified:10 Apr 2014 02:45

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