Genomic variance estimates: With or without disequilibrium covariances?

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
C LehermeierC-C Schön

Abstract

Whole-genome regression methods are often used for estimating genomic heritability: the proportion of phenotypic variance that can be explained by regression on marker genotypes. Recently, there has been an intensive debate on whether and how to account for the contribution of linkage disequilibrium (LD) to genomic variance. Here, we investigate two different methods for genomic variance estimation that differ in their ability to account for LD. By analysing flowering time in a data set on 1,057 fully sequenced Arabidopsis lines with strong evidence for diversifying selection, we observed a large contribution of covariances between quantitative trait loci (QTL) to the genomic variance. The classical estimate of genomic variance that ignores covariances underestimated the genomic variance in the data. The second method accounts for LD explicitly and leads to genomic variance estimates that when added to error variance estimates match the sample variance of phenotypes. This method also allows estimating the covariance between sets of markers when partitioning the genome into subunits. Large covariance estimates between the five Arabidopsis chromosomes indicated that the population structure in the data led to strong LD also betwe...Continue Reading

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Citations

Feb 28, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sebastian MichelHermann Bürstmayr
May 26, 2018·G3 : Genes - Genomes - Genetics·Felix Enciso-RodriguezGustavo de Los Campos
Sep 13, 2017·Genetics·Hwasoon KimGustavo de Los Campos
Aug 7, 2019·Genetics·Nicholas SchreckMartin Schlather
Oct 9, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Antoine AllierLaurence Moreau
Feb 19, 2019·Plant Methods·Filipe Couto AlvesGustavo de Los Campos
Jun 29, 2018·Frontiers in Genetics·Daniel GianolaChris-Carolin Schön
Jan 23, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Antoine AllierAlain Charcosset
Nov 21, 2018·Frontiers in Plant Science·Heike MolenaarHans-Peter Piepho
Dec 13, 2019·Theoretical Population Biology·Daniel GianolaChris-Carolin Schön
Oct 15, 2020·G3 : Genes - Genomes - Genetics·Motoyuki IshimoriHiroyoshi Iwata
Aug 25, 2018·Trends in Genetics : TIG·Gustavo de Los CamposLouis Lello
Oct 1, 2019·Genetics·Nicholas SchreckMartin Schlather
Dec 17, 2021·Heredity·Letícia A de C LaraGregor Gorjanc

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