means_floweringTime {heritability}

Flowering time from Atwell et al. (2010): accession means.

Description

Accession means for the flowering time data contained in LD and LDV.

Usage

data(means_LD); data(means_LDV)

Format

Data-frames with flowering time means:

genotype

a factor, the levels being the accession or ecotype identifiers

LD

Flowering time under long days, in number of days

LDV

Flowering time under long days and vernalization, in number of days

Details

Following Kruijer et al. (appendix A) these means were defined as the least-squares estimate for the factor accession, in a linear model containing both accession and replicate effects. Consequently there are differences compared to Atwell et al. (2010), where just the arithmetic averages are considered.

References

• Atwell, S., Y. S. Huang, B. J. Vilhjalmsson, G. Willems, M. Horton, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.

• Kruijer, W. et al. (2015) Marker-based estimation of heritability in immortal populations. Genetics, Vol. 199(2), p. 1-20.

See Also

Together with the covariance matrices contained in R_matrix_LD and R_matrix_LDV, the means contained in means_LD and means_LDV can be used to estimate heritability, using the function marker_h2_means. For the corresponding genetic relatedness matrix, see K_atwell. For the individual plant data, see floweringTime.

Examples

data(means_LD)
data(means_LDV)