means_floweringTime function

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

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

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)