K_arabidopsis: Marker-based relatedness matrices for 3 populations of...

In heritability: Marker-Based Estimation of Heritability Using Individual Plant or Plot Data

Marker-based relatedness matrices for 3 populations of Arabidopsis thaliana.

Description

Marker-based relatedness matrices based on the SNP-data from Horton et al. (2012). Three matrices are provided: (a) K_atwell, for the 199 accessions studied in Atwell et al. (2010). (b) K_hapmap, for a subset of 350 accessions taken from the Arabidopsis hapmap (Li et al., 2010). (c) K_swedish, for 304 Swedish accessions. All of these are part of the world-wide regmap of 1307 accessions, described in Horton et al. (2012).

Usage

data(K_atwell); data(K_hapmap); data(K_swedish)

Format

Matrices whose row- and column names are the ecotype or seed-stock IDs of the accessions.

Details

The matrices were computed using equation (2.2) in Astle and Balding (2009); see also Goddard et al. (2009). The heritability-package does not contain functions to construct relatedness matrices from genotypic data, but such functions can be found in many other software packages. For example, GCTA (Yang et al., 2011), LDAK (Speed et al., 2012), Fast-LMM (Lippert, 2011) and GEMMA (Zhou and Stephens, 2012).

References

• W. Astle and D.J. Balding (2009) Population Structure and Cryptic Relatedness in Genetic Association Studies. Statistical Science, Vol. 24, No. 4, 451-471.

• 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.

• Goddard, M.E., Naomi R. Wray, Klara Verbyla and Peter M. Visscher (2009) Estimating Effects and Making Predictions from Genome-Wide Marker Data. Statistical Science, Vol. 24, No. 4, 517-529.

• Horton, M. W., A. M. Hancock, Y. S. Huang, C. Toomajian, S. Atwell, et al. (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nature Genetics 44: 212-216.

• Li, Y., Y. Huang, J. Bergelson, M. Nordborg, and J. O. Borevitz (2010) Association mapping of local climate-sensitive quantitative trait loci in arabidopsis thaliana. PNAS vol. 107, number 49.

• Lippert, C., J. Listgarten, Y. Liu, C.M. Kadie, R.I. Davidson, et al. (2011) FaST linear mixed models for genome-wide association studies. Naure methods 8: 833-835.

• Speed, D., G. Hemani, M. R. Johnson, and D.J. Balding (2012) Improved heritability estimation from genome-wide snps. the American journal of human genetics 91: 1011-1021.

• Yang, J., S.H. Lee, M.E. Goddard, and P.M. Visscher (2011) GCTA: a tool for genomewide complex trait analysis. the American journal of human genetics 88: 76-82.

• Zhou, X., and M. Stephens, (2012) Genome-wide efficient mixed-model analysis for association studies. Nature genetics 44: 821-824.

See Also

For phenotypic data for the population described in Atwell et al. (2010), see LD and LDV. For phenotypic data for the hapmap, see BT_LW_H and LA_H. For phenotypic data for the Swedish regmap, see LA_S.

Examples

data(K_atwell)
data(K_hapmap)
data(K_swedish)

heritability documentation built on Aug. 24, 2023, 9:08 a.m.