trout {qtlbook}

Rainbow trout doubled haploid data

Description

Data from doubled haploid individuals derived from a cross between Oregon State University (OSU) and Clearwater (CW) River rainbow trout clonal lines.

Usage

trout

Format

An object of class cross. See qtl::read.cross() for details.

Details

Doubled haploid individuals were produced from a cross between Oregon State University (OSU) and Clearwater (CW) river rainbow trout (Oncorhynchus mykiss) clonal lines. Eggs from one of eight outbred females, two from Troutlodge (TL) and six from Spokane (SP), were irradiated to destroy maternal nuclear DNA and fertilized with sperm from a single F_1 male. The first embryonic cleavage was blocked by heat shock to restore diploidy. There are a total of 554 individuals, with between 8 and 168 individuals from each of the eight females.

The primary phenotype is time to hatch (tth). An additional "phenotype", female, indicates maternal cytoplasmic environment (the source of the egg).

There are genotype data on 171 markers on 28 linkage groups. The linkage groups are named as in Nichols et al. (2002), though a pair of markers are assigned to linkage group "un", as they don't connect to any of the linkage groups in Nichols et al. (2002).

Note that the data have cross type "dh" (for doubled haploids); in R/qtl they are treated just like a backcross, except that genotypes are referred to as the homozygotes.

Source

Krista M. Nichols, Department of Biological Sciences, Purdue University, [e-mail]

References

Nichols, K. M., Broman, K. W., Sundin, K., Young, J. M., Wheeler, P. A. and Thorgaard, G. H. (2007) Quantitative trait loci by maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics 175, 335–347.

Nichols, K. M., Young, W. P., Danzmann, R. G., Robison, B. D., Rexroad, C., Noakes, M., Phillips, R. B., Bentzen, P., Spies, I., Knudsen, K., Allendorf, F. W., Cunningham, B. M., Brunelli, J., Zhang, H., Ristow, S., Drew, R., Brown, K. H., Wheeler, P. A. and Thrgaard, G. H. (2002) A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34, 102–115.

See Also

link{gutlength}, link{iron}, link{myocard}, link{nf1}, link{ovar}

Examples

data(trout)
library(qtl)
plot(trout)