Generation F8 of an advanced intercross line between Red Junglefowl and White Leghorn chickens: one Red Junglefowl male crossed with three White Leghorn females, then kept as a closed line of about 100 birds per generation with no backcrossing. Every bird is eight generations from the pure parents.
Format
A list with:
- genotypes
Integer matrix, 572 birds x 514 autosomal SNPs, counting White Leghorn (species 2) alleles (0, 1, 2;
NAmissing).- groups
"F8"for every bird. No pure birds were genotyped.- map
Data frame with
snp,chromosome,position(cM per meiosis, approximate: the authors' F8 map divided by 3.09, their genome-wide map expansion over eight generations) andposition_f8(cM on the authors' F8 map).- truth
Data frame with
group,n,generation,hybrid_age(8),backcrosses(0) andbreeders.- description
A short description.
Source
Johnsson M (2017) Open field phenotypes and genotypes (R/qtl csv format). figshare, doi:10.6084/m9.figshare.1265060 . CC0 1.0.
Truth
All birds are F8, so the hybrid age is 8, with no backcrosses and no arrivals. The line was kept at about 100 birds per generation from F3 to F7 and produced the F8 from 122 F7 parents; the mating scheme is not reported. The loss of heterozygosity (mean H about 0.47 instead of 0.5) suggests about 50 effective breeders. The founders were outbred, so not every marker was fixed between them, which also lowers H. Which allele is White Leghorn is not stated by the authors; it was inferred from the Z chromosome (excluded here), where White Leghorn alleles make up one third of copies because of the direction of the founding cross.
Licence
The genotypes are from figshare and were released under CC0 1.0 (public domain dedication). Markers with partial calls, on the Z chromosome or on an unplaced scaffold were dropped, and genotypes were recoded.
References
Johnsson M, Williams MJ, Jensen P, Wright D (2016) Genetical genomics of behavior: a novel chicken genomic model for anxiety behavior. Genetics 202:327-340. doi:10.1534/genetics.115.179010
Johnsson M, Gustafson I, Rubin C-J, et al. (2012) A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication. PLoS Genetics 8:e1002914. doi:10.1371/journal.pgen.1002914
Examples
# every SNP already counts White Leghorn alleles
g <- chickens$genotypes
mk <- data.frame(column = seq_len(ncol(g)), name = colnames(g), flip = FALSE,
freq1 = 0, freq2 = 1)
sc <- hybrid_scores(g, mk)
colMeans(sc[, c("S", "H")])
#> S H
#> 0.4774355 0.4719910