The MapMaker version 3.0 computer program was used for linkage analysis.
Only the data for segregation in a 2 2 ratio in each tetrad was used for linkage analysis.
The polymorphic markers screened in bulk segregant analysis (BSA) (Michelmore et al. 1991) were used for linkage analysis and molecular mapping.
a d Phenotypes of leaf hairs in vertical (a, c) and horizontal (b, d) view of IR24 and IRGC105715 (a, b) and IR24 and IL-hairy (c, d). e Graphical genotype of IL-hairy used for linkage analysis in BC5F2.
Of the 27 InDel markers designed at regular intervals, four were polymorphic and these markers were used for linkage analysis using 151 F2:3 mapping populations similar to the earlier approaches (Jena et al. 2006; He et al. 2013; Wu et al. 2014).
A combined total of 8269 single nucleotide polymorphisms (SNPs) and microsatellite markers were used for linkage analysis.
The physical map was used for linkage analysis which enabled comparison of linkage maps of sub-populations.
To confirm whether deletions found in the BAC sequence of 11K16 occurred in other individuals, we determined genomic sequences encompassing exons 3 4 of the OnubOR5b genes using other BAC clones, as well as in one female and four male BF1 progeny from the crosses between O. nubilalis and O. scapulalis used for linkage analysis.
In a subsequent association study using the same LCL samples and HAPMAP SNP data rather than the microsatellite data used for linkage analysis, SNPs variants encompassing the TYMS gene were subsequently identified as significantly associated with 5FU cytotoxicity in the CEPH cell lines [7].
