These scores were then tested for association with skin lesion status using mixed linear regression models adjusting for sex, age, and genotyping batch implemented in genome-wide efficient mixed model association (GEMMA) (Zhou and Stephens 2012).
Orthologs of TFs were identified by a procedure based on the analysis of phylogenetic trees for protein domains in MicrobesOnline [ 54] and validated by bidirectional genome-wide similarity searches with 30% of identity threshold using the Smith-Waterman algorithm implemented in the Genome Explorer program [ 58].
Reciprocal BLASTing was implemented in SEED genome viewer for each ORF that differed between isolates to identify functional homologs.
NtRFC1 has been implemented in maintaining genome stability and transcriptional gene silencing [ 45], and thus could function to repress the expression of germ-cell genes within the vegetative cell and simultaneously to regulate the tobacco germ-cell chromatin status.
Data were analyzed using the mixed linear model (MLM) in efficient mixed-model association (EMMA) as implemented in the genome association and prediction integrated tool (GAPIT) in R (Lipka et al. 2012) using a marker-based kinship matrix derived within GAPIT from a subset of 927 markers giving a minimum inter-marker distance of 1 cM.
The latter methodology, sequencing-by-synthesis, is implemented in the Genome Sequencer GS-FLX System (454 Life Sciences), which produces several hundred thousand DNA reads of at least 200 bp; this is done by monitoring the release of pyrophosphate during the growth of a DNA chain driven by a DNA polymerase [ 6].
Such methods have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates.
These methods have been most successfully implemented in fungal genomes [ 3, 4], and have long been used in prokaryotic genomes [ 5, 6], where gene order is far less variable than in eukaryotes.
Second, we use the method of Yang et al. (2010) as implemented in the Genome-wide Complex Trait Analysis (GCTA) software (Yang et al. 2011).
A LMM is used to estimate the PVE by measured SNPs for a phenotype, as implemented in the Genome-wide Complex Trait Analysis (GCTA) software package (Yang et al. 2011).
Number and distribution of SNPs was determined using the Probabilistic variant detection plug-in with default settings with L1, L17 and L71 reads mapped to a reference genome, as implemented in CLC genomics workbench.
