Specifically, coding SNP data from WES can be used to establish multiphasic exome analyses based on linkages and SNVs [ 4, 9].
Two tests of gene flow, one based on linkage disequilibrium and a MCMC analysis based on coalescence, suggest that the two species might be exchanging alleles at the per locus.
In this study, 2 procedures were used to analyze a data set from a whole-genome scan, one based on linkage analysis information and the other combing linkage disequilibrium and linkage analysis (LDLA), to determine the quantitative trait loci (QTL) influencing milk production traits in sheep.
Based on linkage disequilibrium and association with asthma, eight SNPs and one CpG site were selected for further analyses.
We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding.
RK undertook the event-based data linkage of transition events, refined the E strategies based on linkage comparisons, and led the analysis.
Individual Cbf genes were selected based on an expression study in rye [ 30] and linkage mapping in barley and diploid wheat [ 6, 8], Vrn1 based on linkage mapping and a real-time PCR expression study in wheat [ 18, 31], Ice2 based on an expression study in wheat [ 4], and Dhn1 and Dhn3 based on an expression study in barley [ 14].
In total 13 loci were defined of which six were based on linkage data and seven were based on cytogenetic data.
A set of markers representing the linkage map at a uniform distance of 0.2 cM was retained from the larger set of GBS SNPs scored, with missing marker data imputed based on linkage intensities and flanking non-missing markers using the Full Sib Family Haplotype Imputation algorithm [ 52].
Association analysis is based on linkage disequilibrium (LD) and complements conventional linkage mapping for the identification of genes and QTLs for traits of interest.
