Theoretically, allele frequencies from the unselected base population should be used to construct G [ 20], which could be estimated after using linear regression to predict gene content (number of copies of a particular allele in a genotype of an individual) of non-genotyped ancestors, based on the available information of genotypes and pedigree [ 22].
If phase information of genotypes to identify haplotypes is not available, P ij is estimated using maximum likelihood methods, which is the same as computing the Pearson correlation coefficient r between additive genotypes X i and X j.
Thus, in view of a significant association, the following contrasts of genotypes are defined by merging information of the genotype distribution [ 4], and estimated with the odds ratio (OR) and its 95% confidence interval (CI): (i) the additive contrast, which is defined as the comparison between the extreme genotypes - mtmt vs. wtwt- (in this contrast the heterozygotes are ignored.
During the analysis, the information of a genotype is converted to one of the DCNs in a one to one manner using oligonucleotide ligation assay (encoding).
Dimension reduction [ 4, 5] could be an alternative approach to retain the most relevant information of the genotype data [ 6, 7] in a low-dimensional vector space.
Nonetheless, it was recently demonstrated that the precious information of mitochondrial genotype may be retrieved from off-target DNA in human WES studies, even when designed for nuclear DNA exclusively [ 6].
We then used a likelihood-based method with the program ADMIXTURE [ 78] to investigate the ancestry information of soybean genotypes, using PLINK [ 79] for genotype quality control.
Multiple imputation yields a set of m complete data matrices of genotype information.
With co-dominant inheritance, the information of microsatellite genotyping can estimate the effective population sizes in ancestral and present populations (Ge et al. [2014]), Hardy-Weinberg Equilibrium (Ge et al. [2012]), and levels of introgression (Liao et al. [2012]).
This suggests that the PC enable the most relevant information of the genotypes to be conveyed for this line.
