Due to the immense amount of computation, however, we could not perform the analysis using the whole SNPs at the same time.
For instance, LASSO includes about 100 SNPs for n = 1600 and p1 = 200 and about 500 SNPs for n = 1600 and p1 = 1600, which indicates that we can construct prediction models without using the whole SNPs.
The percentage of variation accounted for by the first two axes was higher with the SNPs from the A than from the C genome when we used the whole SNP set where the markers from the A genome were overrepresented.
Using the whole set of SNPs, the LD decay rate of the population was estimated at 326 kb in euchromatin, where r 2 = 0.23 (half of its maximum value).
For three of the main continental groups (Africans, East Asians, Europeans) ancestry was first estimated using the whole HapMap SNP database as a proxy for global genome ancestry; these estimates were subsequently compared to those obtained from pre-designed AIM panels.
The genetic backgrounds of the three selected near-isogenic lines (NILs) were assayed using the whole-genome SNP array RICE6K.
The genomic components of these NILs were detected using the whole-genome SNP (Single nucleotide polymorphism) array, RICE6K, suggesting that the recurrent parent genome (RPG) recovery of the NILs was 87.88, 87.70 and 86.62 %, respectively.
We then used the whole set of 4D SNPs to calculate the cluster membership for each accession with 10,000 iterations.
This file gives the position of all the QTL detected using the whole dataset, with the top SNP corresponding to the SNP with the highest effect in the QTL region.
As described above, when using the whole sample, two additional SNPs became nominally significant.
