Flowchart of NGS-QCbox pipeline illustrating the two modes of usage namely <i>quick</i> and <i>complete</i>.

<p>NGS-QCbox comprises of two workflow modes namely <i>quick</i> and <i>complete</i>. In <i>quick</i> mode, read/base level metrics are computed in parallel using Raspberry, an in-house tool, both before and after quality trimming. On the other hand, <i>complete</i> mode is full-fledged quality control and variant calling pipeline that integrates quick mode and additionally generates genome coverage information in parallel. Quality of the data generated could be assessed using this information.</p

Selected genotypes possessing desirable allelic combination for multiple traits.

<p>Selected genotypes possessing desirable allelic combination for multiple traits.</p

Genetic and population structure of the peanut ‘reference set’.

<p>This figure shows (a) grouping of genotypes based on SSR and DArT marker genotyping data, (b) principle co-ordinate analysis (PCoA) based on SSR and DArT marker genotyping data. In the case of SSR as well as DArT based PCoA, cultivated genotypes are clustered in two groups and the wild species genotypes are clustered in one group. (c) the population structure in the reference set at different values of K (K = 1 to K = 15), and (d) presence of three subgroups based on mean Fst values.</p

Global distribution of genotypes containing linked-marker allele(s) for different economically important traits in peanut.

<p>An attempt has been made to show passport-based geographical distribution of genotypes that had favourable alleles for markers showing association and explaining >20% phenotypic variation for the trait. Genotypes containing favourable alleles for different traits have been represented by circles in different colors.</p

Linkage disequilibrium (LD) decay in the peanut ‘reference set’ based on mapped SSR marker data.

<p>The simulation trend line within 20 cM showed that the LD declined to below 0.1 within 20 cM. Hence, the estimated LD decay in the ‘reference set’ is 15.0 cM.</p

Genomewide distribution of trait-associated markers for different traits.

<p>Mapped SSR markers that showed trait association are represented on linkage groups (A01 to A10 and B01 to B10) while unmapped DArT features are assigned to A0 linkage group for representation.</p

Allelic effect of selected marker-trait associations (MTAs) with ≥20% phenotypic variance for 15 traits.

<p>Allelic effect of selected marker-trait associations (MTAs) with ≥20% phenotypic variance for 15 traits.</p