Ct variation and expression stability analysis of each candidate reference gene among different tissue samples using NormFinder.

<p>(a) Boxplot depicting absolute Ct values, which was calculated using GenEx program. Lower and upper boxes indicate the 25th and 75th percentile, respectively. The median is depicted by the line and all outliers are indicated by dots. (b) Gene expression stability graph using NormFinder algorithm based on stability values. Lower the stability value indicates higher stability of the housekeeping gene. The direction of the arrow indicates the most and least stable housekeeping genes.</p

Validation of selected housekeeping genes under drought stress conditions.

<p>Expression profiling of candidate gene responsible for universal stress protein A-like (<i>uspA</i>) protein in drought imposed tissues (root, stem and leaves). The expression value of candidate gene was normalized with stable, combination of stable and least stable genes namely (i) <i>IF4α</i> (ii) <i>TUB6</i> (iii) <i>HSP90</i> (iv) <i>IF4α + TUB6</i> (v) <i>IF4α + HSP90</i> (vi) <i>IF4α + TUB6+HSP90</i> (vii) <i>ACT1</i> and (viii) <i>18SrRNA</i>. The relative quantitative values of selected drought responsive candidate gene were obtained after scaling to control samples. EDR: vegetative root stressed; LDR: reproductive root stressed; EDS: vegetative stem stressed; LDS: reproductive stem stressed; EDL: vegetative leaves stressed; LDL: reproductive leaves stressed.</p

Details of primers used for qRT-PCR analysis.

<p>Details of primers used for qRT-PCR analysis.</p

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

Principal component analysis depicting correlation among samples based on gene expression data.

<p>Samples formed two clusters representing early stage of seed development (Cl-I) and late pod wall development (Cl-II). Red color depicts the cluster of samples from the early stage of seed development, while green color depicts cluster of sample that represents pod wall development.</p

Assessment of genetic diversity across groups of wild and cultivated chickpea using DArT markers.

<p>No. of polymorphic alleles (N), No. of Different Alleles (Na), No. of Effective Alleles (Ne, = 1/(Sum pi∧2)), Shannon’s Information Index (I = −1 * Sum (pi * Ln (pi))), Expected Heterozygosity (He = 1−Sum pi∧2) and Unbiased Expected Heterozygosity (UHe = (2N/(2N−1)) * He).</p

Distribution of Gene Ontology annotation assigned by Blast2GO.

<p>Summary of level 2 GO annotation into three categories, biological processes (A), molecular functions (B), and cellular components (C) are represented in a pie-chart.</p

Assessment of genetic diversity across chickpea germplasm based on seed type.

<p>No. of polymorphic alleles (N), No. of Different Alleles (Na), No. of Effective Alleles (Ne, = 1/(Sum pi∧2)), Shannon’s Information Index (I = −1* Sum (pi * Ln (pi))), Expected Heterozygosity (He = 1−Sum pi∧2) and Unbiased Expected Heterozygosity (UHe = (2N/(2N−1)) * He).</p

Polymorphism information content (PIC) value of markers used in study.

<p>a. PIC value of SNP markers used for diversity analysis. b. PIC value of DArT markers used for diversity analysis.</p

Summary statistics for Illumina sequencing data and mapping to the pigeonpea genome.

<p>Summary statistics for Illumina sequencing data and mapping to the pigeonpea genome.</p