Study of arbitrarily amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) markers for genetic diversity and population structure in Kalmegh [Andrographis paniculata (Burm. f.) Nees]

• This is first study where arbitrarily amplified and gene targeted markers were used for genetic diversity and population structure study of Andrographis paniculata.
• UPGMA tree and PCoA showed lack of agro-ecological isolation in Andrographis paniculata accessions collected from five agro-ecological regions of India.
• AMOVA has indicated that more than 90% of variation was present within the population.
• PIC, Rp value and correspondence between UPGMA tree and population structure suggested that CBDP markers were better markers for genetic diversity study.

Andrographis paniculata is a medicinal herb also known as ‘King of Bitter’. This herb was studied using arbitrary amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) molecular markers. Thirty-nine accessions were collected from five agro-ecological regions of India. Eighteen RAPD and five ISSR primers generated a total of 124 and 32 amplicons with an average of 6.89 and 6.4 amplicons per primer respectively. Similarly, 22 SCoT and 19CBDP primers were used to characterize A. paniculata accessions. A total of 132 and 97 amplicons were generated, with an average of 6.0 and 5.11 amplicons per primer, respectively. Polymorphic information content (PIC) for RAPD and ISSR primers ranged from 0.32 to 0.45 and 0.25–0.42, with resolving power (Rp) ranging from 2.13 to 10.03 and 2.46–3.96, respectively. PIC values ranged from 0.09 to 0.48 and 0.30–0.46, with an average value of 0.34 and 0.41 per primer for SCoT and CBDP markers, respectively. The resolving power for SCoT and CBDP primers ranged from 2.36 to 10.54 and 1.39–13.15 per primer, respectively. Unweighted pair group method with arithmetic mean (UPGMA) based clustering grouped 39 accessions into three broad clusters based on all four marker systems studied, did not correlate with their agro-ecological regions. Population structure based analysis divided 39 accessions into seven populations, six populations and four populations using RAPD, ISSR and SCoT markers respectively. Whereas only three populations were observed using CBDP primers which corresponded to the grouping observed with the UPGMA. Analysis of molecular variance (AMOVA) based analysis showed that the maximum variation (10%) among agro-ecological regions was observed using CBDP primers; whereas, minimum variation (2%) was observed using SCoT markers. Taken together, our data suggest CBDP markers are better markers for genetic diversity study in A. paniculata.