Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Abstract

Kalmegh (Andrographis paniculata (Burm. F.) Nees) is one of the most important medicinal plants and has been widely explored as traditional medicine. To exploit its natural genetic diversity and initiations of molecular breeding to develop novel cultivars or varieties, developments of genomic resources are essential. Four microsatellite-enriched genomic libraries—(CT)14, (GT)12, (AG)15 and (AAC)8—were constructed using the genomic DNA of A. paniculata. Initially, 183 recombinant colonies were screened for the presence of CT, GT, AG, and AAC microsatellite repeats, out of which 47 clones found positive for the desired simple sequence repeats (SSRs). It was found that few colonies had more than one desirable SSR. Thus, a sum of 67 SSRs were designed and synthesized for their validation among 42 A. paniculata accessions. Out of the 67 SSRs used for genotyping, only 41 were found to be polymorphic. The developed set of g-SSR markers showed substantial genetic variability among the selected A. paniculata accessions, with an average polymorphic information content (PIC) value of 0.32. Neighbor-joining tree analysis, population structure analysis, analysis of molecular variance (AMOVA), and principal coordinate analysis (PCoA) illustrated the considerable genetic diversity among them. The novel g-SSR markers developed in the present study could be important genomic resources for future applications in A. paniculata.

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

“…Thus, more detailed studies with larger sampling sizes from extended geographical regions could draw a concrete inference ( Sahoo et al., 2021 ). Previously, evaluation of genetic diversity among the geographically isolated germplasm of A.paniculata was carried out using various dominant molecular markers ( Lattoo et al., 2008 ; Minz et al., 2013 ; Tiwari et al., 2016 ; Kumar et al., 2020 ; Hiremath et al., 2020 ) the outcomes of which are in line with our results. However, in the present study, metabolic pathway specific EST-SSR markers were designed and used to determine the genetic diversity among twenty-four ecotypes of A. paniculata .…”

“…Bayesian model-based population structuring considered individuals with a probability score of >0.80 as genetically pure and a score of<0.80 as admixed type ( Figure 6B ). Mixing of pure individuals with few admixed accessions was observed in both the populations derived from model-based study, which could be due to the breeding behavior of the studied plant ( Kumar et al., 2020 ). AMOVA and PCoA also explained substantial genetic diversity among the studied accessions of six agroecologically grouped populations.…”

“…In the recent past, the introgression of molecular markers has augmented the accumulation of genetic gains achieved by morpho-chemical descriptors based characterization. In kalmegh, an array of genetic diversity studies has been done using agro-morphological traits ( Nagvanshi and Tirkey, 2016 ), phytochemical traits ( Sabu et al., 2001 ; Archana et al., 2016 ), and molecular markers, including RAPD, ISSR, SCoT, CBDP and Genomic SSRs ( Padmesh et al., 1999 ; Maison et al., 2005 ; Kumar and Shekhawat, 2009 ; Wijarat et al., 2011 ; Ghosh et al., 2014 ; Tiwari et al., 2016 ; Kumar et al., 2020 ). Compared with dominant markers, the reproducibility and reliability of SSR (simple sequence repeat) markers are high due to co-dominance, high polymorphism, uniform distribution throughout the genome, and multi-allelic nature ( Varshney et al., 2005 ).…”

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study

“…Population Structure analysis also showed differentiation among T. cordifolia , T. sinensis , and T. rumphii study based on g-SSR markers. Similar studies were also reported in medicinal plants like Andrographis paniculate [ 48 ]. The genomic SSR markers developed in T. cordifolia were found transferable in the species Tinospora rumphii and Tinospora sinensis .…”

Development of Chloroplast Microsatellite Markers and Evaluation of Genetic Diversity and Population Structure of Cutleaf Groundcherry (Physalis angulata L.) in China

“…The design of microsatellite (simple sequence repeat, SSR) markers is based on conserved nucleotide sequences on both sides of simple repeat sequences, and the polymorphism among alleles is reflected by detecting the difference in the number of repeats [16]. SSRs are widely distributed in the nuclear and organellar genomes of eukaryotes [17][18][19][20]. SSR markers are considered to be among the most ideal molecular markers for the study of plant genetics [14,18].…”