Utilization of intron-flanking EST-specific markers in the genetic characterization of Artemisia annua genotypes from the trans-Himalayan region of Ladakh, India.

Genetic variation was assessed utilizing intron-flanking EST-specific markers among genotypes of Artemesia annua collected from two sampling sites viz. Nubra (9,600 ft) and Leh (11,500 ft) valleys of the trans-Himalayan region, Ladakh, India. The available ESTs (3,60,906) sequences of A. annua were aligned with the genomic sequences of Arabidopsis to developed ‘intron-flanking’ EST-PCR based primers. These primers anneal with the conserved region of exon (flanking to the intron) and amplified the introns. Out of the 39 primers selected and tested on 20 genotypes of A. annua, we successfully exploited 81 codominant intron length polymorphism (ILP) markers, with an average of 2.08 markers per primer and 92.04% polymorphism detection. Clustering of genotypes revealed distribution of genotypes into 2 distinct clusters with respect to their site of collection. Significantly, this study demonstrates that Arabidopsis genome sequence can be useful in developing gene-specific PCR-based markers for other non-model plant species like A. annua in the absence of genome sequences.