Development of Novel InDel Markers for Breeding Applications in Pomegranate (<scp><i>Punica granatum</i></scp> L.)

ABSTRACT The present study aims to enrich the genetic marker resources that are amenable for future trait mapping and quality improvement programmes in pomegranate. We analysed 140 well‐characterized genes that belonged to seven important gene families involved in the growth and development of pomegranate. We retrieved 140 representative genes for seven gene families from four draft genomes of pomegranate, cvs. Tunisia, Dabenzi, Taishanhong and Bhagawa, using BLASTn homology search. A total of 245 InDel primers were designed based on the comparison among four pomegranate genomes for the representative gene sequences, focusing on a size difference of at least 8 base pairs (bp). One hundred forty‐eight (60.41%) markers were in silico verified through e‐PCR on the Tunisia genome and further confirmed on the other three genomes, and we identified 107 polymorphic markers with an average PIC value of 0.62. By using 148 InDel markers physically mapped on the genome, we found that Tunisia had the highest syntenic relations with the Bhagawa (100%), Dabenzi (97.97%) and Taishanhong (97.30%) genomes. Experimental validation of 54 InDel primers on six pomegranate genotypes identified a set of 37 (71.15%) polymorphic markers, 24 of which had PIC values of ≥ 0.48. An investigation on genetic diversity and phenotype correlations in 16 pomegranate genotypes using 16 InDel markers demonstrated the utility of these markers. The developed InDel markers are an excellent resource for diverse applications in pomegranate including genetic diversity, trait mapping, gene discovery and gene editing.