Development of the chloroplast genome-based InDel markers in Niitaka (Pyrus pyrifolia) and its application

Pears ( Pyrus spp.) are one of the most important fruit crops in temperate regions and are self-incompatible. Large numbers of interspecific hybrids occur naturally and, have been artificially produced in breeding programs. Also, many pear cultivars were generated from intraspecific crossing. Some varieties have been cultivated for a long time, but their breeding history remains unknown. The P. pyrifolia cv. Niitaka is one of key varieties in the Korean pear breeding program. Therefore, its complete chloroplast (cp) genome was determined, and its phylogenetic relationships with other Pyrus species and P. pyrifolia cultivars were addressed. The cp genome has a total of 133 genes, including 93 protein-coding genes, 32 tRNA genes, and eight rRNA genes. We found many SNPs in the ‘Niitaka’ cp genes when compared with that in another Korean cultivar ‘Wonwhang’ (BioSample SAMN05196235). The primer sets for six genes that had two or more SNPs in their sequence were used to amplify and sequence 27 Pyrus and one Malus cultivars. Of these, we found dramatic InDel polymorphisms in the ndhA and clpP genes. Phylogenetic relationships using the sequences of these two genes in 28 samples showed that they could mainly be classified into two groups of P. pyrifolia . Group I constitutes Niitaka and all cultivars that contain chloroplast maternally inherited from Niitaka, and group II constitutes the other cultivars of P. pyrifolia . We have developed a useful polymorphic molecular marker to confirm the maternal parent in the interspecific hybrids of Niitaka and previous mothers of Niitaka, (such as Amanogawa). Furthermore, these two genes could identify and greatly aid in understanding the subspecies classification in Pyrus .