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

Abstract

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.

A Comprehensive Study of the Genus Sanguisorba (Rosaceae) Based on the Floral Micromorphology, Palynology, and Plastome Analysis

“…In particular, DNA barcodes are widely used to identify herbal medicines [92][93][94]. In addition, because information on the cp genome can be easily recognized with the development of NGS technology, many studies have reported the development of markers using genetic variations such as indels and SNPs through genome comparison [95][96][97].…”

The First Glimpse of Streptocarpus ionanthus (Gesneriaceae) Phylogenomics: Analysis of Five Subspecies’ Chloroplast Genomes

“…ionanthus subspecies is expected. Interestingly, some studies such as Pyrus cultivars [38] report a relatively high variability among low taxonomic ranks.…”

Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots

“…For the mutations of sequences, the single nucleotide polymorphism (SNP) and deletion or insertion (InDels) of nucleotide bases are the most common variations in the sequences of plastome (Decesare, Hodkinson & Barth, 2010;Kim et al, 2015). These variations have provided ideal information for developing polymorphic markers for numerous applications such as molecular barcoding (Okoth et al, 2016;Zong et al, 2019), phylogenetic reconstruction (Peterson, Romaschenko & Johnson, 2010), biogeographic studies (Kress et al, 2009;Xie et al, 2019), assessment of the maternal line of hybrid species (Schroeder, Höltken & Fladung, 2011;Tomar et al, 2014;Chung et al, 2019), and clarification of the evolutionary relationship between cultivated and crop wild relatives (Gao et al, 2019). Currently, with the advancement of next-generation sequencing technologies (NGS), sequencing of chloroplast genomes and the development of plastid genetic markers have become feasible in various plant genetic researches (Brozynska, Furtado & Henry, 2014;Bi et al, 2018).…”