Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

Abstract

the rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. the chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. comparative genome analysis showed that the iR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. the phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species. Chloroplasts are vital and unique components of photosynthetic cells in plants and algae. They are responsible for multiple functions, e.g., assimilation of carbon and nitrogen, synthesis of amino acids and fatty acids, etc., and play important roles in plant growth and development 1. Chloroplasts may have originated from cyanobacteria through endosymbiosis 2,3 , and chloroplasts possess their own deoxyribonucleic acid (DNA). In the majority of plant species, the chloroplast genome (cp genome) is inherited maternally, with the exception of certain gymnosperms, in which the cp genome is paternally inherited 4. In recent years, knowledge about the organization and evolution of the cp genome has rapidly improved because of the development of DNA sequencing technology and bioinformatics methods. The cp genome is relatively conserved in angiosperms, and its size ranges from 107 to 218 kb, including 100-200 encoding genes 5. A typical angiosperm cp genome has circular DNA, including two small inverted repeats (IRa and IRb), a large single copy (LSC) region and a small single copy (SSC) region 6. Compared to nuclear DNA, the cp genome is small, single-stranded, relatively conserved and has uniparental inheritance, and its nucleotide m...

The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea

“…One of the evidences which reflects this situation is that the number of angiosperm complete chloroplast genomes deposited in NCBI is 9,323 covering 6,727 species as of 11 Jan 2021. These chloroplast genome sequences have been analyzed for the identification of phylogenetic positions [ 18 – 20 ] and for developing useful molecular markers [ 21 , 22 ]. It presents that sequence variations of complete chloroplast genomes are enough information to conduct the studies for those purposes that complete chloroplast genomes can be also used to reveal the relationship between morphological plasticity and genetic diversity of C. album s. str.…”

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

“…In angiosperms, IGSs 3'trnV-UAC-ndhC, rpl32-trnL-UAG , trnQ- UUG-5'rps16, rps4-trnT-UGU , psbZ-trnG-GCC , rpl33-rps18, psbL-trnS-GCU , psbM-trnD-GUC , trnM-CAU-aptE, accD-trnM, rrn5-rrn4.5, infA-rps8, etc. (Shaw et al 2007;Wu et al 2018;Chincoya et al 2020;Khan et al 2020;Li et al 2020a;Niu et al 2020;Mekbib et al 2020) and rpl16 intron (Kelchner et al 1997) have proven to be highly variable in different species. However, these so-called highly variable regions may exhibit unequal levels of variation across different taxonomic groups of angiosperms, and even do not show high levels of variation in some genus.…”

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

“…These markers are useful tools for identifying maternal parent putative hybrid progeny. Nonetheless, cpSSR markers may be deficient in identifying hybrids as these chloroplast associated markers provide only maternal data ( Li et al., 2020 ). Other main drawbacks that hinder the effective use of cpSSRs include lack of variation in some species or occurrence of very narrow genetic diversity, unavailability of general primers, the effects of size homoplasy, heteroplasmy phenomenon, and interspecific hybridization mediated cytoplasmic introgression.…”