Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis

Abstract

The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale , representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S . vavilovii was very similar to S . cereale , which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S . sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

“…In our previous studies the phylogenetic indels context were not analysed because algorithms describing substitution models are not able to model indel-type changes and they are removed by tree-creating programs. However, basic data on length and number of indels were obtained [ 38 ]. The number of identified indels in cpDNA was not very high compared to the results presented by other authors [ 65 ].…”

“…The region trnT (UGU)- trnL (UAA)5′exon shows a high frequency of insertions or deletions, depending on the species, which makes it possible to use them as genetic markers [ 38 ].…”

“…In our previous study, a total of 45 indels in mtDNA have been identified [ 38 ]. It is comparable to the results of other authors in plant mtDNA.…”

“…Chinese Spring) [ 77 ]. We determined 0 to 40 (in nad 4/1-2 ) indels with sizes ranging from 1 bp to 5 bp in the rps12-nad3 (2) and nad4/1-2 regions, respectively [ 38 ].…”

Genetic Diversity and Classification of the Cytoplasm of Chinese Elite Foxtail Millet [Setaria italica (L.) P. Beauv.] Parental Lines Revealed by Chloroplast Deoxyribonucleic Acid Variation

“…Both types of cytoplasmic genomes, mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA), represent important genetic material in addition to the nuclear genome of plants. Their distinct features, including small genome sizes, high conservation, and the absence of sexual recombination make mtDNA and cpDNA useful tools for determining phylogenetic relationships and studying plant populations (Avise, 2000; Provan et al, 2001; Norouzi et al, 2012; Cheng et al, 2015; Skuza et al, 2019). Recently, molecular markers derived from cpDNA and mtDNA have been designed and used for research on cytoplasmic variation in soybean ( Glycine max ) (Shimamoto et al, 2000), rice (Rajendrakumar et al, 2007), Lolium species (McGrath et al, 2007), and Brassica species (Wang et al, 2012b; Zamani-Nour et al, 2013; Shu et al, 2016).…”