Date Published: February 27, 2019
Publisher: Public Library of Science
Author(s): Lidia Skuza, Izabela Szućko, Ewa Filip, Tomasz Strzała, Tzen-Yuh Chiang.
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.
Rye is a difficult object of genetic and breeding studies. The reason is the open-pollination, self-incompatibility and the relationship between heterozygosity and productivity, which arises as a result of inter-chromosomal gene interactions . Rye has the largest genome ~ 7.9 Gbp among all diploid Triticeae , which is in 90% consisting of repetitive sequences. The genus Secale is also very diverse–it includes annual, perennial, self-pollinating and open-pollinating species of various morphologies. The classification system of the American Germplasm Resources Information Network (GRIN, http://www.arsgrin.gov) currently includes four species to the genus Secale: annual S. cereale L., annual S. sylvestre Host and S. vavilovii Grossh and perennial S. strictum (Presl.) Presl. (syn. S. montanum) [3,4]. All species within the genus Secale are diploid with 14 chromosomes, they cross with each other easily, and crossbreeding results in partially fertile hybrids [5,6]. Only Secale sylvestre has different characteristics (low crossability with other species, the lowest amount of t-heterochromatin  and the smallest genome (7.23 pg) and is probably the most distant species [5,8], as indicated by many research results [9–15]. Rye (Secale cereale L.) is also an important and rich source of valuable genes encoding, e.g., high protein content, resistance to diseases as well as morphological and biochemical traits for wheat and a synthetic wheat–rye hybrid triticale (× Triticosecale Wittmack) improvement.
The plant material consisted of 35 accessions of the genus Secale, 13 cultivated and non-cultivated species and subspecies of rye, obtained from several world collections (Center for Biological Diversity Conservation in Powsin–Warsaw, Poland; United States Department of Agriculture–Agricultural Research Service, USA; Nordic Genetic Resource Center, Sweden). The list of species, along with the accession numbers for each sample, is given in S1 Table.
The genetic information contained in both chloroplast (cpDNA) and mitochondrial DNA (mtDNA) is often analyzed in phylogenetic and population studies. However, for most species, including rye, the data is incomplete. So far, rye mtDNA has not been fully sequenced, while in 2014, complete data on the S. cereale chloroplast genome sequence has been published . Only in 2007, Isik et al.  analyzed the organelle genomes of S. cereale cultivars originated from different geographical regions using the PCR-RFLP method. The study used 7 cpDNA fragments and 4 mtDNA fragments for both coding and non-coding regions. Each amplified sequence was digested with 13 different restriction enzymes. The study of Isik et al.  proved that the mitochondrial genome, as compared to the chloroplast genome, showed a higher level of organelle polymorphism between analyzed rye cultivars. Our research , consisting in the analysis of mtDNA of seven species and subspecies of rye based on the RFLP method, showed the division of the analyzed taxa into two groups. The first included Secale cereale ssp. segetale and Secale sylvestre, and the second group comprised the remaining of the analyzed species (Secale strictum, Secale strictum ssp. kuprijanovii and Secale vavilovii, Secale cereale and Secale strictum ssp. africanum), which did not overlap with the existing classification system.
The use of non-coding sequences of chloroplast and mitochondrial DNA provided new data on genetic diversity within the genus Secale. Such sequences have so far not been used in any analysis of phylogenetic relationships in rye. The results obtained in this study clearly indicated disproportions in the available information regarding various non-coding cpDNA regions used in phylogenetic studies, and some of them–due to high variability–can be successfully used in the analyses of closely related species.