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

Lidia Skuza,Jan Bocianowski,Ewa Filip,Izabela Szućko

doi:10.3390/ijms21249421

Abstract

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

Highlights

Rye (Secale cereale L.) is commonly grown in the fields of Northern and Eastern Europe
The potential use of SPInDel profiles for species identification purposes requires the existence of ‘species-specific SPInDel profiles’: those that are only found in one species within a taxonomic group and allow their unequivocal identification
The results obtained in this study clearly indicated disproportions in the available information regarding various non-coding cpDNA and mtDNA regions used in phylogenetic studies, and some of them—due to high variability—can be successfully used in the analyses of closely related species

Summary

Introduction

Rye (Secale cereale L.) is commonly grown in the fields of Northern and Eastern Europe. S. cereale L. is highly tolerant to diverse environmental stresses, as drought and frost [1,2]. It contains genes conferring biotic stress resistance against various diseases In view of that the wild and weedy forms may crossbreed with cultivated rye [5], these taxa, along with the landraces, constitute gene pools for desirable genes. They can be regarded as genetic resource reservoirs for new niches and future breeding programs of wheat, triticale and other crops [6]. Understanding genetic structuring of the genus Secale and distribution of genetic diversity within the genus is extremely important

Methods

Results

Discussion

Conclusion