Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)

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Abstract

Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum.

Materials and methods. As a result of the work, intergenic spacers trnY–trnT, trnH–psbA and rpoB–trnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed.

Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoB–trnC. Based on rpoB–trnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).

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About the authors

Elena A. Dyachenko

Federal State Institution Research Center of Biotechnology of the Russian Academy of Sciences

Author for correspondence.
Email: dyachenko-el@yandex.ru
ORCID iD: 0000-0002-0570-9751
SPIN-code: 4525-9700

PhD, Researcher, Laboratory of Plant System Biology

Russian Federation, Moscow

Elena V. Semenova

Federal State Budgetary Scientific Institution Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources

Email: e.semenova@vir.nw.ru
ORCID iD: 0000-0002-2637-1091
SPIN-code: 4667-9935

PhD, Main Researcher, Department of Leguminous Crops Genetic Resources

Russian Federation, Saint Petersburg

Elena Z. Kochieva

Federal State Institution Research Center of Biotechnology of the Russian Academy of Sciences

Email: ekochieva@yandex.ru
ORCID iD: 0000-0002-6091-0765

Dr. Sci. (Biol.), Main Researcher, Laboratory of Plant System Biology

Russian Federation, Moscow

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2. Figure: 1. Identified haplotypes in the rpoB – trnC sequence in the pea species P. sativum (Ps) (a) and P. fulvum (Pf) (b). EL - samples of P. sativum subsp. elatius; T - samples of P. sativum subsp. transcaucasicum

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3. Figure: 2. Dendrogram of genetic similarity of 38 samples of the genus Pisum and species of the genera Lathyrus and Vavilovia of the tribe Fabeae based on the total sequence of the analyzed regions of the chloroplast genome (trnH – psbA, trnY – trnT, rpoB – trnC) (ML method, model T92 + G)

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Copyright (c) 2021 Dyachenko E.A., Semenova E.V., Kochieva E.Z.

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