Diversity of PsSym29 and PsNRLK1 genes in the VIR germplasm collection of pea (Pisum sativum L.)

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Abstract

BACKGROUND: N.I. Vavilov Institute of Plant Genetic Resources (VIR) (Saint Petersburg, Russia) maintains a large collection of pea (Pisum sativum L.). Earlier, several growth and yield parameters were recorded for plants of 99 accessions grown under inoculation with nodule bacteria and arbuscular mycorrhizal fungi.

MATERIALS AND METHODS: Polymorphism of genes encoding symbiotic receptor kinase PsSym29 [participating in the autoregulation of nodulation (AON) system] and closely related receptor kinase PsNRLK1 (with yet unknown function in symbiosis) was assessed in 99 pea genotypes from the VIR collection. Nucleotide diversity, Tajima’s D, and Fay and Wu’s H statistics were calculated using DNAsp 5.0 software. The significance of associations of allelic state of the sequenced genes with the growth and yield parameters was tested by two-way ANOVA followed by FDR correction and by regression analysis.

RESULTS: Nucleotide diversity and the ratio of synonymous to non-synonymous substitutions was greater in PsNRLK1 as compared to PsSym29. The analysis of Fay and Wu’s H in sliding window revealed signatures of positive selection in one site of PsSym29 and in three sites of PsNRLK1 gene sequences located in 1st exons encoding LRR (leucine rich repeat) domains. No significant associations of allelic state of neither PsSym29 nor PsNRLK1 genes was found with plant growth and yield parameters.

CONCLUSIONS: The sequences of both PsSym29 and PsNRLK1 genes undergo positive selection, but the conditions in which specific allelic states of the genes become adaptive are to be elucidated in future.

About the authors

Vladimir A. Zhukov

All-Russia Research Institute for Agricultural Microbiology; Saint Petersburg State University; Sirius University of Science and Technology

Author for correspondence.
Email: vzhukov@arriam.ru
ORCID iD: 0000-0002-2411-9191
SPIN-code: 2610-3670
Scopus Author ID: 35325957900

Cand. Sci. (Biol.), PhD, Leading Research Associate, Head of the Laboratory of Genetics of Plant-Microbe Interactions

Russian Federation, Saint Petersburg; Saint Petersburg; Saint Petersburg

Aleksandr I. Zhernakov

All-Russia Research Institute for Agricultural Microbiology; Saint Petersburg State University

Email: AZhernakov@arriam.ru
ORCID iD: 0000-0001-8961-9317
Scopus Author ID: 16403813100

Junior Research Associate, Laboratory of Genetics of Plant-Microbe Interactions

Russian Federation, Saint Petersburg; Saint Petersburg

Maria Yu. Belozerova

Saint Petersburg State University

Email: m-kitty@mail.ru

Student

Russian Federation, Saint Petersburg

Irina E. Dodueva

Saint Petersburg State University

Email: wildtype@yandex.ru
SPIN-code: 8061-2388

PhD, Cand. Sci. (Biol.), Associate Professor, Department of Genetics and Biotechnology

Russian Federation, Saint Petersburg

Maria A. Lebedeva

Saint Petersburg State University

Email: mary_osipova@mail.ru
SPIN-code: 6000-6307

PhD, Cand. Sci. (Biol.), Senior Research Associate, Department of Genetics and Biotechnology

Russian Federation, Saint Petersburg

Ludmila A. Lutova

Saint Petersburg State University

Email: la.lutova@gmail.com
SPIN-code: 3685-7136

Dr. Sci. (Biol.), Professor, Department of Genetics and Biotechnology

Russian Federation, Saint Petersburg

Igor A. Tikhonovich

All-Russia Research Institute for Agricultural Microbiology; Saint Petersburg State University

Email: igor.tikhonovich49@mail.ru
SPIN-code: 6685-9419

Dr. Sci. (Biol.), Professor RAS, Dean of Faculty of Biology

Russian Federation, Saint Petersburg; Saint Petersburg

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2. Fig. 1. Nucleotide diversity, Tajima’s D, and Fay and Wu’s H statistics calculated for PsSym29 and PsNRLK1 gene sequences, and the domain structure of the proteins encoded by the genes. Amino acid substitutions in sites with detected signals of positive selection are indicated. SP — signal peptide, LRR — leucine rich repeats, TM — transmembrane domain, kinase — protein kinase domain

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3. Appendix Fig. S1. The heatmap diagram illustrating expression levels (normalized RPKM values) of the PsNRLK1 and PsSYM29 genes in different pea organs according to transcriptomic data by S. Alves-Carvalho et al. [14]. The heatmap was generated using Morpheus software (https://software.broadinstitute.org/morpheus)

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Copyright (c) 2022 Zhukov V.A., Zhernakov A.I., Belozerova M.Y., Dodueva I.E., Lebedeva M.A., Lutova L.A., Tikhonovich I.A.

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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
 


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