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Samarina L, Fedorina J, Kuzmina D, Malyukova L, Manakhova K, Kovalenko T, Matskiv A, Xia E, Tong W, Zhang Z, Ryndin A, Orlov YL, Khlestkina EK. Analysis of Functional Single-Nucleotide Polymorphisms (SNPs) and Leaf Quality in Tea Collection under Nitrogen-Deficient Conditions. Int J Mol Sci 2023; 24:14538. [PMID: 37833988 PMCID: PMC10572165 DOI: 10.3390/ijms241914538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
This study discusses the genetic mutations that have a significant association with economically important traits that would benefit tea breeders. The purpose of this study was to analyze the leaf quality and SNPs in quality-related genes in the tea plant collection of 20 mutant genotypes growing without nitrogen fertilizers. Leaf N-content, catechins, L-theanine, and caffeine contents were analyzed in dry leaves via HPLC. Additionally, the photochemical yield, electron transport efficiency, and non-photochemical quenching were analyzed using PAM-fluorimetry. The next generation pooled amplicon-sequencing approach was used for SNPs-calling in 30 key genes related to N metabolism and leaf quality. The leaf N content varied significantly among genotypes (p ≤ 0.05) from 2.3 to 3.7% of dry mass. The caffeine content varied from 0.7 to 11.7 mg g-1, and the L-theanine content varied from 0.2 to 5.8 mg g-1 dry leaf mass. Significant positive correlations were detected between the nitrogen content and biochemical parameters such as theanine, caffeine, and most of the catechins. However, significant negative correlations were observed between the photosynthetic parameters (Y, ETR, Fv/Fm) and several biochemical compounds, including rutin, Quercetin-3-O-glucoside, Kaempferol-3-O-rutinoside, Kaempferol-3-O-glucoside, Theaflavin-3'-gallate, gallic acid. From our SNP-analysis, three SNPs in WRKY57 were detected in all genotypes with a low N content. Moreover, 29 SNPs with a high or moderate effect were specific for #316 (high N-content, high quality) or #507 (low N-content, low quality). The use of a linear regression model revealed 16 significant associations; theaflavin, L-theanine, and ECG were associated with several SNPs of the following genes: ANSa, DFRa, GDH2, 4CL, AlaAT1, MYB4, LHT1, F3'5'Hb, UFGTa. Among them, seven SNPs of moderate effect led to changes in the amino acid contents in the final proteins of the following genes: ANSa, GDH2, 4Cl, F3'5'Hb, UFGTa. These results will be useful for further evaluations of the important SNPs and will help to provide a better understanding of the mechanisms of nitrogen uptake efficiency in tree crops.
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Affiliation(s)
- Lidiia Samarina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Jaroslava Fedorina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Daria Kuzmina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Karina Manakhova
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Tatyana Kovalenko
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China; (E.X.)
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
| | - Yuriy L. Orlov
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 344002 Sochi, Russia; (L.M.); (A.M.)
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Elena K. Khlestkina
- Center of Genetics and Life Sciences Sirius University of Science and Technology, Olimpiyskiy Ave. b.1, 354340 Sirius, Russia; (L.S.); (J.F.); (D.K.); (K.M.); (T.K.); (E.K.K.)
- Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 196632 Saint Petersburg, Russia
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Samarina L, Wang S, Malyukova L, Bobrovskikh A, Doroshkov A, Koninskaya N, Shkhalakhova R, Matskiv A, Fedorina J, Fizikova A, Manakhova K, Loshkaryova S, Tutberidze T, Ryndin A, Khlestkina E. Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( Camellia sinensis (L.) Kuntze). Front Plant Sci 2023; 14:1145793. [PMID: 37235017 PMCID: PMC10206121 DOI: 10.3389/fpls.2023.1145793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Songbo Wang
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandr Bobrovskikh
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Doroshkov
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Jaroslava Fedorina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Anastasia Fizikova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Karina Manakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Svetlana Loshkaryova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Tsiala Tutberidze
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Elena Khlestkina
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg, Russia
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