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Ahmed AA, Ghoneim M, Ali MAA, Amer A, Głowacka A, Ahmed MAA. Comparative studies of four cumin landraces grown in Egypt. Sci Rep 2024; 14:7990. [PMID: 38580717 PMCID: PMC10997781 DOI: 10.1038/s41598-024-57637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
One of the significant aromatic plants applied in food and pharma is cumin. Despite its massive trading in Egypt, there are no comprehensive reports on cumin landraces profile screening. This study aimed to investigate the variation in seeds' physical and biochemical profiles and genetic diversity as well as assess the efficiency of seeds' germination under salinity stress. Consequently, during the 2020/2021 growing season, four common cumin seed landraces were gathered from various agro-climatic regions: El Gharbia, El Menia, Assiut, and Qena. Results showed a significant variation in physical profile among the four seeds of landraces. In addition, Assiut had the highest percentage of essential oil at 8.04%, whilst Qena had the largest amount of cumin aldehyde, the primary essential oil component, at 25.19%. Lauric acid was found to be the predominant fatty acid (54.78 to 62.73%). According to ISSR amplification, El Menia presented a negative unique band, whereas other landraces offered a positive band. Additionally, the cumin genotypes were separated into two clusters by the dendrogram, with El Gharbia being located in an entirely separate cluster. There were two sub-clusters within the other cluster: El Menia in one and Assiut and Qena in the other. Moreover, the germination sensitivity to the diverse salinity concentrations (control, 4, 8, 12, and 16 dS/m) findings showed that landraces exhibited varying responses to increased salinity when El Gharbia and El Menia showed a moderate response at four dS/m. Whilst, Qena landraces showed supreme values among other landraces under 12 and 16 dS/m. The majority of the examined features had strong positive associations over a range of salinity levels, according to phenotypic correlation coefficient analysis. To accomplish the aims of sustainable agriculture in Egypt, it would be imperative that the potential breeding program for cumin landraces consider this screening study.
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Affiliation(s)
- Abeer A Ahmed
- Seed Technology Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Marwa Ghoneim
- Cell Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Mahmoud A A Ali
- Horticultural Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Alia Amer
- Medicinal and Aromatic Plants Research Department, Horticulture Research Institute, Agricultural Research Center, Giza, Egypt.
| | - Aleksandra Głowacka
- Department of Plant Cultivation Technology and Commodity Sciences, University of Life Sciences in Lublin, 13 Akademicka Street, 20-950, Lublin, Poland
| | - Mohamed A A Ahmed
- Plant Production Department (Horticulture - Medicinal and Aromatic Plants), Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt.
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Lee YK, Park JE, Lee M, Mifflin R, Xu Y, Novak R, Zhang Y, Hardwick JP. Deletion of hepatic small heterodimer partner ameliorates development of nonalcoholic steatohepatitis in mice. J Lipid Res 2023; 64:100454. [PMID: 37827334 PMCID: PMC10665942 DOI: 10.1016/j.jlr.2023.100454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 09/02/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023] Open
Abstract
Small heterodimer partner (SHP, Nr0b2) is an orphan nuclear receptor that regulates bile acid, lipid, and glucose metabolism. Shp-/- mice are resistant to diet-induced obesity and hepatic steatosis. In this study, we explored the potential role of SHP in the development of nonalcoholic steatohepatitis (NASH). A 6-month Western diet (WD) regimen was used to induce NASH. Shp deletion protected mice from NASH progression by inhibiting inflammatory and fibrotic genes, oxidative stress, and macrophage infiltration. WD feeding disrupted the ultrastructure of hepatic mitochondria in WT mice but not in Shp-/- mice. In ApoE-/- mice, Shp deletion also effectively ameliorated hepatic inflammation after a 1 week WD regimen without an apparent antisteatotic effect. Moreover, Shp-/- mice resisted fibrogenesis induced by a methionine- and choline-deficient diet. Notably, the observed protection against NASH was recapitulated in liver-specific Shp-/- mice fed either the WD or methionine- and choline-deficient diet. Hepatic cholesterol was consistently reduced in the studied mouse models with Shp deletion. Our data suggest that Shp deficiency ameliorates NASH development likely by modulating hepatic cholesterol metabolism and inflammation.
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Affiliation(s)
- Yoon-Kwang Lee
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.
| | - Jung Eun Park
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Mikang Lee
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Ryan Mifflin
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Yang Xu
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Robert Novak
- Department of Pathology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Yanqiao Zhang
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA
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Terletskaya NV, Khapilina ON, Turzhanova AS, Erbay M, Magzumova S, Mamirova A. Genetic Polymorphism in the Amaranthaceae Species in the Context of Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:3470. [PMID: 37836210 PMCID: PMC10575142 DOI: 10.3390/plants12193470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/13/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023]
Abstract
The adaptive potential and biochemical properties of the Amaranthaceae species make them promising for introduction into agriculture and markets, particularly in arid conditions. Molecular genetic polymorphism analysis is the most powerful tool for studying plant resources; therefore, the current study aimed to investigate the polymorphisms of allelic variations in the ARF and SOD gene families, as well as the genetic diversity of six Amaranthaceae species, using retrotransposon-based fingerprinting with the multi-locus EPIC-PCR profiling approach. Additionally, the iPBS PCR amplification was employed for genome profiling, revealing variations in genetic diversity among the studied Amaranthaceae samples. The observed genetic diversity in Amaranthaceae species contributes to their enhanced tolerance to adverse environmental conditions. The knowledge about the genetic diversity of genes crucial in plant development and stress resistance can be useful for the genetic improvement of cultivated Amaranthaceae species.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan;
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan;
| | - Oxana N. Khapilina
- National Center for Biotechnology, Qorghalzhyn 13, Astana 010000, Kazakhstan; (A.S.T.); (S.M.)
| | - Ainur S. Turzhanova
- National Center for Biotechnology, Qorghalzhyn 13, Astana 010000, Kazakhstan; (A.S.T.); (S.M.)
| | - Malika Erbay
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan;
| | - Saule Magzumova
- National Center for Biotechnology, Qorghalzhyn 13, Astana 010000, Kazakhstan; (A.S.T.); (S.M.)
| | - Aigerim Mamirova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan;
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan;
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Johnson G, Canty SWJ, Lichter‐Marck IH, Wagner W, Wen J. Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11519. [PMID: 37342166 PMCID: PMC10278939 DOI: 10.1002/aps3.11519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 06/22/2023]
Abstract
Premise The preservation of plant tissues in ethanol is conventionally viewed as problematic. Here, we show that leaf preservation in ethanol combined with proteinase digestion can provide high-quality DNA extracts. Additionally, as a pretreatment, ethanol can facilitate DNA extraction for recalcitrant samples. Methods DNA was isolated from leaves preserved with 96% ethanol or from silica-desiccated leaf samples and herbarium fragments that were pretreated with ethanol. DNA was extracted from herbarium tissues using a special ethanol pretreatment protocol, and these extracts were compared with those obtained using the standard cetyltrimethylammonium bromide (CTAB) method. Results DNA extracted from tissue preserved in, or pretreated with, ethanol was less fragmented than DNA from tissues without pretreatment. Adding proteinase digestion to the lysis step increased the amount of DNA obtained from the ethanol-pretreated tissues. The combination of the ethanol pretreatment with liquid nitrogen freezing and a sorbitol wash prior to cell lysis greatly improved the quality and yield of DNA from the herbarium tissue samples. Discussion This study critically reevaluates the consequences of ethanol for plant tissue preservation and expands the utility of pretreatment methods for molecular and phylogenomic studies.
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Affiliation(s)
- Gabriel Johnson
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Steven W. J. Canty
- Smithsonian Marine StationFort PierceFlorida34949USA
- Working Land and Seascapes, Smithsonian InstitutionWashingtonD.C.20013USA
| | - Isaac H. Lichter‐Marck
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos Angeles, 612 Charles E. Young Dr. SouthLos AngelesCalifornia90095USA
- Department of Integrative Biology and Jepson herbariumUniversity of California, Berkeley1001 Valley Life Sciences Bldg.BerkeleyCalifornia94720USA
| | - Warren Wagner
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
| | - Jun Wen
- Department of Botany/MRC 166National Museum of Natural History, Smithsonian InstitutionWashingtonD.C.20560USA
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Terletskaya NV, Turzhanova AS, Khapilina ON, Zhumagul MZ, Meduntseva ND, Kudrina NO, Korbozova NK, Kubentayev SA, Kalendar R. Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies. Genes (Basel) 2023; 14:genes14040794. [PMID: 37107552 PMCID: PMC10137911 DOI: 10.3390/genes14040794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Representatives of the Crassulaceae family’s genus Rhodiola are succulents, making them distinctive in a changing environment. One of the most significant tools for analyzing plant resources, including numerous genetic processes in wild populations, is the analysis of molecular genetic polymorphism. This work aimed to look at the polymorphisms of allelic variations of the superoxide dismutase (SOD) and auxin response factor (ARF) gene families, as well as the genetic diversity of five Rhodiola species, using the retrotransposons-based fingerprinting approach. The multi-locus exon-primed intron-crossing (EPIC-PCR) profiling approach was used to examine allelic variations in the SOD and ARF gene families. We implemented the inter-primer binding site (iPBS) PCR amplification technique for genome profiling, which demonstrated a significant level of polymorphism in the Rhodiola samples studied. Natural populations of Rhodiola species have a great capacity for adaptation to unfavorable environmental influences. The genetic variety of wild populations of Rhodiola species leads to their improved tolerance of opposing environmental circumstances and species evolutionary divergence based on the diversity of reproductive systems.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan;
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan; (N.D.M.); (N.O.K.); (N.K.K.)
| | - Ainur S. Turzhanova
- National Center for Biotechnology, Qorghalzhyn Hwy 13, Astana 010000, Kazakhstan; (A.S.T.); (O.N.K.)
| | - Oxana N. Khapilina
- National Center for Biotechnology, Qorghalzhyn Hwy 13, Astana 010000, Kazakhstan; (A.S.T.); (O.N.K.)
| | - Moldir Z. Zhumagul
- Astana International University, Kabanbai Batyr 8, Astana 010000, Kazakhstan;
- Astana Botanical Garden, Orunbur 16, Astana 010000, Kazakhstan;
| | - Nataliya D. Meduntseva
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan; (N.D.M.); (N.O.K.); (N.K.K.)
| | - Nataliya O. Kudrina
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan; (N.D.M.); (N.O.K.); (N.K.K.)
- National Center for Biotechnology, Qorghalzhyn Hwy 13, Astana 010000, Kazakhstan; (A.S.T.); (O.N.K.)
| | - Nazym K. Korbozova
- Institute of Genetic and Physiology, Al-Farabi Avenue 93, Almaty 050040, Kazakhstan; (N.D.M.); (N.O.K.); (N.K.K.)
- National Center for Biotechnology, Qorghalzhyn Hwy 13, Astana 010000, Kazakhstan; (A.S.T.); (O.N.K.)
| | | | - Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Astana 010000, Kazakhstan
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
- Correspondence: ; Tel.: +358-294158869
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Liu D, Li Q, Luo J, Huang Q, Zhang Y. An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness. BMC Genomics 2023; 24:125. [PMID: 36927488 PMCID: PMC10022144 DOI: 10.1186/s12864-023-09211-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Current solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios. RESULTS We report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20% PEG 8000, 2 M NaCl and 16.3 mM MgCl2, and 1.25 mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency. CONCLUSION We have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.
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Affiliation(s)
- Danli Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qiujia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China.
- College of Life Science and Engineering, Foshan University, Foshan, China.
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Buonfiglio PI, Menazzi S, Francipane L, Lotersztein V, Ferreiro V, Elgoyhen AB, Dalamón V. Mitochondrial DNA variants in a cohort from Argentina with suspected Leber's hereditary optic neuropathy (LHON). PLoS One 2023; 18:e0275703. [PMID: 36827238 PMCID: PMC9956067 DOI: 10.1371/journal.pone.0275703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
The present study investigates the spectrum and analysis of mitochondrial DNA (mtDNA) variants associated with Leber hereditary optic neuropathy (LHON) in an Argentinean cohort, analyzing 3 LHON-associated mitochondrial genes. In 32% of the cases, molecular confirmation of the diagnosis could be established, due to the identification of disease-causing variants. A total of 54 variants were observed in a cohort of 100 patients tested with direct sequencing analysis. The frequent causative mutations m.11778G>A in MT-ND4, m.3460G>A in MT-ND1, and m.14484T>C in MT-ND6 were identified in 28% of the cases of our cohort. Secondary mutations in this Argentinean LHON cohort were m.11253T>C p.Ile165Thr in MT-ND4, identified in three patients (3/100, 3%) and m.3395A>G p.Tyr30Cys in MT-ND1, in one of the patients studied (1%). This study shows, for the first time, the analysis of mtDNA variants in patients with a probable diagnosis of LHON in Argentina. Standard molecular methods are an effective first approach in order to achieve genetic diagnosis of the disease, leaving NGS tests for those patients with negative results.
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Affiliation(s)
- Paula I. Buonfiglio
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Menazzi
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Liliana Francipane
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Vanesa Lotersztein
- Servicio de Genética, Hospital Militar Central “Dr. Cosme Argerich”, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Ana Belén Elgoyhen
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- División Genética, Hospital de Clínicas “José de San Martín”, Ciudad Autónoma de Buenos Aires, Argentina
- Servicio de Genética, Hospital Militar Central “Dr. Cosme Argerich”, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio Genos, Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
| | - Viviana Dalamón
- Laboratorio de Fisiología y Genética de la Audición, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas - INGEBI / CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
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Pozharskiy A, Kostyukova V, Taskuzhina A, Nizamdinova G, Kisselyova N, Kalendar R, Karimov N, Gritsenko D. Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses. Heliyon 2022; 8:e10095. [PMID: 36033267 PMCID: PMC9399970 DOI: 10.1016/j.heliyon.2022.e10095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/27/2022] [Accepted: 07/21/2022] [Indexed: 12/01/2022] Open
Abstract
The tomato is one of the most important vegetable crops. The successful development of tomato cultures in Kazakhstan depends on the implementation of intensive agricultural methods, including breeding and selecting for new tomato varieties resistant to plant pathogens. Common tomato viruses, although not detected in our country to date, may potentially have a deleterious impact on agriculture if allowed to spread. The implementation of tomato breeding programs based on molecular markers of resistance is therefore an important preventive measure for protecting the agriculture and food safety of Kazakhstan. In the present work, we used nine molecular markers associated with resistance to three tomato viruses, i.e., tomato mosaic virus (ToMV), tomato spot wilt virus (TSWV), and tomato yellow leaf curl virus (TYLCV), to test the local breeding collection for the presence of genetic resistance factors. Two tomato varieties, 'Zhiraf' (Russia) and 'Sunnik' (Armenia), were revealed to possess the resistant allele marker PrRuG86-151 against ToMV; three hybrid forms had the same allele in the heterozygous state. One hybrid, based on the 'Mirsini' F1 variety from the Netherlands, had resistance to TSWV, which was confirmed by four markers: NCSw003, NCSw007, NCSw011, and NCSw012. Two cultivars, 'Nicola' and 'Malinovyi Slon' (Russia), and the local hybrid based on 'Yarkiy Rumyanets' had two to three resistant alleles of markers based on locus Tm-3 of resistance to TYLCV. The obtained results have demonstrated that the collection of tomato varieties involved in breeding programs in Kazakhstan lacks well-known genetic resistance factors to the considered tomato viruses. Thus, the prospective breeding programs require introduction of known resistant genetic resources to establish resistance to viruses using marker-assisted selection.
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Affiliation(s)
- Alexandr Pozharskiy
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan.,Al Farabi Kazakh National University, 050040, Almaty, Kazakhstan
| | - Valeriya Kostyukova
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan.,Al Farabi Kazakh National University, 050040, Almaty, Kazakhstan
| | - Aisha Taskuzhina
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan.,Al Farabi Kazakh National University, 050040, Almaty, Kazakhstan
| | - Gulnaz Nizamdinova
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
| | - Nina Kisselyova
- Fruit and Vegetable Research Institute, 050060, Almaty, Kazakhstan
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014, University of Helsinki, Finland.,National Laboratory Astana, Nazarbayev University, 010000, Nur-Sultan, Kazakhstan
| | - Nurlybek Karimov
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
| | - Dilyara Gritsenko
- Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
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Xu X, Li M, Zou JX, Zheng YS, Li DD. EgMYB108 regulates very long-chain fatty acid (VLCFA) anabolism in the mesocarp of oil palm. PLANT CELL REPORTS 2022; 41:1449-1460. [PMID: 35362736 DOI: 10.1007/s00299-022-02868-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
EgMYB108 regulates VLCFA anabolism in oil palm. Very long-chain fatty acids (VLCFAs), which are fatty acids with more than 18 C, can not only be used as a form of triglyceride (TAG) but also provide precursors for the biosynthesis of cuticle wax, and they exist in plant epidermal cells in the form of wax in higher plants. However, which and how transcriptional factors (TFs) regulate this process is largely unknown in oil palm. In this study, a MYB transcription factor (EgMYB108) with high expression in the mesocarp of oil palm fruit was characterized. Overexpression of EgMYB108 promoted not only total lipid content but also VLCFA accumulation in oil palm embryoids. Subsequently, transient transformation in protoplasts and qRT-PCR analysis indicated that the EgKCS5 and EgLACS4 genes were significantly increased with the overexpression of EgMYB108. Furthermore, yeast one‑hybrid assays, dual-luciferase assays and EMSAs demonstrated that EgMYB108 binds to the promoters of EgKCS5 and EgLACS4 and regulates their transcription. Finally, EgMYB108 interacts with the promoters of EgLACS and EgKCS simultaneously and finally improves the VLCFA and total lipid contents; a pathway summarizing this interaction was depicted.. The results provide new insight into the mechanism by which EgMYB108 regulates lipid and VLCFA accumulation in oil palm.
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Affiliation(s)
- Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Menghan Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Ji-Xin Zou
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yu-Sheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Sanya, 572025, Hainan, China.
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Moon YJ, Lee SY, Oh SW. A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens. Foods 2022; 11:foods11030322. [PMID: 35159473 PMCID: PMC8833899 DOI: 10.3390/foods11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.
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Pusz-Bochenska K, Pérez-López E, Dumonceaux TJ, Olivier C, Wist TJ. Rapid Molecular Diagnostics in the Field and Laboratory to Detect Plant Pathogen DNA in Potential Insect Vectors. Methods Mol Biol 2022; 2536:179-199. [PMID: 35819606 DOI: 10.1007/978-1-0716-2517-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A variety of sensitive and specific molecular diagnostic assays has been described for detecting nucleic acids in biological samples that may harbor pathogens of interest. These methods include very rapid, isothermal nucleic acid amplification methods that can be deployed outside of the laboratory environment, such as loop-mediated isothermal DNA amplification (LAMP) and recombinase-polymerase amplification (RPA). However, all molecular diagnostic assays must be preceded by nucleic acid extraction from the biological samples of interest, which provides suitable template molecules for the assays. To exploit the features of the amplification assays and be utilized outside of the lab, these methods must be rapid and avoid the need for typical laboratory chemicals and equipment. We describe a protocol for the extraction of DNA from field-collected insects that can be implemented at the point of collection and used to detect the presence of DNA sequences from potential plant pathogens that may be vectored by the insects. This protocol provides template DNA that is suitable for PCR, LAMP, and RPA. The FTA PlantSaver card-based DNA extraction product was also confirmed to amplify the mitochondrial cytochrome oxidase 1 (CO1) universal barcode that could later be sequenced to identify any insect. Lastly, we provide an example using field-collected insects, Neokolla (Graphocephala) heiroglyphica, and demonstrate the detection of the plant pathogen Xylella fastidiosa in carrier insects using PCR, RPA, and LAMP.
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Affiliation(s)
- Karolina Pusz-Bochenska
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Edel Pérez-López
- Université Laval, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département de Phytologie, Québec City, QC, Canada
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chrystel Olivier
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Tyler J Wist
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada.
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12
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Khapilina O, Turzhanova A, Danilova A, Tumenbayeva A, Shevtsov V, Kotukhov Y, Kalendar R. Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult. BIOTECH 2021; 10:23. [PMID: 35822797 PMCID: PMC9245474 DOI: 10.3390/biotech10040023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/25/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022] Open
Abstract
Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.
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Affiliation(s)
- Oxana Khapilina
- National Center for Biotechnology, Korgalzhin Hwy 13/5, Nur-Sultan 010000, Kazakhstan; (A.T.); (A.T.); (V.S.)
| | - Ainur Turzhanova
- National Center for Biotechnology, Korgalzhin Hwy 13/5, Nur-Sultan 010000, Kazakhstan; (A.T.); (A.T.); (V.S.)
| | - Alevtina Danilova
- Altai Botanical Garden, Yermakova Str 1, Ridder 070000, Kazakhstan; (A.D.); (Y.K.)
| | - Asem Tumenbayeva
- National Center for Biotechnology, Korgalzhin Hwy 13/5, Nur-Sultan 010000, Kazakhstan; (A.T.); (A.T.); (V.S.)
| | - Vladislav Shevtsov
- National Center for Biotechnology, Korgalzhin Hwy 13/5, Nur-Sultan 010000, Kazakhstan; (A.T.); (A.T.); (V.S.)
| | - Yuri Kotukhov
- Altai Botanical Garden, Yermakova Str 1, Ridder 070000, Kazakhstan; (A.D.); (Y.K.)
| | - Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, University of Helsinki, FI-00014 Helsinki, Finland
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13
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Kalendar R, Shustov AV, Schulman AH. Palindromic Sequence-Targeted (PST) PCR, Version 2: An Advanced Method for High-Throughput Targeted Gene Characterization and Transposon Display. FRONTIERS IN PLANT SCIENCE 2021; 12:691940. [PMID: 34239528 PMCID: PMC8258406 DOI: 10.3389/fpls.2021.691940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 05/28/2023]
Abstract
Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that are in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for combining of sequence-specific primers with designed capturing primers capable of annealing to unknown DNA targets, thereby offering the rapidity and effectiveness of PCR. This study presents a methodological improvement to the previously described GW technique known as palindromic sequence-targeted PCR (PST-PCR). Like PST-PCR, this new method (called PST-PCR v.2) relies on targeting of capturing primers to palindromic sequences arbitrarily present in natural DNA templates. PST-PCR v.2 consists of two rounds of PCR. The first round uses a combination of one sequence-specific primer with one capturing (PST) primer. The second round uses a combination of a single (preferred) or two universal primers; one anneals to a 5' tail attached to the sequence-specific primer and the other anneals to a different 5' tail attached to the PST primer. The key advantage of PST-PCR v.2 is the convenience of using a single universal primer with invariable sequences in GW processes involving various templates. The entire procedure takes approximately 2-3 h to produce the amplified PCR fragment, which contains a portion of a template flanked by the sequence-specific and capturing primers. PST-PCR v.2 is highly suitable for simultaneous work with multiple samples. For this reason, PST-PCR v.2 can be applied beyond the classical task of GW for studies in population genetics, in which PST-PCR v.2 is a preferred alternative to amplified fragment length polymorphism (AFLP) or next-generation sequencing. Furthermore, the conditions for PST-PCR v.2 are easier to optimize, as only one sequence-specific primer is used. This reduces non-specific random amplified polymorphic DNA (RAPD)-like amplification and formation of non-templated amplification. Importantly, akin to the previous version, PST-PCR v.2 is not sensitive to template DNA sequence complexity or quality. This study illustrates the utility of PST-PCR v.2 for transposon display (TD), which is a method to characterize inter- or intra-specific variability related to transposon integration sites. The Ac transposon sequence in the maize (Zea mays) genome was used as a sequence tag during the TD procedure to characterize the Ac integration sites.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Alan H. Schulman
- Viikki Plant Science Centre, HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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Erper I, Ozer G, Kalendar R, Avci S, Yildirim E, Alkan M, Turkkan M. Genetic Diversity and Pathogenicity of Rhizoctonia spp. Isolates Associated with Red Cabbage in Samsun (Turkey). J Fungi (Basel) 2021; 7:jof7030234. [PMID: 33801129 PMCID: PMC8004240 DOI: 10.3390/jof7030234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/31/2023] Open
Abstract
A total of 132 Rhizoctonia isolates were recovered from red cabbage plants with root rot and wirestem symptoms in the province of Samsun (Turkey) between 2018 and 2019. Based on the sequence analysis of the internal transcribed spacer (ITS) region located between the 18S and 28S ribosomal RNA genes and including nuclear staining, these 124 isolates were assigned to multinucleate Rhizoctonia solani, and eight were binucleate Rhizoctonia. The most prevalent anastomosis group (AG) was AG 4 (84%), which was subdivided into AG 4 HG-I (81%) and AG 4 HG-III (3%), followed by AG 5 (10%) and AG-A (6%), respectively. The unweighted pair group method phylogenetic tree resulting from the data of 68 isolates with the inter-PBS amplification DNA profiling method based on interspersed retrotransposon element sequences confirmed the differentiation of AGs with a higher resolution. In the greenhouse experiment with representative isolates (n = 24) from AGs on red cabbage (cv. Rondale), the disease severity index was between 3.33 and 4.0 for multinucleate AG isolates and ranged from 2.5 to 3.17 for AG-A isolates. In the pathogenicity assay of six red cabbage cultivars, one isolate for each AG was tested using a similar method, and all cultivars were susceptible to AG 4 HG-I and AG 4 HG-III isolates. Redriver and Remale were moderately susceptible, while Rescue, Travero, Integro, and Rondale were susceptible to the AG 5 isolate. The results indicate that the most prevalent and aggressive AGs of Rhizoctonia are devastating pathogens to red cabbage, which means that rotation with nonhost-crops for these AGs may be the most effective control strategy. This is the first comprehensive study of Rhizoctonia isolates in red cabbage using a molecular approach to assess genetic diversity using iPBS-amplified DNA profiling.
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Affiliation(s)
- Ismail Erper
- Department of Plant Protection, Faculty of Agriculture, Ondokuz Mayis University, Atakum, 55139 Samsun, Turkey; (S.A.); (E.Y.)
- Department of Plant Protection, Faculty of Agriculture, Kyrgyz Turkish Manas University, Bishkek 720044, Kyrgyzstan
- Correspondence: (I.E.); (R.K.); Tel.: +9036-2457-6034 (I.E.); +3585-0448-3505 (R.K.)
| | - Goksel Ozer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (G.O.); (M.A.)
| | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, 00014 Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
- Correspondence: (I.E.); (R.K.); Tel.: +9036-2457-6034 (I.E.); +3585-0448-3505 (R.K.)
| | - Sirin Avci
- Department of Plant Protection, Faculty of Agriculture, Ondokuz Mayis University, Atakum, 55139 Samsun, Turkey; (S.A.); (E.Y.)
| | - Elif Yildirim
- Department of Plant Protection, Faculty of Agriculture, Ondokuz Mayis University, Atakum, 55139 Samsun, Turkey; (S.A.); (E.Y.)
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey; (G.O.); (M.A.)
| | - Muharrem Turkkan
- Department of Plant Protection, Faculty of Agriculture, Ordu University, 52200 Ordu, Turkey;
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Khapilina O, Raiser O, Danilova A, Shevtsov V, Turzhanova A, Kalendar R. DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai. PeerJ 2021; 9:e10674. [PMID: 33510974 PMCID: PMC7798630 DOI: 10.7717/peerj.10674] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan's Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.
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Affiliation(s)
| | - Olesya Raiser
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | | | | | | | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Aqmola, Kazakhstan
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16
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Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET. FRONTIERS IN PLANT SCIENCE 2021; 12:747886. [PMID: 35082803 PMCID: PMC8784781 DOI: 10.3389/fpls.2021.747886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- *Correspondence: Ruslan Kalendar
| | - Akmaral Baidyussen
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
- Yuri Shavrukov
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