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Ishwarya Lakshmi VG, Sreedhar M, JhansiLakshmi V, Gireesh C, Rathod S, Bohar R, Deshpande S, Laavanya R, Kiranmayee KNSU, Siddi S, Vanisri S. Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice. Front Genet 2022; 13:914131. [PMID: 35899197 PMCID: PMC9309266 DOI: 10.3389/fgene.2022.914131] [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: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Rice (Oryza sativa L.) is an important source of nutrition for the world's burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (StΓ₯l)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers.
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Affiliation(s)
- V. G. Ishwarya Lakshmi
- Department of Genetics and Plant Breeding, College of Agriculture, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - M. Sreedhar
- Administrative Office, PJTSAU, Hyderabad, India
| | | | - C. Gireesh
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Santosha Rathod
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Rajaguru Bohar
- CGIAR Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - R. Laavanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Sreedhar Siddi
- Agricultural Research Station, PJTSAU, Peddapalli, India
| | - S. Vanisri
- Institute of Biotechnology, PJTSAU, Hyderabad, India
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Bai Q, He B, Cai Y, Lian H, Zhang Q, Liang D, Wang Y. Genetic Diversity and Population Structure of Schima superba From Southern China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.879512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tree Schima superba is important for afforestation and fire prevention in southern China. The wood of this tree can also be used for furniture and buildings. However, the lack of genetic background and genomic information for this species has lowered wood yield speed and quality improvement. Here, we aimed to discover genome-wide single nucleotide polymorphisms (SNPs) in 302 S. superba germplasms collected from southern China and to use these SNPs to investigate the population structure. Using genotyping by sequencing, a total of 785 high-quality SNP markers (minor allele frequency [MAF] β₯ 0.05) were identified from 302 accessions collected from seven geographical locations. Population structure analyses and principal coordinate analyses (PCoAs) indicated that these germplasm resources can be clearly separated into different populations. The S. superba accessions originating from Yunnan (YN) and Guangxi (GX) fell into the same population, separate from the accessions originating from Guangdong (GD), which indicated that these two regions should be regarded as major provenances of this species. In addition, two independent core germplasm sets with abundant genetic polymorphisms were constructed to support the breeding work. The identification of SNP markers, analyses of population genetics, and construction of core germplasm sets will greatly promote the molecular breeding work of S. superba.
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Molecular sexual determinants in Pistacia genus by KASP assay. Mol Biol Rep 2022; 49:5473-5482. [PMID: 35235154 DOI: 10.1007/s11033-022-07285-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 02/18/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Pistacia is a genus of dioecious plant species whose trees can take 4-5Β years to reach the economically valuable fruit-bearing stage. The fruits have great importance as raw material in the food, healthcare, and baking industries. For that reason, the identification of individual plants in the early juvenile period for the pollination and positioning of trees is crucial for growers. The objective of this study is to develop markers for each Pistacia species that can help in screening the sex of plant seedlings before they reach the reproductive stage, without waiting for morphological characteristics to appear. METHODS AND RESULTS Within this context, by using the power of the kompetitive allele-specific PCR (KASP) assay technology as a marker screening system, we successfully discriminated seven out of eight Pistacia species: P. atlantica, P. integerrima, P. khinjuk, P. mutica, P. terebinthus, P. vera, and P. lentiscus. We used a high-throughput DNA sequence read archive (SRA) to assemble a reference genome that was employed in our studies as a de novo bioinformatics method. Four genomic regions from SRA and three single-nucleotide polymorphism (SNP) positions from Kafkas et al. BMC Genomics 16:98, 2015) were selected and sequenced with collected plant material from predominantly the AntepfΔ±stΔ±gΔ± Research Institute Collection Garden, and eight species were aligned intraspecifically for SNP mining. In total, 12 SNP markers were converted to KASP markers, and 5 of them (SNP-PIS-133396, SNP-PIS-167992, P-ATL-91951-565, P-INT-91951-256, P-KHI-91951-115) showed clear allelic discrimination between male and female plants. SNP-PIS-167992 and P-ATL-91951-565 were identified as the best marker assays because they showed allelic frequency differences for all individuals and for both homozygous and heterozygous characters. These markers could be the most comprehensive ones for the whole genus because they showed discriminative power for several species. CONCLUSIONS This study is the first one to use the KASP assay for sex discrimination in Pistacia species, and it can be regarded as a precursor study for sex discrimination by KASP for plants in general.
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Kalendar R, Shustov AV, Akhmetollayev I, Kairov U. Designing Allele-Specific Competitive-Extension PCR-Based Assays for High-Throughput Genotyping and Gene Characterization. Front Mol Biosci 2022; 9:773956. [PMID: 35300118 PMCID: PMC8921500 DOI: 10.3389/fmolb.2022.773956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/02/2022] [Indexed: 12/03/2022] Open
Abstract
Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer's 3' end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available (http://primerdigital.com/tools/). Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success.
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Affiliation(s)
- Ruslan Kalendar
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- PrimerDigital Ltd., Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Ulykbek Kairov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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Feng B, Wang X, Chen S, Zhang Y, Su X, Song S. Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2915-2923. [PMID: 34553046 PMCID: PMC8451692 DOI: 10.1080/23802359.2021.1972857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum, Allium fistulosum, and Allium cepa, but genetically close to Allium tuberosum. The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera. In addition, two KASP markers for discriminating the Dongfeng samples from the other four A. victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.
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Affiliation(s)
- Bo Feng
- Jilin Agricultural University, Changchun, Jilin, China.,Jilin Provincial Academy of Forestry Sciences, Changchun, Jilin, China
| | - Xiufeng Wang
- Jilin Academy of Vegetable and Flower Sciences, Changchun, Jilin, China
| | - Shanshan Chen
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yue Zhang
- Jilin Academy of Vegetable and Flower Sciences, Changchun, Jilin, China
| | - Xuejiao Su
- Jilin Agricultural University, Changchun, Jilin, China
| | - Shuyao Song
- Jilin Agricultural University, Changchun, Jilin, China
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Liu Y, Song Q, Kang W, Yang F, Yan W. The complete chloroplast genome sequence of Rubus sachalinensis LΓ©vl. Mitochondrial DNA B Resour 2021; 6:1621-1622. [PMID: 34027073 PMCID: PMC8118508 DOI: 10.1080/23802359.2021.1926354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Yue Liu
- Department of Medical College, Qinghai University, Xining, PR China
| | - QingYun Song
- Department of Medical College, Qinghai University, Xining, PR China
| | - WenJuan Kang
- Department of Medical College, Qinghai University, Xining, PR China
| | - Fang Yang
- Department of Medical College, Qinghai University, Xining, PR China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, PR China
| | - Wei Yan
- Department of Medical College, Qinghai University, Xining, PR China
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Ma KB, Yang SJ, Jo YS, Kang SS, Nam M. Development of Kompetitive Allele Specific PCR markers for identification of persimmon varieties using genotyping-by-sequencing. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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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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Kamnev ΠΠ, Antonova OY, Dunaeva SΠ, Gavrilenko TA, Chukhina IG. [Molecular markers in the genetic diversity studies of representatives of the genus Rubus L. and prospects of their application in breeding]. Vavilovskii Zhurnal Genet Selektsii 2020; 24:20-30. [PMID: 33659777 PMCID: PMC7893148 DOI: 10.18699/vj20.591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Π ΠΎΠ΄ Rubus L. (ΡΠ΅ΠΌΠ΅ΠΉΡΡΠ²ΠΎ Rosaceae Juss.), ΠΏΠΎ ΠΎΡΠ΅Π½ΠΊΠ°ΠΌ ΡΠ°Π·Π½ΡΡ
ΡΠΈΡΡΠ΅ΠΌΠ°ΡΠΈΠΊΠΎΠ², ΡΠΎΡΡΠΎΠΈΡ ΠΈΠ· 12β16 ΠΏΠΎΠ΄ΡΠΎΠ΄ΠΎΠ², ΠΎΠ±ΡΠ΅Π΄ΠΈΠ½ΡΡΡΠΈΡ
~750 Π²ΠΈΠ΄ΠΎΠ². Π‘Π°ΠΌΡΠ΅ ΠΊΡΡΠΏΠ½ΡΠ΅ ΠΏΠΎ ΡΠΈΡΠ»Ρ Π²ΠΈΠ΄ΠΎΠ² ΠΏΠΎΠ΄ΡΠΎΠ΄Ρ β Idaeobatus (Focke) Focke, ΠΊ ΠΊΠΎΡΠΎΡΠΎΠΌΡ ΠΎΡΠ½ΠΎΡΡΡΡΡ ΠΌΠ°Π»ΠΈΠ½Ρ, ΠΈ ΡΠΈΠΏΠΎΠ²ΠΎΠΉ ΠΏΠΎΠ΄ΡΠΎΠ΄ Rubus (=Eubatus Focke), Π²ΠΊΠ»ΡΡΠ°ΡΡΠΈΠΉ Π²ΠΈΠ΄Ρ Π΅ΠΆΠ΅Π²ΠΈΠΊ. ΠΡΠ΅Π΄ΡΡΠ°Π²ΠΈΡΠ΅Π»ΠΈ ΡΠΎΠ΄Π° Rubus ΠΎΠ±Π»Π°Π΄Π°ΡΡ Π²ΡΡΠΎΠΊΠΎΠΉ ΠΏΠΈΡΠ΅Π²ΠΎΠΉ ΠΈ Ρ
ΠΎΠ·ΡΠΉΡΡΠ²Π΅Π½Π½ΠΎΠΉ ΡΠ΅Π½Π½ΠΎΡΡΡΡ, Π° ΡΠ°ΠΊΠΆΠ΅ Π»Π΅ΠΊΠ°ΡΡΡΠ²Π΅Π½Π½ΡΠΌΠΈ ΡΠ²ΠΎΠΉΡΡΠ²Π°ΠΌΠΈ. Π‘Π΅Π»Π΅ΠΊΡΠΈΠΎΠ½Π½ΡΠ΅ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½Ρ Π½Π° ΡΠ°ΡΡΠΈΡΠ΅Π½ΠΈΠ΅ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΡ ΠΈ ΡΠΎΠ·Π΄Π°Π½ΠΈΠ΅ Π½ΠΎΠ²ΡΡ
ΡΠΎΡΡΠΎΠ² ΠΌΠ°Π»ΠΈΠ½ ΠΈ Π΅ΠΆΠ΅Π²ΠΈΠΊ, ΡΡΡΠΎΠΉΡΠΈΠ²ΡΡ
ΠΊ Π±ΠΈΠΎΡΠΈΡΠ΅ΡΠΊΠΈΠΌ ΠΈ Π°Π±ΠΈΠΎΡΠΈΡΠ΅ΡΠΊΠΈΠΌ ΡΡΡΠ΅ΡΡΠΎΡΠ°ΠΌ ΠΈ ΠΎΡΠ»ΠΈΡΠ°ΡΡΠΈΡ
ΡΡ Π²ΡΡΠΎΠΊΠΈΠΌ ΠΊΠ°ΡΠ΅ΡΡΠ²ΠΎΠΌ ΠΏΠ»ΠΎΠ΄ΠΎΠ². Π‘ΠΎΠ²ΡΠ΅ΠΌΠ΅Π½Π½ΡΠ΅ ΡΠ΅Π»Π΅ΠΊΡΠΈΠΎΠ½Π½ΠΎ-Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΈΠ΅ ΠΏΡΠΎΠ³ΡΠ°ΠΌΠΌΡ Π²ΡΠ΅ ΡΠΈΡΠ΅ Π²ΠΊΠ»ΡΡΠ°ΡΡ Π΄ΠΎΡΡΠΈΠΆΠ΅Π½ΠΈΡ ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΠΎΠΉ Π³Π΅Π½Π΅ΡΠΈΠΊΠΈ ΠΈ Π³Π΅Π½ΠΎΠΌΠΈΠΊΠΈ. Π Π΄Π°Π½Π½ΠΎΠΉ ΡΡΠ°ΡΡΠ΅ ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»Π΅Π½ ΠΎΠ±Π·ΠΎΡ ΡΡΠ½Π΄Π°ΠΌΠ΅Π½ΡΠ°Π»ΡΠ½ΡΡ
ΠΈ ΠΏΡΠΈΠΊΠ»Π°Π΄Π½ΡΡ
ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠΉ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΡ ΠΊΡΠ»ΡΡΠΈΠ²ΠΈΡΡΠ΅ΠΌΡΡ
ΠΈ Π΄ΠΈΠΊΠΎΡΠ°ΡΡΡΡΠΈΡ
Π²ΠΈΠ΄ΠΎΠ² ΡΠΎΠ΄Π° Rubus, Π²ΡΠΏΠΎΠ»Π½Π΅Π½Π½ΡΡ
Π½Π° ΠΎΡΠ½ΠΎΠ²Π΅ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ² ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΠΎΠ³ΠΎ ΠΌΠ°ΡΠΊΠΈΡΠΎΠ²Π°Π½ΠΈΡ. Π Π°ΡΡΠΌΠΎΡΡΠ΅Π½Ρ ΠΎΡΠ½ΠΎΠ²Π½ΡΠ΅ ΡΠΈΠΏΡ ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΡΡ
ΠΌΠ°ΡΠΊΠ΅ΡΠΎΠ² (RFLP, RAPD, SSR, ISSR, AFLP, SCAR, SSCP, ΡΠ΅ΡΡΠΎΡΡΠ°Π½ΡΠΏΠΎΠ·ΠΎΠ½Π½ΡΠ΅ ΠΌΠ°ΡΠΊΠ΅ΡΡ ΠΈ Ρ. Π΄.) ΠΈ ΠΎΠ±Π»Π°ΡΡΠΈ ΠΈΡ
ΠΏΡΠΈΠΌΠ΅Π½Π΅Π½ΠΈΡ Π² ΠΈΠ·ΡΡΠ΅Π½ΠΈΠΈ ΠΏΡΠ΅Π΄ΡΡΠ°Π²ΠΈΡΠ΅Π»Π΅ΠΉ ΡΠΎΠ΄Π° Rubus. ΠΡΠΈΠ²Π΅Π΄Π΅Π½Ρ ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΡ ΡΠ°Π±ΠΎΡ ΠΏΠΎ ΠΈΡΠΏΠΎΠ»ΡΠ·ΠΎΠ²Π°Π½ΠΈΡ ΠΌΠ΅ΡΠΎΠ΄ΠΎΠ² ΠΠΠ-ΠΌΠ°ΡΠΊΠΈΡΠΎΠ²Π°Π½ΠΈΡ Π΄Π»Ρ ΡΠ΅ΡΠ΅Π½ΠΈΡ ΡΠ°ΠΌΡΡ
ΡΠ°Π·Π½ΡΡ
Π·Π°Π΄Π°Ρ, Π²ΠΊΠ»ΡΡΠ°Ρ: ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΠ΅ ΠΌΠ΅ΠΆΠ²ΠΈΠ΄ΠΎΠ²ΠΎΠ³ΠΎ ΠΈ Π²Π½ΡΡΡΠΈΠ²ΠΈΠ΄ΠΎΠ²ΠΎΠ³ΠΎ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠ³ΠΎ ΡΠ°Π·Π½ΠΎΠΎΠ±ΡΠ°Π·ΠΈΡ, ΡΠΈΠ»ΠΎΠ³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΡΠ²ΡΠ·Π΅ΠΉ Π²ΠΈΠ΄ΠΎΠ² ΠΈ Π½Π°Π΄Π²ΠΈΠ΄ΠΎΠ²ΡΡ
ΡΠ°ΠΊΡΠΎΠ½ΠΎΠ², Π²ΡΡΡΠ½Π΅Π½ΠΈΠ΅ ΡΠΏΠΎΡΠ½ΡΡ
Π²ΠΎΠΏΡΠΎΡΠΎΠ² ΡΠΈΡΡΠ΅ΠΌΠ°ΡΠΈΠΊΠΈ, Π³Π΅Π½ΠΎΡΠΈΠΏΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ ΠΈ ΡΡΠΎΡΠ½Π΅Π½ΠΈΠ΅ ΡΠΎΠ΄ΠΎΡΠ»ΠΎΠ²Π½ΡΡ
ΡΠΎΡΡΠΎΠ² ΠΌΠ°Π»ΠΈΠ½ ΠΈ Π΅ΠΆΠ΅Π²ΠΈΠΊ, ΠΈΠ·ΡΡΠ΅Π½ΠΈΠ΅ ΡΠΎΠΌΠ°ΠΊΠ»ΠΎΠ½Π°Π»ΡΠ½ΠΎΠΉ ΠΈΠ·ΠΌΠ΅Π½ΡΠΈΠ²ΠΎΡΡΠΈ ΠΈ Π΄Ρ. ΠΠ°ΠΈΠ±ΠΎΠ»Π΅Π΅ Π²Π°ΠΆΠ½ΡΠΌ ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠΎΠΌ Π² ΠΏΡΠ°ΠΊΡΠΈΡΠ΅ΡΠΊΠΎΠΌ ΠΏΠ»Π°Π½Π΅ ΡΠ²Π»ΡΠ΅ΡΡΡ ΡΠΎΠ·Π΄Π°Π½ΠΈΠ΅ Π½Π°ΡΡΡΠ΅Π½Π½ΡΡ
ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΠΎ-Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΠΊΠ°ΡΡ Π΄Π»Ρ ΡΠ°Π·Π½ΡΡ
Π²ΠΈΠ΄ΠΎΠ² ΠΌΠ°Π»ΠΈΠ½ ΠΈ Π΅ΠΆΠ΅Π²ΠΈΠΊ, Π½Π° ΠΊΠΎΡΠΎΡΡΡ
Π»ΠΎΠΊΠ°Π»ΠΈΠ·ΠΎΠ²Π°Π½Ρ ΠΌΠ½ΠΎΠ³ΠΎΡΠΈΡΠ»Π΅Π½Π½ΡΠ΅ Π³Π΅Π½Ρ ΠΈ QTL, Π΄Π΅ΡΠ΅ΡΠΌΠΈΠ½ΠΈΡΡΡΡΠΈΠ΅ ΡΠ°Π·Π»ΠΈΡΠ½ΡΠ΅ Ρ
ΠΎΠ·ΡΠΉΡΡΠ²Π΅Π½Π½ΠΎ ΡΠ΅Π½Π½ΡΠ΅ ΠΏΡΠΈΠ·Π½Π°ΠΊΠΈ. Π ΡΠΎ ΠΆΠ΅ Π²ΡΠ΅ΠΌΡ Π½Π΅ΠΎΠ±Ρ
ΠΎΠ΄ΠΈΠΌΠΎ ΠΎΡΠΌΠ΅ΡΠΈΡΡ, ΡΡΠΎ ΡΠΈΡΠ»ΠΎ ΠΌΠ°ΡΠΊΠ΅ΡΠΎΠ², ΠΏΠ΅ΡΡΠΏΠ΅ΠΊΡΠΈΠ²Π½ΡΡ
Π΄Π»Ρ ΠΏΡΠΎΠ²Π΅Π΄Π΅Π½ΠΈΡ ΡΡΡΠ΅ΠΊΡΠΈΠ²Π½ΠΎΠ³ΠΎ ΠΌΠΎΠ»Π΅ΠΊΡΠ»ΡΡΠ½ΠΎΠ³ΠΎ ΡΠΊΡΠΈΠ½ΠΈΠ½Π³Π°, ΠΏΠΎΠΊΠ° Π΅ΡΠ΅ Π½Π΅Π΄ΠΎΡΡΠ°ΡΠΎΡΠ½ΠΎ.
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Affiliation(s)
- Π Π Kamnev
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia Altai State University, Barnaul, Russia
| | - O Yu Antonova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - S Π Dunaeva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - T A Gavrilenko
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - I G Chukhina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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10
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Zengin G, Ferrante C, Senkardes I, Gevrenova R, Zheleva-Dimitrova D, Menghini L, Orlando G, Recinella L, Chiavaroli A, Leone S, Brunetti L, Picot-Allain CMN, Rengasamy KR, Mahomoodally MF. Multidirectional biological investigation and phytochemical profile of Rubus sanctus and Rubus ibericus. Food Chem Toxicol 2019; 127:237-250. [PMID: 30914354 DOI: 10.1016/j.fct.2019.03.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 02/06/2023]
Abstract
In the present study, the biological properties, including, the enzyme inhibitory and antioxidant activities, as well as, the phytochemical profile of the ethyl acetate, methanol, and water extracts of Rubus sanctus Schreb. and Rubus ibericus Juz. leaves were determined using in vitro bioassays. Wide range of phytochemicals, including, hydroxybenzoic acids, hydroxycinnamic acids, acylquinic acids, ellagitannins, flavonoids, and triterpenoid saponins were determined using UHPLC-ESI/HRMS technique. The ethyl acetate and methanol extracts of the studied Rubus species effectively inhibited acetyl and butyryl cholinesterase. On the other hand, R. sanctus water extract showed low inhibition against Ξ±-amylase and prominent inhibitory action against Ξ±-glucosidase. Data collected from this study reported the radical scavenging and reducing potential of the studied Rubus species. Investigation of the protective effects of the different extracts of R. sanctus and R. ibericus in experimental model of ulcerative colitis was performed. The extracts were also tested on spontaneous migration of human colon cancer cells (HCT116) in wound healing experimental paradigm. Only R. sanctus methanol extract inhibited spontaneous HCT116 migration in the wound healing test. Our results suggested that R. sanctus and R. ibericus may be potential candidates as sources of biologically-active compounds for the development of nutraceuticals, pharmaceuticals, and/or cosmetics.
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Affiliation(s)
- Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University, Konya, Turkey.
| | - Claudio Ferrante
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | - Ismail Senkardes
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Reneta Gevrenova
- Department of Pharmacognosy, Faculty of Pharmacy, Medical University of Sofia, Bulgaria
| | | | - Luigi Menghini
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | - Giustino Orlando
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy.
| | - Lucia Recinella
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | - Annalisa Chiavaroli
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | - Sheila Leone
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | - Luigi Brunetti
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Chieti, 66100, Italy
| | | | - Kannan Rr Rengasamy
- Department of Bio-resources and Food Science, Konkuk University, Seoul, South Korea
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