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Ibrahim EA, Alhaithloul HAS, Shamseldin SAM, Awaly SBH, El-Latif Hesham A, Abdelkader MFM, Alqahtani MM, Alzuaibr FM, Alasmari A, Sukar NA, Diyasty MZ, Abdein MA. Morphological, Biochemical, and Molecular Diversity Assessment of Egyptian Bottle Gourd Cultivars. Genet Res (Camb) 2024; 2024:4182158. [PMID: 38205231 PMCID: PMC10781529 DOI: 10.1155/2024/4182158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The genetic variability and relationships between ten bottle gourd cultivars were evaluated based on morphological, biochemical, and molecular parameters. The results displayed high variability among selected cultivars in terms of photosynthetic pigments, total free amino acids, total phenol content, isozymes pattern, and protein electrophoresis. Furthermore, differences in molecular markers were revealed by the SCoT technique. The peroxidase (POD) and polyphenyl oxidase (PPO) isozymes patterns did not detect significant differences in bands among cultivars. The protein patterns revealed seventeen bands ranging from 126 to 9 kDa and five polymorphic bands representing 29.41%. On the other hand, eight SCoT primers were used to evaluate the genetic variability and relationships between the ten Egyptian bottle gourd cultivars. The results of SCoT analysis detected 44 amplicons with 50% polymorphism. In addition, the results of the phylogenetic tree that is constructed based on the similarity coefficient revealed by SCoT analysis confirm the results of biochemical analysis indicating a genetic relationship between the most efficient bottle gourd cultivars (S1 and S2 cultivars). In addition, there is a genetic relationship among the less efficient bottle gourd cultivars (S4 and S5 cultivars). These results could be beneficial to distinguish among bottle gourd cultivars in the plant breeding programs.
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Affiliation(s)
- Ehab A. Ibrahim
- Department of Cross-Pollinated Vegetable Research, Horticulture Research Institute, Agricultural Research Centre, Giza 12619, Egypt
| | | | - Sahar A. M. Shamseldin
- Botany Department, Women's College for Arts, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Sara B. H. Awaly
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni Suef 62521, Egypt
| | - Mohamed F. M. Abdelkader
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh 12372, Saudi Arabia
| | - Mesfer M. Alqahtani
- Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University, P.O. Box 1040, Ad-Dawadimi, Shaqra 11911, Saudi Arabia
| | | | - Abdulrahman Alasmari
- Biology Department, College of Science, Tabuk University, Tabuk 71491, Saudi Arabia
| | - Noha A. Sukar
- Agricultural Botany (Genetics) Department, Faculty of Agriculture (Girls), Al-Azhar University, Cairo, Egypt
| | - Mohamed Z. Diyasty
- Genetic Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Abdein
- Seeds Development Department, El-Nada Misr Scientific Research and Development Projects, Turrell, Mansoura 35511, Egypt
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Kulyan R, Samarina L, Shkhalakhova R, Kuleshov A, Ukhatova Y, Antonova O, Koninskaya N, Matskiv A, Malyarovskaya V, Ryndin A. InDel and SCoT Markers for Genetic Diversity Analysis in a Citrus Collection from the Western Caucasus. Int J Mol Sci 2023; 24:ijms24098276. [PMID: 37175981 PMCID: PMC10179493 DOI: 10.3390/ijms24098276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Citrus collections from extreme growing regions can be an important source of tolerant germplasms for the breeding of cold-tolerant varieties. However, the efficient utilization of these germplasms requires their genetic background information. Thus, efficient marker systems are necessary for the characterization and identification of valuable accessions. In this study, the efficiency of 36 SCoT markers and 60 InDel markers were evaluated as part of the broad citrus collection of the Western Caucasus. The interspecific and intraspecific genetic diversity and genetic structures were analyzed for 172 accessions, including 31 species and sets of the locally derived cultivars. Single markers, such as SCoT18 (0.84), SCoT20 (0.93), SCoT23 (0.87), SCoT31 (0.88), SCoT36 (0.87) и LG 1-4 (0.94), LG 4-3 (0.86), LG 7-11 (0.98), and LG 8-10 (0.83), showed a high discriminating power, indicating the good applicability of these markers to assess intraspecific diversity of the genus Citrus. Overall, SCoT markers showed a higher level of polymorphism than InDel markers. According to analysis of population structure, SCoT and InDel markers showed K = 9 and K = 5 genetic clusters, respectively. The lowest levels of genetic admixtures and diversity were observed among the locally derived satsumas and lemons. The highest level of genetic admixtures was observed in the lime group. Phylogenetic relationships indicated a high level of interspecific genetic diversity but a low level of intraspecific diversity in locally derived satsumas and lemons. The results provide new insight into the origin of citrus germplasms and their distribution in colder regions. Furthermore, they are important for implementing conservation measures, controlling genetic erosion, developing breeding strategies, and improving breeding efficiency.
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Affiliation(s)
- Raisa Kulyan
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexandr Kuleshov
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Yulia Ukhatova
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
- Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia
| | - Olga Antonova
- "Sirius University of Science and Technology", Olimpiyskiy Ave. b.1, 354340 Sirius, Kransnodar Region, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Valentina Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, 354002 Sochi, Russia
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Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran. BIOCHEM SYST ECOL 2023. [DOI: 10.1016/j.bse.2023.104618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Cornea-Cipcigan M, Pamfil D, Sisea CR, Margaoan R. Characterization of Cyclamen genotypes using morphological descriptors and DNA molecular markers in a multivariate analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1100099. [PMID: 36778673 PMCID: PMC9909266 DOI: 10.3389/fpls.2023.1100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Morphological and molecular characterization of germplasm is essential for the improvement of cultivated plants efforts. This study investigated the genetic diversity of 32 Cyclamen genotypes comprising 16 C. persicum varieties and 16 Cyclamen species using multivariate analysis for 36 morphological traits (19 quantitative and 17 qualitative) and molecular characterization (SRAP and SCoT markers). The color CIELab parameters were collected via PCE-CSM7 that separately measured the leaves dark and silvery patterns and the flower's slip (region of the petal top), eye (the region of the petal base) and sepal. Genetic diversity was also evaluated using Shannon Wiener (H') and Simpson's (λ) Indices, and Pilou evenness (J) using the library vegan from R software. According to the principal component analysis, the variables that contributed the most were leaf pattern color, leaf abaxial surface color, pedicel coiling, leaf and stem number. The color indicators of Cyclamen leaves showed decreased L* values in darker colored genotypes, whereas increased a* values were noticed in flower eye and lower in slip. Molecular characterization was based on 26 SRAP and 12 SCoT markers that produced clearly repeatable DNA bands and exhibited significant levels of polymorphism. Based on the morphological traits and molecular markers data, the UPGMA method for hierarchical clustering technique was used to generate the dendrograms, and their entanglement was obtained using the Tanglegram algorithm from the dendextend package with the R software. Entanglement analysis (0.30) between dendrograms obtained from the morphological and genetic analysis using SRAP markers showed a high association. Comparison between color measurements of flowers (entanglement=0.45) and leaves (entanglement=0.47) with SCoT analysis revealed differences at species level, discriminating between similar genotypes. Combined phenotypic and molecular analysis improved the comprehensive estimation of real diversity in the investigated Cyclamen genotypes. The findings of the present study are useful for quantifying diversity and genetic variability in Cyclamen breeding and genetic investigations.
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Affiliation(s)
- Mihaiela Cornea-Cipcigan
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Doru Pamfil
- Research Centre for Biotechnology in Agriculture Affiliated to Romanian Academy, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristian Radu Sisea
- Department of Horticulture and Business in Rural Development, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Rodica Margaoan
- Laboratory of Cell Analysis and Spectrometry, Advanced Horticultural Research Institute of Transylvania, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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Cai Y, Gao Y, Zhang Z, Liu H, Wang Y, Ma Y, Li Y, Feng S, Wang H. Development and Application of a Cultivar-Specific Sequence-Characterized Amplified Region (SCAR) Marker for the Detection of Chrysanthemum morifolium Ramat. 'Daboju'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050604. [PMID: 35270074 PMCID: PMC8912837 DOI: 10.3390/plants11050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemummorifolium Ramat. 'Daboju' is a C. morifolium cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of C. morifolium 'Daboju' are very similar to those of other C. morifolium cultivars, they are often confused in practice. However, the medicinal value and practical use of C. morifolium depends on using the correct rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, similar C. morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in C. morifolium 'Daboju' (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 C. morifolium cultivars, ten C. morifolium 'Daboju' populations, and different simulated adulterations of 'Daboju' with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested C. morifolium 'Daboju' samples but failed in the absence of 'Daboju'. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from C. morifolium 'Daboju'. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of C. morifolium 'Daboju'. It can play an important role in ensuring the quality of medicinal preparations and protecting C. morifolium 'Daboju' germplasm resources in breeding programs and in identifying lines generated from this cultivar.
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Affiliation(s)
- Yuchen Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Yadi Gao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhao Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huijie Liu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yifan Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yuxin Ma
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yixin Li
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
| | - Huizhong Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
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Population Analysis of Diospyros lotus in the Northwestern Caucasus Based on Leaf Morphology and Multilocus DNA Markers. Int J Mol Sci 2022; 23:ijms23042192. [PMID: 35216308 PMCID: PMC8877681 DOI: 10.3390/ijms23042192] [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: 12/31/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 01/02/2023] Open
Abstract
Diospyros lotus is the one of the most frost-tolerant species in the Diospyros genera, used as a rootstock for colder regions. Natural populations of D. lotus have a fragmented character of distribution in the Northwestern Caucasus, one of the coldest regions of Diospyros cultivation. To predict the behavior of D. lotus populations in an extreme environment, it is necessary to investigate the intraspecific genetic diversity and phenotypic variability of populations in the colder regions. In this study, we analyzed five geographically distant populations of D. lotus according to 33 morphological leaf traits, and the most informative traits were established, namely, leaf length, leaf width, leaf index (leaf to length ratio) and the length of the fourth veins. Additionally, we evaluated the intraspecific genetic diversity of D. lotus using ISSR and SCoT markers and proposed a new parameter for the evaluation of genetic polymorphism among populations, in order to eliminate the effect of sample number. This new parameter is the relative genetic polymorphism, which is the ratio of polymorphism to the number of samples. Based on morphological and genetic data, the northernmost population from Shkhafit was phenotypically and genetically distant from the other populations. The correspondence between several morphological traits (leaf width, leaf length and first to fifth right vein angles) and several marker bands (SCoT5, SCoT7, SCoT30: 800–1500 bp; ISSR13, ISSR14, ISSR880: 500–1000 bp) were observed for the Shkhafit population. Unique SCoT and ISSR fragments can be used as markers for breeding purposes. The results provide a better understanding of adaptive mechanisms in D. lotus in extreme environments and will be important for the further expansion of the cultivation area for persimmon in colder regions.
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