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Manchanda P, Sharma D, Kaur G, Kaur H, Vanshika. Exploring the Significance of Somaclonal Variations in Horticultural Crops. Mol Biotechnol 2024:10.1007/s12033-024-01214-6. [PMID: 38896180 DOI: 10.1007/s12033-024-01214-6] [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: 04/17/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024]
Abstract
Genetic and epigenetic variations produced via cell and tissue culture open up new sources of variability intra-species which can be used to improve crops. The use of in vitro generated somaclonal variations for selecting novel variants aids in the development of novel genotypes having desirable agronomic traits that can be released as varieties or utilized for breeding purposes. Horticultural crops give higher yield and productivity per unit area than other crops, as well as provide good economic returns which have led to an increase in their potential benefits throughout time. The last three to four decades have seen the selection and release of a number of valuable somaclonal variants, many of which possess remarkable features including disease resistance, high yield, improved nutritional quality and abiotic stress tolerance. Generating somaclonal variations has given breeders a novel alternative option for obtaining genetic diversity in horticultural crops and without advanced technologies. The variations introduced through tissue culture process, methods to determine and validate genetic changes in vitro regenerated plantlets, along with prospective application of such variations in horticultural crops' improvement are reviewed in the present work.
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Affiliation(s)
- Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Deepansh Sharma
- Department of Plant Pathology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Gurpreet Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Vanshika
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
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Jara-Seguel P, Urrutia-Estrada J. Chilean Plants Cytogenetic Database: An Online Resource for Embryophytes of the Southern Cone. Methods Mol Biol 2023; 2703:193-200. [PMID: 37646946 DOI: 10.1007/978-1-0716-3389-2_14] [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: 09/01/2023]
Abstract
Chilean Plants Cytogenetic Database (CPCD) is a resource available online in electronic format, providing a cytogenetics catalog for continental and insular Chilean plants that are representative of the floras of the Southern Cone. In the last update carried out in 2021, we increased the cytogenetic data for 499 Chilean native species, and from here on we will include a new section with chromosome number data for 683 exotic species classified as invaders in Chile. Aspects on the coverage, features, and uses of the CPCD are presented here, including background information accumulated since its inception in 2010 to the present. With the new update, the database currently stores cytogenetic information for species belonging to the divisions Bryophyta, Pteridophyta, Pinophyta, and Magnoliophyta, thus contributing to the largest community resource on plant cytogenetics in the world.
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Affiliation(s)
- Pedro Jara-Seguel
- Departamento de Ciencias Biológicas y Químicas & Núcleo de Estudios Ambientales, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile.
| | - Jonathan Urrutia-Estrada
- Laboratorio de Invasiones Biológicas, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile
- Instituto de Ecología y Biodiversidad, IEB, Concepción, Chile
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Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids. Int J Mol Sci 2022; 23:ijms231911406. [PMID: 36232706 PMCID: PMC9570356 DOI: 10.3390/ijms231911406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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Sassone AB, Hojsgaard DH, Giussani LM, Brassac J, Blattner FR. Genomic, karyological and morphological changes of South American garlics (Ipheion) provide insights into mechanisms of speciation in the Pampean region. Mol Ecol 2021; 30:3716-3729. [PMID: 34087027 DOI: 10.1111/mec.16009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 01/15/2023]
Abstract
Speciation proceeds through mechanisms that promote reproductive isolation and shape the extent of genetic variation in natural populations, and thus its study is essential to understand the evolutionary processes leading to increased biodiversity. Chromosomal rearrangements are known to facilitate reproductive isolation by hybrid sterility and favour speciation events. The genus Ipheion (Amaryllidaceae, Allioideae) is unique as its species exhibit a remarkable karyological variability but lack population-level genetic data. To unveil the diversification processes acting upon the formation of new lineages within Ipheion in the Pampas of South America, we combined morphology and karyology approaches with genotyping-by-sequencing. Our phylogenomic and population genomics results supported the taxonomic division of Ipheion into three morphological and genetically well-differentiated groups. The origin of Ipheion uniflorum was traced back to its current southern distribution area in the southern Pampean region (in Argentina), from where it had expanded to the north reaching Uruguay. Our results further suggested that chromosome rearrangements and ploidy shifts had triggered speciation events, first during the origin of I. uniflorum and later during its subsequent diversification into I. recurvifolium and I. tweedieanum, in both cases reinforced by extrinsic factors and biogeographical settings. The current study illustrates the analytical power of multidisciplinary approaches integrating phylo- and population genomics with classic analyses to reveal evolutionary processes in plants.
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Affiliation(s)
- Agostina B Sassone
- Instituto de Botánica Darwinion, CONICET-ANCEFN, Buenos Aires, Argentina.,Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Diego H Hojsgaard
- Department of Systematics, Biodiversity, and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany
| | - Liliana M Giussani
- Instituto de Botánica Darwinion, CONICET-ANCEFN, Buenos Aires, Argentina
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Li J, Zhu K, Wang Q, Chen X. Genome size variation and karyotype diversity in eight taxa of Sorbus sensu stricto (Rosaceae) from China. COMPARATIVE CYTOGENETICS 2021; 15:137-148. [PMID: 34055237 PMCID: PMC8159915 DOI: 10.3897/compcytogen.v15i2.58278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/28/2021] [Indexed: 05/27/2023]
Abstract
Eight taxa of Sorbus Linnaeus, 1753 sensu stricto (Rosaceae) from China have been studied karyologically through chromosome counting, chromosomal measurement and karyotype symmetry. Genome size was also estimated by flow cytometry. Six taxa, S. amabilis Cheng ex T.T.Yu et K.C.Kuan, 1963, S. hupehensis var. paucijuga (D.K. Zang et P.C. Huang, 1992) L.T. Lu, 2000, S. koehneana C.K. Schneider, 1906, S. pohuashanensis (Hance, 1875) Hedlund, 1901, S. scalaris Koehne, 1913 and S. wilsoniana C.K. Schneider, 1906 are diploids with 2n = 34, whereas two taxa, S. filipes Handel-Mazzetti,1933 and S. ovalis McAllister, 2005 are tetraploid with 2n = 68. In general, the chromosome size is mainly small, and karyotypes are symmetrical with predominance of metacentric chromosomes. Genome size variation of diploids and tetraploids is 1.401 pg -1.676 pg and 2.674 pg -2.684 pg, respectively. Chromosome numbers of S. amabilis and S. hupehensis var. paucijuga, and karyotype and genome size of eight taxa studied are reported for the first time. This study emphasised the reliability of flow cytometry in genome size determination to infer ploidy levels in Chinese native Sorbus species.
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Affiliation(s)
- Jiabao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, ChinaNanjing Forestry UniversityNanjingChina
| | - Kailin Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, ChinaNanjing Forestry UniversityNanjingChina
| | - Qin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, ChinaNanjing Forestry UniversityNanjingChina
| | - Xin Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, ChinaNanjing Forestry UniversityNanjingChina
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Beena VL, S. Suhara Beevy. Intervarietal Karyomorphological Studies on Two Species of Passiflora L. (Passifloraceae). CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720050126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Choi B, Weiss-Schneeweiss H, Temsch EM, So S, Myeong HH, Jang TS. Genome Size and Chromosome Number Evolution in Korean Iris L. Species (Iridaceae Juss.). PLANTS (BASEL, SWITZERLAND) 2020; 9:E1284. [PMID: 32998465 PMCID: PMC7650623 DOI: 10.3390/plants9101284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 01/13/2023]
Abstract
Chromosome numbers, karyotypes, and genome sizes of 14 Iris L. (Iridaceae Juss.) species in Korea and their closely related taxon, Sisyrinchium rosulatum, are presented and analyzed in a phylogenetic framework. To date, understanding the chromosomal evolution of Korean irises has been hampered by their high chromosome numbers. Here, we report analyses of chromosome numbers and karyotypes obtained via classic Feulgen staining and genome sizes measured using flow cytometry in Korean irises. More than a two-fold variation in chromosome numbers (2n = 22 to 2n = 50) and over a three-fold genome size variation (2.39 pg to 7.86 pg/1 C) suggest the putative polyploid and/or dysploid origin of some taxa. Our study demonstrates that the patterns of genome size variation and chromosome number changes in Korean irises do not correlate with the phylogenetic relationships and could have been affected by different evolutionary processes involving polyploidy or dysploidy. This study presents the first comprehensive chromosomal and genome size data for Korean Iris species. Further studies involving molecular cytogenetic and phylogenomic analyses are needed to interpret the mechanisms involved in the origin of chromosomal variation in the Iris.
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Affiliation(s)
- Bokyung Choi
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea;
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria; (H.W.-S.); (E.M.T.)
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria; (H.W.-S.); (E.M.T.)
| | - Soonku So
- Korea National Park Research Institute, 171, Dangu-ro, Wonju-si 26441, Gangwon-do, Korea; (S.S.); (H.-H.M.)
| | - Hyeon-Ho Myeong
- Korea National Park Research Institute, 171, Dangu-ro, Wonju-si 26441, Gangwon-do, Korea; (S.S.); (H.-H.M.)
| | - Tae-Soo Jang
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea;
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Costa L, Jimenez H, Carvalho R, Carvalho-Sobrinho J, Escobar I, Souza G. Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:320. [PMID: 32318079 PMCID: PMC7155398 DOI: 10.3389/fpls.2020.00320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Horace Jimenez
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Jefferson Carvalho-Sobrinho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Inelia Escobar
- Department of Botany, University of Concepción, Concepción, Chile
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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Sassone AB, Giussani LM. Reconstructing the phylogenetic history of the tribe Leucocoryneae (Allioideae): Reticulate evolution and diversification in South America. Mol Phylogenet Evol 2018; 127:437-448. [DOI: 10.1016/j.ympev.2018.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/08/2018] [Accepted: 04/21/2018] [Indexed: 12/13/2022]
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