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Theerawitaya C, Praseartkul P, Taota K, Tisarum R, Samphumphuang T, Singh HP, Cha-Um S. Investigating high throughput phenotyping based morpho-physiological and biochemical adaptations of indian pennywort (Centella asiatica L. urban) in response to different irrigation regimes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107927. [PMID: 37544120 DOI: 10.1016/j.plaphy.2023.107927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
Indian pennywort (Centella asiatica L. Urban; Apiaceae) is a herbaceous plant used as traditional medicine in several regions worldwide. An adequate supply of fresh water in accordance with crop requirements is an important tool for maintaining the productivity and quality of medicinal plants. The objective of this study was to find a suitable irrigation schedule for improving the morphological and physiological characteristics, and crop productivity of Indian pennywort using high-throughput phenotyping. Four treatments were considered based on irrigation schedules (100, 75, 50, and 25% of field capacity denoted by I100 [control], I75, I50, and I25, respectively). The number of leaves, plant perimeter, plant volume, and shoot dry weight were sustained in I75 irrigated plants, whereas adverse effects on plant growth parameters were observed when plants were subjected to I25 irrigation for 21 days. Leaf temperature (Tleaf) was also retained in I75 irrigated plants, when compared with control. An increase of 2.0 °C temperature was detected in the Tleaf of plants under I25 irrigation treatment when compared with control. The increase in Tleaf was attributed to a decreased transpiration rate (R2 = 0.93), leading to an elevated crop water stress index. Green reflectance and leaf greenness remained unchanged in plants under I75 irrigation, while significantly decreased under I50 and I25 irrigation. These decreases were attributed to declined leaf osmotic potential, increased non-photochemical quenching, and inhibition of net photosynthetic rate (Pn). The asiatic acid and total centellosides in the leaf tissues, and centellosides yield of plants under I75 irrigation were retained when compared with control, while these parameters were regulated to maximal when exposed to I50 irrigation. Based on the results, I75 irrigation treatment was identified as the optimum irrigation schedule for Indian pennywort in terms of sustained biomass and a stable total centellosides. However, further validation in the field trials at multiple locations and involving different crop rotations is recommended to confirm these findings.
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Affiliation(s)
- Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Patchara Praseartkul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Kanyarat Taota
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Thapanee Samphumphuang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Faculty of Science, Panjab University, Chandigarh, 160014, India
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand.
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Mathavaraj S, Sabu KK. Genetic diversity and structure revealed by genomic microsatellite markers in Centella asiatica (L.) Urb., a plant with medicinal potential. Mol Biol Rep 2021; 48:7387-7396. [PMID: 34716865 DOI: 10.1007/s11033-021-06748-5] [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: 09/18/2020] [Accepted: 09/15/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Around the world, medicinal plants are utilised for various purposes. Centella asiatica is one of the important medicinal plants widely used in many medicinal systems. Nevertheless, analysis of the genetic diversity would pave the way for its most suitable utilisation. METHODS AND RESULTS The present study analyses the genetic diversity and structure of eighty C. asiatica accessions collected from the southern states of India, using ten genomic microsatellite markers. The mean Nei's gene diversity (0.46) indicates considerable genetic diversity. Analysis of molecular variance (82.48%) exhibited significant genetic variance between samples within the population. The cluster analysis brought out the structure of the analysed populations as three subpopulations based on the genetic differentiation. CONCLUSIONS The study showed significant intra-population variation, predominant inbreeding and population differentiation in C. asiatica. The findings will help better understanding of the genetic structure and gene pool of the plant.
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Affiliation(s)
- Sakthipriya Mathavaraj
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, 695562, India
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Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
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Pootakham W, Naktang C, Kongkachana W, Sonthirod C, Yoocha T, Sangsrakru D, Jomchai N, U-Thoomporn S, Romyanon K, Toojinda T, Tangphatsornruang S. De novo chromosome-level assembly of the Centella asiatica genome. Genomics 2021; 113:2221-2228. [PMID: 34022344 DOI: 10.1016/j.ygeno.2021.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/05/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
Centella asiatica is a herbaceous, perennial species indigenous to India and Southeast Asia. C. asiatica possesses several medicinal properties: anti-aging, anti-inflammatory, wound healing and memory enhancing. The lack of available genomics resources significantly impedes the improvement of C. asiatica varieties through molecular breeding. Here, we combined the 10× Genomics linked-read technology and the long-range HiC technique to obtain the genome assembly. The final assembly contained nine pseudomolecules, corresponding to the haploid chromosome number in C. asiatica. These nine chromosomes covered 402,536,584 bases or 93.6% of the 430-Mb assembly. Comparative genomics analyses based on single-copy orthologous genes showed that C. asiatica and the common ancestor of Coriandrum sativum (coriander) and Daucus carota (carrot) diverged about 48 million years ago. This assembly provides a valuable reference genome for future molecular studies, varietal development through marker-assisted breeding and comparative genomics studies in C. asiatica.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Kanokwan Romyanon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, Sheng O, Mayer C, Yi G, Deng G. Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana. Genes (Basel) 2020; 11:genes11121479. [PMID: 33317074 PMCID: PMC7763637 DOI: 10.3390/genes11121479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
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Affiliation(s)
- Manosh Kumar Biswas
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- Correspondence: (M.K.B.); (G.D.)
| | - Mita Bagchi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- The College of Economics and Managements, South China Agricultural University, Guangzhou 510640, China
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, West Bengal 700064, India;
| | - Jennifer Ann Harikrishna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuxuan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany;
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Correspondence: (M.K.B.); (G.D.)
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Baldemir A, Topçu H, Paksoy MY, Motalebipour EZ, Kafkas S. First microsatellite markers for Scaligeria lazicaBoiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1301784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Ayşe Baldemir
- Department of Pharmaceutical Botany, Faculty of Pharmacy, University of Erciyes, Kayseri, Turkey
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, University of Cukurova, Adana, Turkey
| | - Mehmet Yavuz Paksoy
- Department of Environmental Engineering, Faculty of Engineering, University of Tunceli, Tunceli, Turkey
| | | | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Cukurova, Adana, Turkey
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Ferraz dos Santos L, Moreira Fregapani R, Falcão LL, Togawa RC, Costa MMDC, Lopes UV, Peres Gramacho K, Alves RM, Micheli F, Marcellino LH. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao. PLoS One 2016; 11:e0151074. [PMID: 26949967 PMCID: PMC4780773 DOI: 10.1371/journal.pone.0151074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/23/2016] [Indexed: 01/25/2023] Open
Abstract
The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches’ broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.
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Affiliation(s)
- Lucas Ferraz dos Santos
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662–900 Ilhéus-BA, Brazil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, 70770–917, Brazil
| | | | - Loeni Ludke Falcão
- Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, 70770–917, Brazil
| | | | | | | | | | | | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662–900 Ilhéus-BA, Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- * E-mail:
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