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Liao X, Zhao Y, Li H, Hou W, Tang X, Zhou R. A simple and rapid method for isolating high-quality RNA from kenaf with high polysaccharide and polyphenol contents. Biotechniques 2023; 75:218-226. [PMID: 37880956 DOI: 10.2144/btn-2023-0077] [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: 10/27/2023] Open
Abstract
The extraction of high-quality RNA from kenaf is essential for genetic and molecular biology research. However, the presence of high levels of polysaccharide and polyphenol compounds in kenaf poses challenges for RNA isolation. We proposed a simplified, time-saving and cost-effective method for isolating high quantities of RNA from various kenaf tissues. This method exhibited superior efficiency in RNA isolation compared with the conventional cetyltrimethylammonium bromide method and demonstrated greater adaptability to different samples than commercial kits. Furthermore, the high-quality RNA obtained from this method was successfully utilized for RT-PCR, real-time RT-PCR and northern blot analysis. Moreover, this proposed protocol also enables the acquisition of both high-quality and -quantity gDNA through RNase A treatment. In addition, the effectiveness of this approach in isolating high-quality RNA from other plant species has been experimentally confirmed.
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Affiliation(s)
- Xiaofang Liao
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yanhong Zhao
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Hongwei Li
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
- Faculty of Mechanical & Energy Engineering, Shaoyang University, Shaoyang, 422099, China
| | - Wenhuan Hou
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Xingfu Tang
- Cash Crop Research Institute of Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Ruiyang Zhou
- Key Laboratory of Plant Genetic & Breeding, College of Agriculture, Guangxi University, Nanning, 530005, China
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Olayide P, Alexandersson E, Tzfadia O, Lenman M, Gisel A, Stavolone L. Transcriptome and metabolome profiling identify factors potentially involved in pro-vitamin A accumulation in cassava landraces. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107713. [PMID: 37126903 DOI: 10.1016/j.plaphy.2023.107713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a predominant food security crop in several developing countries. Its storage roots, rich in carbohydrate, are deficient in essential micronutrients, including provitamin A carotenoids. Increasing carotenoid content in cassava storage roots is important to reduce the incidence of vitamin A deficiency, a public health problem in sub-Saharan Africa. However, cassava improvement advances slowly, mainly due to limited information on the molecular factors influencing β-carotene accumulation in cassava. To address this problem, we performed comparative transcriptomic and untargeted metabolic analyses of roots and leaves of eleven African cassava landraces ranging from white to deep yellow colour, to uncover regulators of carotenoid biosynthesis and accumulation with conserved function in yellow cassava roots. Sequence analysis confirmed the presence of a mutation, known to influence β-carotene content, in PSY transcripts of deep yellow but not of pale yellow genotypes. We identified genes and metabolites with expression and accumulation levels significantly associated with β-carotene content. Particularly an increased activity of the abscisic acid catabolism pathway together with a reduced amount of L-carnitine, may be related to the carotenoid pathway flux, higher in yellow than in white storage roots. In fact, NCED_3.1 was specifically expressed at a lower level in all yellow genotypes suggesting that it could be a potential target for increasing carotenoid accumulation in cassava. These results expand the knowledge on metabolite compositions and molecular mechanisms influencing carotenoid biosynthesis and accumulation in cassava and provide novel information for biotechnological applications and genetic improvement of cassava with high nutritional values.
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Affiliation(s)
- Priscilla Olayide
- Swedish University of Agricultural Sciences, Sundsvägen 10, SE-234 22, Lomma, Sweden; International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, 200001, Oyo State, Nigeria.
| | - Erik Alexandersson
- Swedish University of Agricultural Sciences, Sundsvägen 10, SE-234 22, Lomma, Sweden.
| | - Oren Tzfadia
- Institute of Tropical Medicine, Kronenburgstraat 43/3, 2000, Antwerpen, Belgium.
| | - Marit Lenman
- Swedish University of Agricultural Sciences, Sundsvägen 10, SE-234 22, Lomma, Sweden.
| | - Andreas Gisel
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, 200001, Oyo State, Nigeria; Institute of Biomedical Technologies, CNR, Via Amendola 122/D, Bari, Italy.
| | - Livia Stavolone
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, 200001, Oyo State, Nigeria; Institute for Sustainable Plant Protection CNR, Via Amendola 122/D, Bari, Italy.
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Wang C, Hou X, Qi N, Li C, Luo Y, Hu D, Li Y, Liao W. An optimized method to obtain high-quality RNA from different tissues in Lilium davidii var. unicolor. Sci Rep 2022; 12:2825. [PMID: 35181714 PMCID: PMC8857280 DOI: 10.1038/s41598-022-06810-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
The high quality, yield and purity total RNA samples are essential for molecular experiments. However, harvesting high quality RNA in Lilium davidii var. unicolor is a great challenge due to its polysaccharides, polyphenols and other secondary metabolites. In this study, different RNA extraction methods, namely TRIzol method, the modified TRIzol method, Kit method and cetyltrimethylammonium bromide (CTAB) method were employed to obtain total RNA from different tissues in L. davidii var. unicolor. A Nano drop spectrophotometer and 1% agarose gel electrophoresis were used to detect the RNA quality and integrity. Compared with TRIzol, Kit and CTAB methods, the modified TRIzol method obtained higher RNA concentrations from different tissues and the A260/A280 ratios of RNA samples were ranged from 1.97 to 2.27. Thus, the modified TRIzol method was shown to be the most effective RNA extraction protocol in acquiring RNA with high concentrations. Furthermore, the RNA samples isolated by the modified TRIzol and Kit methods were intact, whereas different degrees of degradation happened within RNA samples isolated by the TRIzol and CTAB methods. In addition, the modified TRIzol method could also isolate high-quality RNA from other edible lily bulbs. Taken together, the modified TRIzol method is an efficient method for total RNA isolation from L. davidii var. unicolor.
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Affiliation(s)
- Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Xuemei Hou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Nana Qi
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Changxia Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yanyan Luo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Dongliang Hu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Yihua Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
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Maceda-López LF, Villalpando-Aguilar JL, García-Hernández E, Ávila de Dios E, Andrade-Canto SB, Morán-Velázquez DC, Rodríguez-López L, Hernández-Díaz D, Chablé-Vega MA, Trejo L, Góngora-Castillo E, López-Rosas I, Simpson J, Alatorre-Cobos F. Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots. 3 Biotech 2021; 11:75. [PMID: 33505830 DOI: 10.1007/s13205-020-02620-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 12/26/2020] [Indexed: 12/30/2022] Open
Abstract
Together with their undeniable role in the ecology of arid and semiarid ecosystems, Agave species are emerging as a model to dissect the relationships between crassulacean acid metabolism and high efficiency of light and water use, and as an energy crop for bioethanol production. Transcriptome resources from economically valuable Agaves species, such as Agave tequilana and A. salmiana, as well as hybrids for fibers, are now available, and multiple gene expression landscape analyses have been reported. Key components in molecular mechanisms underlying drought tolerance could be uncovered by analyzing gene expression patterns of roots. This study describes an efficient protocol for high-quality total RNA isolation from phenolic compounds-rich Agave roots. Our methodology involves suitable root handling and collecting in the field and using saving-time commercial kits available. RNA isolated from roots free of lignified out-layers and clean cortex showed high values of quality and integrity according to electrophoresis and microfluidics-based platform. Synthesis of long full-length cDNAs and PCR amplification tested the suitability for downstream applications of extracted RNA. The protocol was applied successfully to A. tequilana roots but can be used for other Agave species that also develop lignified epidermis/exodermis in roots.
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Affiliation(s)
- Luis F Maceda-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - José L Villalpando-Aguilar
- Tecnológico Nacional de México, Instituto Tecnológico de Chiná, Calle 11entre 22 y 28, 24050 Chiná, Mexico
| | - Eleazar García-Hernández
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Emmanuel Ávila de Dios
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Silvia B Andrade-Canto
- Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Dalia C Morán-Velázquez
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Lorena Rodríguez-López
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Demetrio Hernández-Díaz
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Manuel A Chablé-Vega
- Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - Laura Trejo
- CONACYT Research Fellow, Laboratorio de Biodiversidad y Cultivo de Tejidos Vegetales, Instituto de Biología, UNAM, 90640 Santa Cruz Tlaxcala, Tlaxcala Mexico
| | - Elsa Góngora-Castillo
- CONACYT Research Fellow, Centro de Investigacion Cientifica de Yucatan, A.C., Calle 43 No.130 x 32 y 34, Chuburna de Hidalgo, 97205 Mérida, Yucatan Mexico
| | - Itzel López-Rosas
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados, 3681 Irapuato, Mexico
| | - Fulgencio Alatorre-Cobos
- CONACYT Research Fellow, Colegio de Postgraduados Campus Campeche, Carretera Haltunchen-Edzna km 17.5, Sihochac, 24450 Campeche, Mexico
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