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Patel R, Menon J, Kumar S, Nóbrega MB, Patel DA, Sakure AA, Vaja MB. Modern day breeding approaches for improvement of castor. Heliyon 2024; 10:e27048. [PMID: 38463846 PMCID: PMC10920369 DOI: 10.1016/j.heliyon.2024.e27048] [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: 05/08/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Castor (Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety. Modern approaches accelerate the speed of crop breeding as an alternative tool. To achieve this goal, molecular markers are employed in breeding to capture the genetic variability through molecular analysis and population structuring. Allele mining is used to trace the evolution of alleles, identify new haplotypes and produce allele specific markers for use in marker aided selection using Genome wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Plant genetic transformation is a rapid and effective mode of castor improvement is also discussed here. The efforts towards developing stable regeneration protocol provide a wide range of utility like embryo rescue in distant crosses, development of somaclonal variation, haploid development using anther culture and callus development for stable genetic transformation has reviewed in this article. Omics has provided intuitions to the molecular mechanisms of (a)biotic stress management in castor along with dissected out the possible genes for improving the yield. Relating genes to traits offers additional scientific inevitability leading to enhancement and sympathetic mechanisms of yield improvement and several stress tolerance.
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Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Juned Menon
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Márcia B.M. Nóbrega
- Embrapa Algodão, Rua Oswaldo Cruz, nº 1.143, Centenário, CEP 58428-095, Campina Grande, PB, Brazil
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Mahesh B. Vaja
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
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Mahdieh M, Talebi SM, Dehghan T, Tabaripour R, Matsyura A. Molecular genetics, seed morphology and fatty acids diversity in castor (Ricinus communis L., Euphorbiaceae) Iranian populations. Mol Biol Rep 2023; 50:9859-9873. [PMID: 37848759 DOI: 10.1007/s11033-023-08904-5] [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] [Received: 08/13/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. METHODS AND RESULTS The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. CONCLUSIONS The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs.
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Affiliation(s)
- Majid Mahdieh
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Seyed Mehdi Talebi
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran.
| | - Tahereh Dehghan
- Department of Biology, Faculty of Sciences, Arak University, Arak, 38156-8-8349, Iran
| | - Raheleh Tabaripour
- Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
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Sen S, Rathi S, Sahu J, Mandal SC, Ray S, Slama P, Roychoudhury S. In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae. Genes (Basel) 2023; 14:332. [PMID: 36833259 PMCID: PMC9956114 DOI: 10.3390/genes14020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.
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Affiliation(s)
- Surojit Sen
- Department of Zoology, Mariani College, Mariani 785634, India
| | - Sunayana Rathi
- Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat 785013, India
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar 751003, India
| | - Subhash C. Mandal
- Department of Pharmaceutical Technology, Division of Pharmacognosy, Jadavpur University, Kolkata 700032, India
| | - Supratim Ray
- Department of Pharmaceutical Sciences, Assam University, Silchar 788011, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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Carrasco B, Arévalo B, Perez-Diaz R, Rodríguez-Alvarez Y, Gebauer M, Maldonado JE, García-Gonzáles R, Chong-Pérez B, Pico-Mendoza J, Meisel LA, Ming R, Silva H. Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools. PLANTS 2022; 11:plants11162151. [PMID: 36015454 PMCID: PMC9414553 DOI: 10.3390/plants11162151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.
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Affiliation(s)
- Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Talca 3480094, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados (CEAP), Talca 3480094, Chile
| | | | - Yohaily Rodríguez-Alvarez
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Marlene Gebauer
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Jonathan E Maldonado
- Laboratorio de Genómica Funcional y Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile
- Laboratorio de Multiómica Vegetal y Bioinformática, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9160000, Chile
| | | | - Borys Chong-Pérez
- Sociedad de Investigación y Servicios, BioTECNOS Ltda., San Javier 3660000, Chile
| | - José Pico-Mendoza
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador
| | - Lee A Meisel
- Laboratorio de Genética Molecular Vegetal, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830490, Chile
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Herman Silva
- Laboratorio de Genómica Funcional y Bioinformática, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago 8820808, Chile
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Ergun Z. The effects of plant growth substances on the oil content and fatty acid composition of Ricinus communis L.: an in vitro study. Mol Biol Rep 2022; 49:5241-5249. [PMID: 34472005 DOI: 10.1007/s11033-021-06686-2] [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] [Received: 07/16/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Ricinus communis L. (castor bean) is valued for its oil and the performance of oil is closely related to its fatty acid composition. Thus, producing oil in vitro with favored fatty acid profiles is a promising research area and may also offer industrial opportunities. MATERIAL AND METHOD In line with this, the total amount of oil and the fatty acid composition of the samples, which were endosperm and calli obtained by treatment of various doses of plant growth regulators were determined. RESULTS Results showed that the type and amount of the plant growth regulator used in the media affect the fatty acid composition. In detail, the biggest change was shown by Indole-3-Acetic Acid (IAA), in general, using the plant growth regulators at 5 mg L-1, instead of 20 mg L-1, was found to have induced larger differentiations. The effect of a natural plant growth regulator (IAA) on fatty acid profiles was bigger than the synthetic ones (NAA, 1-Naphthaleneacetic acid, and 2,4 D, 2,4-Dichlorophenoxyacetic acid). The media containing 5 mg L-1 of NAA, 20 mg L-1 of NAA, 20 mg L-1 of 2,4 D, or 5 mg L-1 of 2,4 D gave similar results.
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Affiliation(s)
- Zeynep Ergun
- Department of Bioengineering, Faculty of Engineering, Adana Alpaslan Turkes Science and Technology University, Adana, Turkey.
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Song JM, Zhang Y, Zhou ZW, Lu S, Ma W, Lu C, Chen LL, Guo L. Oil plant genomes: current state of the science. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2859-2874. [PMID: 35560205 DOI: 10.1093/jxb/erab472] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhi-Wei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chaofu Lu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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DE Oliveira Neto SS, Zeffa DM, Sartori MMP, Soares DJ, Zanotto MD. Genetic variability in Brazilian castor (Ricinus communis) germplasm assessed by morphoagronomic traits and gray mold reaction. AN ACAD BRAS CIENC 2021; 93:e20190985. [PMID: 34644721 DOI: 10.1590/0001-3765202120190985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/23/2019] [Indexed: 11/22/2022] Open
Abstract
The characterization and conservation of castor accessions in germplasm bank are essential in order to breeding programs achieve its goals. Despite Brazil having the 4th largest castor germplasm bank in the world, castor diversity in Brazil remains little explored. Thus, this study aimed at characterize castor accessions collected in different Brazilian regions by means of 31 morphoagronomic traits and gray mold reaction. Forty accessions of the Universidade do Estado de São Paulo (UNESP), Botucatu, SP, Brazil, germplasm bank were evaluated. Genetic parameters were estimated for the quantitative traits, and the accessions were grouped by Ward method using the standardized Euclidean distance and the simple coincidence index for quantitative and qualitative data, respectively. Qualitative and quantitative traits were important to understand and differentiate castor accessions. The accessions showed a high variation regarding the castor gray mold reaction. The accessions assessed in this study have been preserved and can be used as a source for genetic variability in the development of new castor varieties in breeding programs.
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Affiliation(s)
- Sebastião S DE Oliveira Neto
- UNESP, Faculdade de Ciências Agronômicas, Departamento de Produção e Melhoramento Vegetal, Campus de Botucatu, Avenida Universitária, 3780, Altos do Paraíso, 18610-034 Botucatu, SP, Brazil
| | - Douglas M Zeffa
- Universidade Estadual de Maringá, Departamento de Agronomia, Avenida Colombo, 5790, Zona 7, 87020-900 Maringá, PR, Brazil
| | - Maria M P Sartori
- UNESP, Faculdade de Ciências Agronômicas, Departamento de Produção e Melhoramento Vegetal, Campus de Botucatu, Avenida Universitária, 3780, Altos do Paraíso, 18610-034 Botucatu, SP, Brazil
| | - Dartanhã J Soares
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Algodão, Rua Osvaldo Cruz, 1143, Centenário, 58428-095 Campina Grande, PB, Brazil
| | - Maurício D Zanotto
- UNESP, Faculdade de Ciências Agronômicas, Departamento de Produção e Melhoramento Vegetal, Campus de Botucatu, Avenida Universitária, 3780, Altos do Paraíso, 18610-034 Botucatu, SP, Brazil
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Xu W, Wu D, Yang T, Sun C, Wang Z, Han B, Wu S, Yu A, Chapman MA, Muraguri S, Tan Q, Wang W, Bao Z, Liu A, Li DZ. Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean. Genome Biol 2021; 22:113. [PMID: 33874982 PMCID: PMC8056531 DOI: 10.1186/s13059-021-02333-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/29/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. RESULTS Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. CONCLUSIONS This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Di Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Tianquan Yang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chao Sun
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shibo Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Anmin Yu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mark A Chapman
- Biological Sciences and Centre for Underutilised Crops, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sammy Muraguri
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing Tan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenbo Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhigui Bao
- Shanghai OE Biotech Co., Ltd, Shanghai, 201114, China
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Vivodík M, Gálová Z, Balážová Ž. Genetic divergence in Tunisian castor bean genotypes based on trap markers. POTRAVINARSTVO 2020. [DOI: 10.5219/1292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the present study, the representatives of the genus Ricinus communis collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 30 TRAP primers. The efficacy of the TRAP technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 30 primers for TRAP analysis produced 490 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (TRAP 04 x arb 1, TRAP 22 x arb 3 and TRAP 23 x arb 3) to 13 (TRAP 56 x arb 2), and the amplicon size ranged from 100 to 1600 bp. Of the 490 amplified bands, 377 were polymorphic, with an average of 5.71 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for TRAP 10 x arb 1 (0.555) and the highest PIC values were detected for TRAP 44 x arb 2 (0.961) with an average of 0.770. A dendrogram was constructed from a genetic distance matrix based on profiles of the 30 TRAP primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Moreover, functional TRAP markers would be efficiently useful in genetic studies for castor genetic improvement.
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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Dafni A, Böck B. Medicinal plants of the Bible-revisited. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2019; 15:57. [PMID: 31775790 PMCID: PMC6882220 DOI: 10.1186/s13002-019-0338-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Previous lists number from 55 to 176 plant species as "Biblical Medicinal Plants." Modern studies attest that many names on these lists are no longer valid. This situation arose due to old mistranslations and/or mistakes in botanical identification. Many previously recognized Biblical plants are in no way related to the flora of the Bible lands. Accordingly, the list needs revision. METHODS We re-examine the list of possible medicinal plants in the Bible based on new studies in Hebrew Biblical philology and etymology, new studies on the Egyptian and Mesopotamian medicinal use of plants, on ethnobotany and on archaeobotany. RESULTS In our survey, we suggest reducing this list to 45 plant species. Our contribution comprises 20 "newly" suggested Biblical Medicinal Plants. Only five species are mentioned directly as medicinal plants in the Bible: Fig (Ficus carica), Nard (Nardostachys jatamansi), Hyssop (Origanum syriacum), balm of Gilead (Commiphora gileadensis) and Mandrake (Mandragora officinarum). No fewer than 18 medicinal plants are mentioned in old Jewish post-Biblical sources, in addition to those in the Bible. Most of these plants (15) are known also in Egypt and Mesopotamia while three are from Egypt only. Seven of our suggested species are not mentioned in the Bible or in the Jewish post-Biblical literature but were recorded as medicinal plants from Egypt, as well as from Mesopotamia. It is quite logical to assume that they can be included as Biblical Medicinal Plants. CONCLUSIONS All our suggested Biblical Medicinal Plants are known as such in Ancient Egypt and/or Mesopotamia also. Examination of our list shows that all these plants have been in continuous medicinal use in the Middle East down the generations, as well as being used in the Holy Land today. Precisely in King Solomon's words, "That which has been is what will be, that which is done is what will be done. And there is nothing new under the sun" (Ecclesiastes 1:9).
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Affiliation(s)
- Amots Dafni
- Institute of Evolution and the Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
| | - Barbara Böck
- Institute of Mediterranean and Near Eastern Languages and Cultures (ILC), Spanish National Research Council (CSIC), Madrid, Spain
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12
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Xu W, Yang T, Qiu L, Chapman MA, Li D, Liu A. Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop. PLANT DIRECT 2019; 3:e00173. [PMID: 31641699 PMCID: PMC6802463 DOI: 10.1002/pld3.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil-related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene-trait associations and castor bean breeding.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Tianquan Yang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lijun Qiu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Mark A. Chapman
- Biological Sciences and Centre for Underutilised CropsUniversity of SouthamptonSouthamptonUK
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Aizhong Liu
- Department of Economic Plants and BiotechnologyYunnan Key Laboratory for Wild Plant ResourcesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of ChinaMinistry of EducationSouthwest Forestry UniversityKunmingChina
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Yu A, Li F, Xu W, Wang Z, Sun C, Han B, Wang Y, Wang B, Cheng X, Liu A. Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean. Sci Rep 2019; 9:11950. [PMID: 31420567 PMCID: PMC6697702 DOI: 10.1038/s41598-019-48492-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
Castor bean (Ricinus communis L., Euphorbiaceae) is a critical biodiesel crop and its seed derivatives have important industrial applications. Due to lack of a high-density genetic map, the breeding and genetic improvement of castor bean has been largely restricted. In this study, based on a recombinant inbred line (RIL) population consisting of 200 individuals, we generated 8,896 high-quality genomic SNP markers and constructed a high-resolution genetic map with 10 linkage groups (LGs), spanning 1,852.33 centiMorgan (cM). Based on the genetic map, 996 scaffolds from the draft reference genome were anchored onto 10 pseudo-chromosomes, covering 84.43% of the castor bean genome. Furthermore, the quality of the pseudo-chromosome scale assembly genome was confirmed via genome collinearity analysis within the castor bean genome as well as between castor bean and cassava. Our results provide new evidence that the phylogenetic position of castor bean is relatively solitary from other taxa in the Euphorbiaceae family. Based on the genetic map, we identified 16 QTLs that control seed size and weight (covering 851 candidate genes). The findings will be helpful for further research into potential new mechanisms controlling seed size and weight in castor bean. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits, as well as the accelerated molecular breeding of castor bean in a cost-effective pattern.
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Affiliation(s)
- Anmin Yu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wei Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bo Wang
- Wuhan Genoseq Technology Co., Ltd, Wuhan, 430070, China
| | - Xiaomao Cheng
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
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Agyenim-Boateng KG, Lu J, Shi Y, Zhang D, Yin X. SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China. PLoS One 2019; 14:e0219667. [PMID: 31295303 PMCID: PMC6622549 DOI: 10.1371/journal.pone.0219667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/29/2019] [Indexed: 11/19/2022] Open
Abstract
Castor bean is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Currently, castor bean varieties suffer from low productivity and high risk of insect pests and diseases. It is in urgent need to mine elite genes from wild materials for castor breeding. 29 pairs of polymorphic SRAP primers out of 361 pairs were used to analyse the genetic diversity of 473 wild castor materials from South China. 203 bands were amplified by the 29 pairs of primers, of which 169 bands were polymorphic, with a polymorphic percentage of 83.25%. With an average number of alleles per locus (Ap) of 1.801, average number of effective alleles per locus (Ae) of 1.713 and average percentage of polymorphic loci (P) of 90.04%, these primers were proven to be useful and effective. Nei' genetic distance between the materials ranged from 1.04 to 25.02, with an average of 13.03. At the genetic distance of 25.02, the materials clustered into two major groups, consistent with the result of population structure analysis. However, more subgroups existed between 5.21 and 13.32. Although not all the materials from the same region were clustered in the same group, an obvious trend existed where the groups were related to regions to a great extent. Based on multiple indices, the genetic diversity of materials from Hainan was the lowest. However, there was not much difference between West Guangdong and Guangxi, although the former was slightly higher. Moderate genetic differentiation was observed in wild materials in South China. The genetic differentiation mainly occurred within population, with maximum differentiation in Guangxi, followed by West Guangdong and the minimum in Hainan. Nonetheless, there was an extensive geneflow between populations. The above results provided a direction for the conservation and breeding application of these materials.
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Affiliation(s)
| | - Jiannong Lu
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Yuzhen Shi
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Dan Zhang
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Xuegui Yin
- College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, China
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15
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Vivodík M, Saadaoui E, Balážová Ž, Gálová Z, Petrovičová L. Genetic diversity in Tunisian castor genotypes (Ricinus communis L.) detected using RAPD markers. POTRAVINARSTVO 2019. [DOI: 10.5219/1116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Castor (Ricinus communis L.) is a plant that is commercially very important to the world. It is produced in about 30 countries lying in the tropical belt of the world. It is an important plant for production of industrial oil. Assessment of genetic diversity of a crop species is a prerequisite to its improvement; hence it is important to identify the genetic diversity of castor genetic resources for development of improved cultivars. The present study is focused on estimation of genetic distance between 56 Tunisian castor genotypes, based on 18 RAPD markers. Seeds of castor were obtained from the University of Carthage, National Institute of Research in Rural Engineering, Waters and Forests (INRGREF), Regional Station of Gabí¨s, Tunisia. The ricin genotypes were obtained from 12 regions of Tunisia. The efficacy of the RAPD technique in this study is further supported by the obtained PIC values of the primers used in the analysis. PCR amplification of DNA using 18 primers for RAPD analysis produced 145 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 3 (OPE-07) to 13 (SIGMA-D-01), and the amplicon size ranged from 100 to 1500 bp. Of the 145 amplified bands, 145 were polymorphic, with an average of 8.11 polymorphic bands per primer. The lowest values of polymorphic information content were recorded for RLZ 9 (0.618) and the the highest PIC values were detected for OPD-08 (0.846) with an average of 0.761. A dendrogram was constructed from a genetic distance matrix based on profiles of the 18 RAPD primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into five main clusters. Genetically the closest were four genotypes from cluster 1 (BT-1 - S-5 and K-1 - N-3). Knowledge of the genetic diversity of castor can be used in future breeding programs for increased oil production to meet the ever increasing demand of castor oil for industrial uses as well as for biodiesel production.
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16
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Senthilvel S, Ghosh A, Shaik M, Shaw RK, Bagali PG. Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor. Sci Rep 2019; 9:3003. [PMID: 30816245 PMCID: PMC6395776 DOI: 10.1038/s41598-019-39967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/06/2019] [Indexed: 02/01/2023] Open
Abstract
Castor is a commercially important oilseed crop that provides raw materials for several industries. Currently, the availability of genomic resources for castor is very limited. In this study, genome-wide SNPs were discovered in castor via whole-genome sequencing of 14 diverse lines to an average of 34X coverage. A total of 2,179,759 putative SNPs were detected, and a genotyping array was designed with 6,000 high-quality SNPs representing 2,492 scaffolds of the draft castor genome (87.5% genome coverage). The array was validated by genotyping a panel of 314 inbred castor lines, which resulted in 5,025 scorable SNPs with a high call rate (98%) and reproducibility (100%). Using this array, a consensus linkage map consisting of 1,978 SNP loci was constructed with an average inter-marker distance of 0.55 cM. The genome-wide SNP data, the genotyping array and the dense linkage map are valuable genomic tools for promoting high-throughput genomic research and molecular breeding in castor.
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Affiliation(s)
- S Senthilvel
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India.
| | - Arpita Ghosh
- Xcelris Labs Ltd., Xcellon building, Navrangpura, Ahmedabad, 380009, India
| | - Mobeen Shaik
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India
| | - Ranjan K Shaw
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India
| | - Prashanth G Bagali
- Xcelris Labs Ltd., Xcellon building, Navrangpura, Ahmedabad, 380009, India
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17
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Mosa KA, Gairola S, Jamdade R, El-Keblawy A, Al Shaer KI, Al Harthi EK, Shabana HA, Mahmoud T. The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora. FRONTIERS IN PLANT SCIENCE 2019; 9:1929. [PMID: 30719028 PMCID: PMC6348273 DOI: 10.3389/fpls.2018.01929] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.
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Affiliation(s)
- Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Rahul Jamdade
- Plant Biotechnology Laboratory, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Ali El-Keblawy
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Eman Khalid Al Harthi
- Plant Biotechnology Laboratory, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Hatem A. Shabana
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
| | - Tamer Mahmoud
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, Sharjah, United Arab Emirates
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18
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Almeyda León IH, Alvarez Ojeda MG, Pecina Quintero V, Acosta Díaz E. Caracterización molecular de aguacate criollo de Nuevo León, México. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n2.69551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
México es centro de origen del aguacate (Persea americana Mill.), casi todos los miembros reconocidos del género Persea ocurren primariamente desde la parte central de México hasta gran parte de Centroamérica. El objetivo de este trabajo fue realizar la caracterización molecular de germoplasma de aguacate criollo de Nuevo León. Se utilizó la técnica del DNA Polimórfico Amplificado al Azar (RAPD´s). Se colectaron 27 materiales de aguacate criollo en la región sur y 16 en la región norte del Estado de Nuevo León, México. El nivel de diversidad genética detectado fue del 84%, el cual se considera como alto. Se observaron fragmentos específicos o únicos tipo RAPD´s, presentes en un solo individuo, este tipo de fragmentos son de particular interés ya que pueden estar ligados a un genotipo en particular y servir en el diagnóstico para diferenciar un genotipo o una región específica del genoma. Lo anterior es de particular interés para el aguacate criollo del Estado de Nuevo León, cuyo problema para su comercialización es la corta vida de anaquel que presenta, por lo tanto, encontrar gran variación genética como la detectada en este trabajo incrementa la posibilidad de generar nuevos materiales cuya vida de anaquel sea más prolongada, potenciando su valor comercial y por otro lado se podría aprovechar la característica de algunas variedades que presentan contenidos de aceites esenciales superior a lo registrado en variedades comerciales como el Hass.
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19
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Vivodík M, Saadaoui E, Balážová Ž, Gálová Z, Petrovičová L. Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers. POTRAVINARSTVO 2018. [DOI: 10.5219/873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the chemical and physical properties of castor oil (Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. In the present study, the representatives of the genus castor collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. PCR amplification of DNA using 37 primers for SCoT analysis produced 268 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 4 (SCoT 45, SCoT 31 and ScoT 17) to 10 (SCoT 3, SCoT 11, SCoT 14, SCoT 18 and SCoT 12). Of the 268 amplified bands 230 were polymorphic, with an average of 6.22 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for SCoT 17 (0.411) and the the highest PIC values were detected for SCoT 14 (0.868) with an average of 0.751. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 56 Tunisian castor genotypes were clustered into two main clusters (1 and 2). Of the 56 genotypes of Tunisian castor, 2 unique genotypes were separated (BA-5 and K-4). Genetically the closest were two genotypes from Tunisian region Souassi (S-2 and S-5) in subclaster 2bc. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.
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20
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He S, Xu W, Li F, Wang Y, Liu A. Intraspecific DNA methylation polymorphism in the non-edible oilseed plant castor bean. PLANT DIVERSITY 2017; 39:300-307. [PMID: 30159523 PMCID: PMC6112301 DOI: 10.1016/j.pld.2017.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/25/2017] [Accepted: 05/27/2017] [Indexed: 05/05/2023]
Abstract
Investigation of the relationships of phenotypic and epigenetic variations might be a good way to dissect the genetic or molecular basis of phenotypic variation and plasticity in plants. Castor bean (Ricinus communis L.), an important non-edible oilseed crop, is a mono-species genus plant in the family Euphorbiaceae. Since it displays rich phenotypic variations with low genetic diversity, castor bean is a good model to investigate the molecular basis of phenotypic and epigenetic variations. Cytosine DNA methylation represents a major molecular mechanism of epigenetic occurrence. In this study, epigenetic diversity of sixty landrace accessions collected worldwide was investigated using the methylation-sensitive amplification polymorphism (MSAP) technique. Results showed that the epigenetic diversity (based on the polymorphism of DNA methylated loci) exhibited a medium variation (Ne = 1.395, He = 0.242, I = 0.366) at the population level though the variation was great, ranging from 3.80% to 34.31% among accessions. Both population structure analysis and the phylogenetic construction (using the neighbor-joining criteria) revealed that the two main clades were identified, but they did not display a distinct geographic structure. After inspecting the location of polymorphic methylated loci on genome we identified that the polymorphic methylated loci occur widely in nuclear and organelle genomes. This study provides new data to understand phenotypic and epigenetic variations in castor bean.
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Affiliation(s)
- Shan He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fei Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yue Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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21
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Wang ML, Dzievit M, Chen Z, Morris JB, Norris JE, Barkley NA, Tonnis B, Pederson GA, Yu J. Genetic diversity and population structure of castor (Ricinus communis L.) germplasm within the US collection assessed with EST-SSR markers. Genome 2017; 60:193-200. [PMID: 28094539 DOI: 10.1139/gen-2016-0116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Castor is an important oilseed crop and although its oil is inedible, it has multiple industrial and pharmaceutical applications. The entire US castor germplasm collection was previously screened for oil content and fatty acid composition, but its genetic diversity and population structure has not been determined. Based on the screening results of oil content, fatty acid composition, and country origins, 574 accessions were selected and genotyped with 22 polymorphic EST-SSR markers. The results from cluster analysis, population structure, and principal component analysis were consistent, and partitioned accessions into four subpopulations. Although there were certain levels of admixtures among groups, these clusters and subpopulations aligned with geographic origins. Both divergent and redundant accessions were identified in this study. The US castor germplasm collection encompasses a moderately high level of genetic diversity (pairwise dissimilarity coefficient = 0.53). The results obtained here will be useful for choosing accessions as parents to make crosses in breeding programs and prioritizing accessions for regeneration to improve germplasm management. A subset of 230 accessions was selected and will be planted in the field for establishing a core collection of the US castor germplasm. Further evaluation of the US castor germplasm collection is also discussed.
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Affiliation(s)
- M L Wang
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - M Dzievit
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
| | - Z Chen
- c Department of Crop and Soil Sciences, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J B Morris
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J E Norris
- d Emory University Hospital, Emory University, 1364 Clifton Road, Atlanta, GA 30322, USA
| | - N A Barkley
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - B Tonnis
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - G A Pederson
- a USDA-ARS, Plant Genetic Resources Conservation Unit, 1109 Experiment Street, Griffin, GA 30223, USA
| | - J Yu
- b Department of Agronomy, Iowa State University, 2014 Agronomy Hall, Ames, IA 50011, USA
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Thatikunta R, Siva Sankar A, Sreelakshmi J, Palle G, Leela C, Durga Rani CV, Gouri Shankar V, Lavanya B, Narayana Reddy P, Dudhe MY. Utilization of in silico EST-SSR markers for diversity studies in castor ( Ricinus communis L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:535-545. [PMID: 27924126 PMCID: PMC5120032 DOI: 10.1007/s12298-016-0367-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 05/06/2023]
Abstract
Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSR-containing ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.
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Affiliation(s)
- Ramesh Thatikunta
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - A. Siva Sankar
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - J. Sreelakshmi
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Gouthami Palle
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - C. Leela
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Ch. V. Durga Rani
- Institute of Biotechnology, PJTSAU, Rajendranagar, Hyderabad, 500030 India
| | | | - B. Lavanya
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - P. Narayana Reddy
- Department of Plant Pathology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - M. Y. Dudhe
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030 India
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Hu W, Chen L, Qiu X, Lu H, Wei J, Bai Y, He N, Hu R, Sun L, Zhang H, Shen G. Morphological, Physiological and Proteomic Analyses Provide Insights into the Improvement of Castor Bean Productivity of a Dwarf Variety in Comparing with a High-Stalk Variety. FRONTIERS IN PLANT SCIENCE 2016; 7:1473. [PMID: 27746800 PMCID: PMC5040714 DOI: 10.3389/fpls.2016.01473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/15/2016] [Indexed: 05/16/2023]
Abstract
Ricinus communis displays a broad range of phenotypic diversity in size, with dwarf, common, and large-sized varieties. To better understand the differences in plant productivity between a high-stalk variety and a dwarf variety under normal growth conditions, we carried out a comparative proteomic study between Zhebi 100 (a high stalk variety) and Zhebi 26 (a dwarf variety) combined with agronomic and physiological analyses. Over 1000 proteins were detected, 38 of which differed significantly between the two varieties and were identified by mass spectrometry. Compared with Zhebi 100, we found that photosynthesis, energy, and protein biosynthesis related proteins decreased in abundance in Zhebi 26. The lower yield of the dwarf castor is likely related to its lower photosynthetic rate, therefore we hypothesize that the lower yield of the dwarf castor, in comparing to high stalk castor, could be increased by increasing planting density. Consequently, we demonstrated that at the higher planting density in Zhebi 26 (36,000 seedlings/hm2) can achieve a higher yield than that of Zhebi 100 (12,000 seedlings/hm2). Proteomic and physiological studies showed that for developing dwarf R. communis cultivar that is suitable for large scale-production (i.e., mechanical harvesting), it is imperative to identify the optimum planting density that will contribute to higher leaf area index, higher photosynthesis, and eventually higher productivity.
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Affiliation(s)
- Wenjun Hu
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Lin Chen
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaoyun Qiu
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongling Lu
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jia Wei
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yueqing Bai
- Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest UniversityChongqing, China
| | - Rongbin Hu
- Department of Biological Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Li Sun
- Department of Biological Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Hong Zhang
- Department of Biological Sciences, Texas Tech UniversityLubbock, TX, USA
| | - Guoxin Shen
- Zhejiang Academy of Agricultural SciencesHangzhou, China
- *Correspondence: Guoxin Shen
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24
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Gálová Z, Vivodík M, Balážová Ž, Hlozáková TK. Identification and differentiation of Ricinus communis L. using SSR markers. POTRAVINARSTVO 2015. [DOI: 10.5219/516] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The castor-oil plant (Ricinus communis L.), a member of the spurge family (Euphorbiaceae), is a versatile industrial oil crop that is cultivated in many tropical and subtropical regions of the world. Castor oil is of continuing importance to the global specialty chemical industry because it is the only commercial source of a hydroxylated fatty acid. Castor also has tremendous future potential as an industrial oilseed crop because of its high seed oil content, unique fatty acid composition, potentially high oil yields and ability to be grown under drought and saline conditions. Knowledge of genetic variability is important for breeding programs to provide the basis for developing desirable genotypes. The aim of this study was to assess genetic diversity within the set of 60 ricin genotypes using 10 SSR primers. Ten SSR primers revealed a total of 67 alleles ranging from 4 to 9 alleles per locus with a mean value of 6.70 alleles per locus. The PIC values ranged from 0.719 to 0.860 with an average value of 0.813 and the DI value ranged from 0.745 to 0.862 with an average value of 0.821. Probability of identity (PI) was low ranged from 0.004 to 0.018 with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 60 diverse accessions of castor bean was clustered into six clusters. We could not distinguish 2 genotypes grouped in cluster 1, RM-96 and RM-98, which are genetically the closest. Knowledge on the genetic diversity of castor can be used to future breeding programs of castor.
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25
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Schieltz DM, McWilliams LG, Kuklenyik Z, Prezioso SM, Carter AJ, Williamson YM, McGrath SC, Morse SA, Barr JR. Quantification of ricin, RCA and comparison of enzymatic activity in 18 Ricinus communis cultivars by isotope dilution mass spectrometry. Toxicon 2015; 95:72-83. [PMID: 25576235 PMCID: PMC5303535 DOI: 10.1016/j.toxicon.2015.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/20/2014] [Accepted: 01/06/2015] [Indexed: 11/22/2022]
Abstract
The seeds of the Ricinus communis (Castor bean) plant are the source of the economically important commodity castor oil. Castor seeds also contain the proteins ricin and R. communis agglutinin (RCA), two toxic lectins that are hazardous to human health. Radial immunodiffusion (RID) and the enzyme linked immunosorbent assay (ELISA) are two antibody-based methods commonly used to quantify ricin and RCA; however, antibodies currently used in these methods cannot distinguish between ricin and RCA due to the high sequence homology of the respective proteins. In this study, a technique combining antibody-based affinity capture with liquid chromatography and multiple reaction monitoring (MRM) mass spectrometry (MS) was used to quantify the amounts of ricin and RCA independently in extracts prepared from the seeds of eighteen representative cultivars of R. communis which were propagated under identical conditions. Additionally, liquid chromatography and MRM-MS was used to determine rRNA N-glycosidase activity for each cultivar and the overall activity in these cultivars was compared to a purified ricin standard. Of the cultivars studied, the average ricin content was 9.3 mg/g seed, the average RCA content was 9.9 mg/g seed, and the enzymatic activity agreed with the activity of a purified ricin reference within 35% relative activity.
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Affiliation(s)
- David M Schieltz
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA
| | - Lisa G McWilliams
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA
| | - Zsuzsanna Kuklenyik
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA
| | - Samantha M Prezioso
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Andrew J Carter
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Yulanda M Williamson
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA
| | - Sara C McGrath
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA
| | - Stephen A Morse
- Division of Foodborne, Waterborne and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - John R Barr
- Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway N.E., MS-F50, Atlanta, GA 30341, USA.
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Hayward AC, Tollenaere R, Dalton-Morgan J, Batley J. Molecular marker applications in plants. Methods Mol Biol 2015; 1245:13-27. [PMID: 25373746 DOI: 10.1007/978-1-4939-1966-6_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.
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Affiliation(s)
- Alice C Hayward
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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27
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Hodge DR, Prentice KW, Ramage JG, Prezioso S, Gauthier C, Swanson T, Hastings R, Basavanna U, Datta S, Sharma SK, Garber EAE, Staab A, Pettit D, Drumgoole R, Swaney E, Estacio PL, Elder IA, Kovacs G, Morse BS, Kellogg RB, Stanker L, Morse SA, Pillai SP. Comprehensive Laboratory Evaluation of a Highly Specific Lateral Flow Assay for the Presumptive Identification of Ricin in Suspicious White Powders and Environmental Samples. Biosecur Bioterror 2013; 11:237-50. [DOI: 10.1089/bsp.2013.0053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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Rai KM, Singh SK, Bhardwaj A, Kumar V, Lakhwani D, Srivastava A, Jena SN, Yadav HK, Bag SK, Sawant SV. Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:953-963. [PMID: 23782852 DOI: 10.1111/pbi.12088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/19/2013] [Accepted: 05/04/2013] [Indexed: 06/02/2023]
Abstract
The sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93,363 gene models (21,399 full length) and identified 35,923 gene models which were validated against already sequenced plant genomes. A total of 1,093 transcription factor-encoding genes, 3,135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47,093 novel simple sequence repeats and 66,364 novel single nucleotide polymorphisms. In addition, we developed NBRI-Comprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.
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Affiliation(s)
- Krishan Mohan Rai
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
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29
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Genetic Structure of the Endangered Northeastern Bulrush (Scirpus ancistrochaetus) in Pennsylvania, USA, Using Information from RAPD and SNPs. Biochem Genet 2013; 51:686-97. [DOI: 10.1007/s10528-013-9598-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 12/03/2012] [Indexed: 10/26/2022]
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30
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Rizzardo RAG, Milfont MO, Silva EMSD, Freitas BM. Apis mellifera pollination improves agronomic productivity of anemophilous castor bean (Ricinus communis). AN ACAD BRAS CIENC 2012; 84:1137-45. [PMID: 22990600 DOI: 10.1590/s0001-37652012005000057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 06/01/2012] [Indexed: 11/22/2022] Open
Abstract
Castor bean (Ricinus communis L.) is cultivated mainly for biodiesel production because of its oil-rich seeds; it is assumed to be an anemophylous species. But pollination deficit can lead to low productivity often attributed to other reasons. In this paper, we investigated pollination requirements, pollination mechanism, occurrence of pollination deficit, and the role of biotic pollinators in a large commercial plantation of castor bean. Our results show that R. communis bears a mixed breeding system favoring selfing by geitonogamy, although the wind promotes mostly outcrossing. We also found that the honey bee (Apis mellifera L.) foraging on castor bean can both transfer pollen from male to female flowers within the same raceme and boost the release of airborne pollen by male flowers. Both situations increase geitonogamy rates, raising significantly fruit set and seed yield. This is the first report of an animal foraging activity increasing seed yield in an anemophilous and geitonogamous crop and elucidates the role of biotic pollinators in castor bean reproduction.
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Affiliation(s)
- Rômulo A G Rizzardo
- Departamento de Zootecnia, Universidade Federal do Ceará, Fortaleza, CE, Brasil
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31
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Switchgrass PviCAD1: understanding residues important for substrate preferences and activity. Appl Biochem Biotechnol 2012; 168:1086-100. [PMID: 22915235 DOI: 10.1007/s12010-012-9843-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 08/09/2012] [Indexed: 12/12/2022]
Abstract
Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis. Although plants contain numerous genes coding for CADs, only one or two CADs appear to have a primary physiological role in lignin biosynthesis. Much of this distinction appears to reside in a few key residues that permit reasonable catalytic rates on monolignal substrates. Here, several mutant proteins were generated using switchgrass wild type (WT) PviCAD1 as a template to understand the role of some of these key residues, including a proton shuttling HL duo in the active site. Mutated proteins displayed lowered or limited activity on cinnamylaldehydes and exhibited altered kinetic properties compared to the WT enzyme, suggesting that key residues important for efficient catalysis had been identified. We have also shown that a sorghum ortholog containing EW, instead of HL in its active site, displayed negligible activity against monolignals. These results indicate that lignifying CADs require a specific set of key residues for efficient activity against monolignals.
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32
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Galeano CH, Cortés AJ, Fernández AC, Soler Á, Franco-Herrera N, Makunde G, Vanderleyden J, Blair MW. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean. BMC Genet 2012; 13:48. [PMID: 22734675 PMCID: PMC3464600 DOI: 10.1186/1471-2156-13-48] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/21/2012] [Indexed: 12/19/2022] Open
Abstract
Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.
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Affiliation(s)
- Carlos H Galeano
- Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, 3001, Heverlee, Belgium.
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33
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Understanding ricin from a defensive viewpoint. Toxins (Basel) 2011; 3:1373-92. [PMID: 22174975 PMCID: PMC3237001 DOI: 10.3390/toxins3111373] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/17/2022] Open
Abstract
The toxin ricin has long been understood to have potential for criminal activity and there has been concern that it might be used as a mass-scale weapon on a military basis for at least two decades. Currently, the focus has extended to encompass terrorist activities using ricin to disrupt every day activities on a smaller scale. Whichever scenario is considered, there are features in common which need to be understood; these include the knowledge of the toxicity from ricin poisoning by the likely routes, methods for the detection of ricin in relevant materials and approaches to making an early diagnosis of ricin poisoning, in order to take therapeutic steps to mitigate the toxicity. This article will review the current situation regarding each of these stages in our collective understanding of ricin and how to defend against its use by an aggressor.
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Abstract
The toxin ricin has long been understood to have potential for criminal activity and there has been concern that it might be used as a mass-scale weapon on a military basis for at least two decades. Currently, the focus has extended to encompass terrorist activities using ricin to disrupt every day activities on a smaller scale. Whichever scenario is considered, there are features in common which need to be understood; these include the knowledge of the toxicity from ricin poisoning by the likely routes, methods for the detection of ricin in relevant materials and approaches to making an early diagnosis of ricin poisoning, in order to take therapeutic steps to mitigate the toxicity. This article will review the current situation regarding each of these stages in our collective understanding of ricin and how to defend against its use by an aggressor.
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Affiliation(s)
- Gareth D Griffiths
- Biology Department, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK.
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35
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Pranavi B, Sitaram G, Yamini KN, Dinesh Kumar V. Development of EST-SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids. Genome 2011; 54:684-91. [PMID: 21848404 DOI: 10.1139/g11-033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST-SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.
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Affiliation(s)
- B Pranavi
- Directorate of Oilseeds Research, Rajendranagar, Hyderabad, Andhra Pradesh, India
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36
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Rivarola M, Foster JT, Chan AP, Williams AL, Rice DW, Liu X, Melake-Berhan A, Huot Creasy H, Puiu D, Rosovitz MJ, Khouri HM, Beckstrom-Sternberg SM, Allan GJ, Keim P, Ravel J, Rabinowicz PD. Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 2011; 6:e21743. [PMID: 21750729 PMCID: PMC3131294 DOI: 10.1371/journal.pone.0021743] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 06/10/2011] [Indexed: 11/26/2022] Open
Abstract
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
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MESH Headings
- Base Sequence
- Ricinus communis/classification
- Ricinus communis/genetics
- Ricinus communis/growth & development
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Genetic Variation
- Genome, Chloroplast/genetics
- Genome, Mitochondrial/genetics
- Genome, Plant/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Maximo Rivarola
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Amber L. Williams
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Danny W. Rice
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xinyue Liu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Heather Huot Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Daniela Puiu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - M. J. Rosovitz
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Hoda M. Khouri
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen M. Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Gerard J. Allan
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Pablo D. Rabinowicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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37
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Zaitlin D, Pierce AJ. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa. Genome 2010; 53:1066-82. [DOI: 10.1139/g10-077] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet ( Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea , Saintpaulia, and Streptocarpus , all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia , a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%–26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine–cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon ( Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ∼633 × 106 base pairs, which is approximately 40% of the previously published estimate.
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Affiliation(s)
- David Zaitlin
- Kentucky Tobacco Research and Development Center, 1401 University Drive, University of Kentucky, Lexington, KY 40546, USA
- Department of Microbiology, Immunology and Molecular Genetics, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Andrew J. Pierce
- Kentucky Tobacco Research and Development Center, 1401 University Drive, University of Kentucky, Lexington, KY 40546, USA
- Department of Microbiology, Immunology and Molecular Genetics, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
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38
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Vasconcelos S, Souza AAD, Gusmão CLS, Milani M, Benko-Iseppon AM, Brasileiro-Vidal AC. Heterochromatin and rDNA 5S and 45S sites as reliable cytogenetic markers for castor bean (Ricinus communis, Euphorbiaceae). Micron 2010; 41:746-53. [PMID: 20615717 DOI: 10.1016/j.micron.2010.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 06/10/2010] [Accepted: 06/14/2010] [Indexed: 11/24/2022]
Abstract
The increasing need for renewable energy resources has led to higher demands for biofuel, a scenario where the castor bean (Ricinus communis L.) seed oil represents a promising source of raw material. Despite that, information regarding the genome organization of R. communis is still scarce, impairing the application of modern biotechnological and breeding procedures. The present work brings the first evaluation of the mitotic chromosomes of this species, including 10 potentially interesting accessions for cultivation in semi-arid environments aiming at the biofuel production. The approach included standard staining, fluorochrome staining (CMA/DAPI), fluorescent in situ hybridization (FISH) with rDNA 5S and 45S, as well as silver impregnation. All accessions were diploid with 2n=2x=20, displaying mainly metacentric chromosomes, with CMA-positive bands (GC-rich) in all pairs of the complement. After silver impregnation, one to 14 nucleoli were observed, while the FISH with rDNA 45S revealed two large sites and a variety of minor dots, and the DNAr 5S hybridized in a single pair. The observed features were discussed and compared with literature data regarding pachytene bivalents.
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Affiliation(s)
- Santelmo Vasconcelos
- Department of Genetics, Federal University of Pernambuco, Av. Prof. Moraes Rego s/n, Recife, PE, Brazil
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39
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Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD. Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol 2010; 28:951-6. [PMID: 20729833 PMCID: PMC2945230 DOI: 10.1038/nbt.1674] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/02/2010] [Indexed: 11/11/2022]
Abstract
Castor bean (Ricinus communis) is an oilseed crop that belongs to the spurge (Euphorbiaceae) family, which comprises approximately 6,300 species that include cassava (Manihot esculenta), rubber tree (Hevea brasiliensis) and physic nut (Jatropha curcas). It is primarily of economic interest as a source of castor oil, used for the production of high-quality lubricants because of its high proportion of the unusual fatty acid ricinoleic acid. However, castor bean genomics is also relevant to biosecurity as the seeds contain high levels of ricin, a highly toxic, ribosome-inactivating protein. Here we report the draft genome sequence of castor bean (4.6-fold coverage), the first for a member of the Euphorbiaceae. Whereas most of the key genes involved in oil synthesis and turnover are single copy, the number of members of the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.
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Affiliation(s)
- Agnes P. Chan
- J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Qi Zhao
- J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA
| | - Hernan Lorenzi
- J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA
| | - Joshua Orvis
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Daniela Puiu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | | | - Kristine M. Jones
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Julia Redman
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Grace Chen
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Crop Improvement and Utilization, Albany, CA 94710, USA
| | - Edgar B. Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Melaku Gedil
- International Institute of Tropical Agriculture, Oyo State, Ibadan, Nigeria
| | - Mario Stanke
- Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany
| | - Brian J. Haas
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge MA 02141, USA
| | - Jennifer R. Wortman
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Claire M. Fraser-Liggett
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jacques Ravel
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Pablo D. Rabinowicz
- J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA
- Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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40
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Arif IA, Bakir MA, Khan HA, Al Farhan AH, Al Homaidan AA, Bahkali AH, Sadoon MA, Shobrak M. A brief review of molecular techniques to assess plant diversity. Int J Mol Sci 2010; 11:2079-96. [PMID: 20559503 PMCID: PMC2885095 DOI: 10.3390/ijms11052079] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/24/2010] [Accepted: 04/28/2010] [Indexed: 02/05/2023] Open
Abstract
Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.
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Affiliation(s)
| | | | - Haseeb A. Khan
- Author to whom correspondence should be addressed; E-Mail:
; Tel.: +966-1-4674-712
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