1
|
Reinert S, Gao Q, Ferguson B, Portlas ZM, Prasifka JR, Hulke BS. Seed and floret size parameters of sunflower are determined by partially overlapping sets of quantitative trait loci with epistatic interactions. Mol Genet Genomics 2019; 295:143-154. [PMID: 31559504 DOI: 10.1007/s00438-019-01610-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/10/2019] [Indexed: 11/26/2022]
Abstract
KEY MESSAGE Floret and seed traits are moderately correlated phenotypically in modern sunflower cultivars, but the underlying genetics are mostly independent. Seed traits in particular are governed in part by epistatic effects among quantitative trait loci. Seed size is an important quality component in marketing commercial sunflower (Helianthus annuus L.), particularly for the in-shell confectionery market, where long and broad seed types are preferred as a directly consumed snack food globally. Floret size is also important because corolla tube length was previously shown to be inversely correlated with pollinator visitation, impacting bee foraging potential and pollinator services to the plant. Commercial sunflower production benefits from pollinator visits, despite being self-compatible, and bees are required in hybrid seed production, where "female" and "male" inbred lines are crossed at field scale. Issues with pollination of long-seed confectionery sunflower suggest that there may be an unfavorable correlation between seed and floret traits; thus, our objective was to determine the strength of the correlation between seed and floret traits, and confirm any co-localization of seed and floret trait loci using genome-wide association analysis in the SAM diversity panel of sunflower. Our results indicate that phenotypic correlations between seed and floret traits are generally low to moderate, regardless of market class, a component of population substructure. Association mapping results mirror the correlations: while a few loci overlap, many loci for the two traits are not overlapping or even adjacent. The genetics of these traits, while modestly quantitative and influenced by epistatic effects, are not a barrier to simultaneous improvement of seed length and pollinator-friendly floret traits. We conclude that breeding for large seed size, which is required for the confectionery seed market, is possible without producing florets too long for efficient use by pollinators, which promotes bee foraging and associated pollination services.
Collapse
Affiliation(s)
- Stephan Reinert
- Ecology and Evolutionary Biology Department, University of Colorado, 1900 Pleasant Street, 334 UCB, Boulder, CO, 80309-0334, USA
| | - Qingming Gao
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
- Cibus, 6455 Nancy Ridge Drive, San Diego, CA, 92024, USA
| | - Beth Ferguson
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
| | - Zoe M Portlas
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
- Department of Plant Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Jarrad R Prasifka
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA
| | - Brent S Hulke
- USDA-ARS Edward T Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, ND, 58102-2765, USA.
| |
Collapse
|
2
|
Gonçalves DA, de Souza ID, Rosa ACG, Melo ESP, Goncalves AMB, de Oliveira LCS, do Nascimento VA. Multi-wavelength calibration: Determination of trace toxic elements in medicine plants by ICP OES. Microchem J 2019. [DOI: 10.1016/j.microc.2019.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
3
|
Combination of phenolic profiles, pharmacological properties and in silico studies to provide new insights on Silene salsuginea from Turkey. Comput Biol Chem 2018; 77:178-186. [DOI: 10.1016/j.compbiolchem.2018.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 01/17/2023]
|
4
|
Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata. 3 Biotech 2018; 8:133. [PMID: 29479509 DOI: 10.1007/s13205-018-1162-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/06/2018] [Indexed: 01/13/2023] Open
Abstract
To broaden and delve into the genomic information of Clausena excavata, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of Clausena species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.
Collapse
|
5
|
Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
Collapse
|
6
|
Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
Collapse
Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
| |
Collapse
|
7
|
Hao DC, Xiao PG. Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life. Evol Bioinform Online 2015; 11:197-212. [PMID: 26461812 PMCID: PMC4597484 DOI: 10.4137/ebo.s31326] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/24/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023] Open
Abstract
Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.
Collapse
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, P. R. China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, P. R. China
| |
Collapse
|
8
|
Hao DC, Gu XJ, Xiao PG, Peng Y. Phytochemical and biological research of Fritillaria medicine resources. Chin J Nat Med 2014; 11:330-44. [PMID: 23845541 DOI: 10.1016/s1875-5364(13)60050-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Indexed: 12/30/2022]
Abstract
The genus Fritillaria is a botanical source for various pharmaceutically active components, which have been commonly used in traditional Chinese medicine for thousands of years. Increasing interest in Fritillaria medicinal resources has led to additional discoveries of steroidal alkaloids, saponins, terpenoids, glycosides and many other compounds in various Fritillaria species, and to investigations on their chemotaxonomy, molecular phylogeny and pharmacology. In continuation of studies on Fritillaria pharmacophylogeny, the phytochemistry, chemotaxonomy, molecular biology and phylogeny of Fritillaria and their relevance to drug efficacy is reviewed. Literature searching is used to characterize the global scientific effort in the flexible technologies being applied. The interrelationship within Chinese Bei Mu species and between Chinese species, and species distributed outside of China, is clarified by the molecular phylogenetic inferences based on nuclear and chloroplast DNA sequences. The incongruence between chemotaxonomy and molecular phylogeny is revealed and discussed. It is essential to study more species for both the sustainable utilization of Fritillaria medicinal resources and for finding novel compounds with potential clinical utility. Systems biology and omics technologies will play an increasingly important role in future pharmaceutical research involving the bioactive compounds of Fritillaria.
Collapse
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment, Dalian Jiaotong University, Dalian 116028, China.
| | | | | | | |
Collapse
|
9
|
Wang Y, Xu L, Chen Y, Shen H, Gong Y, Limera C, Liu L. Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing. PLoS One 2013; 8:e66539. [PMID: 23840502 PMCID: PMC3688795 DOI: 10.1371/journal.pone.0066539] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/07/2013] [Indexed: 11/19/2022] Open
Abstract
Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)-based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.
Collapse
Affiliation(s)
- Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yinglong Chen
- School of Earth and Environment, and The UWA’s Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Hong Shen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yiqin Gong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Cecilia Limera
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Horticultural Crop Germplasm Enhancement and Utilization, Ministry of Education of P. R. China
- College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
- * E-mail:
| |
Collapse
|
10
|
Research progress in the phytochemistry and biology of Ilex pharmaceutical resources. Acta Pharm Sin B 2013. [DOI: 10.1016/j.apsb.2012.12.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
11
|
Hao DC, Xiao PG, Ge GB, Liu M. Biological, Chemical, and Omics Research ofTaxusMedicinal Resources. Drug Dev Res 2012. [DOI: 10.1002/ddr.21040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
| | | | - Guang-Bo Ge
- Pharmaceutical resource discovery; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian; China
| | - Ming Liu
- Biotechnology Institute/School of Environment; Dalian Jiaotong University; Dalian; China
| |
Collapse
|