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Hylander K, Nemomissa S, Fischer J, Zewdie B, Ayalew B, Tack AJM. Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world. Commun Biol 2024; 7:714. [PMID: 38858451 PMCID: PMC11164958 DOI: 10.1038/s42003-024-06381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.
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Affiliation(s)
- Kristoffer Hylander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden.
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Joern Fischer
- Leuphana University, Faculty of Sustainability, Scharnhorststrasse 1, 21335, Lueneburg, Germany
| | - Beyene Zewdie
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Biruk Ayalew
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
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2
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Hu XZ, Guo C, Qin SY, Li DZ, Guo ZH. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae). PLANT DIVERSITY 2024; 46:344-352. [PMID: 38798728 PMCID: PMC11119509 DOI: 10.1016/j.pld.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 05/29/2024]
Abstract
Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
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Affiliation(s)
- Xiang-Zhou Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Hernández F, Palmieri L, Brunet J. Introgression and persistence of cultivar alleles in wild carrot (Daucus carota) populations in the United States. AMERICAN JOURNAL OF BOTANY 2023; 110:e16242. [PMID: 37681637 DOI: 10.1002/ajb2.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
PREMISE Cultivated species and their wild relatives often hybridize in the wild, and the hybrids can survive and reproduce in some environments. However, it is unclear whether cultivar alleles are permanently incorporated into the wild genomes or whether they are purged by natural selection. This question is key to accurately assessing the risk of escape and spread of cultivar genes into wild populations. METHODS We used genomic data and population genomic methods to study hybridization and introgression between cultivated and wild carrot (Daucus carota) in the United States. We used single nucleotide polymorphisms (SNPs) obtained via genotyping by sequencing for 450 wild individuals from 29 wild georeferenced populations in seven states and 144 cultivars from the United States, Europe, and Asia. RESULTS Cultivated and wild carrot formed two genetically differentiated groups, and evidence of crop-wild admixture was detected in several but not all wild carrot populations in the United States. Two regions were identified where cultivar alleles were present in wild carrots: California and Nantucket Island (Massachusetts). Surprisingly, there was no evidence of introgression in some populations with a long-known history of sympatry with the crop, suggesting that post-hybridization barriers might prevent introgression in some areas. CONCLUSIONS Our results provide support for the introgression and long-term persistence of cultivar alleles in wild carrots populations. We thus anticipate that the release of genetically engineered (GE) cultivars would lead to the introduction and spread of GE alleles in wild carrot populations.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
- CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Luciano Palmieri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Madison, WI, USA
| | - Johanne Brunet
- Vegetable Crops Research Unit, USDA-ARS, Madison, WI, USA
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4
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Zhang Y, Zhu Q, Shao Y, Jiang Y, Ouyang Y, Zhang L, Zhang W. Inferring Historical Introgression with Deep Learning. Syst Biol 2023; 72:1013-1038. [PMID: 37257491 DOI: 10.1093/sysbio/syad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample sizes, restricted phylogenetic topologies, or hypothesis testing. To overcome these difficulties, we developed a deep learning-based approach, named ERICA, for inferring genome-wide evolutionary relationships and local introgressed regions from sequence data. ERICA accepts sequence alignments of both population genomic data and multiple genome assemblies, and efficiently identifies discordant genealogy patterns and exchanged regions across genomes when compared with other methods. We further tested ERICA using real population genomic data from Heliconius butterflies that have undergone adaptive radiation and frequent hybridization. Finally, we applied ERICA to characterize hybridization and introgression in wild and cultivated rice, revealing the important role of introgression in rice domestication and adaptation. Taken together, our findings demonstrate that ERICA provides an effective method for teasing apart evolutionary relationships using whole genome data, which can ultimately facilitate evolutionary studies on hybridization and introgression.
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Affiliation(s)
- Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Yi Shao
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Yanchen Jiang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
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Bulle M, Sheri V, Aileni M, Zhang B. Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3448. [PMID: 37836188 PMCID: PMC10574609 DOI: 10.3390/plants12193448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.
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Affiliation(s)
- Mallesham Bulle
- Agri Biotech Foundation, Agricultural University Campus, Rajendranagar, Hyderabad 500030, India
| | - Vijay Sheri
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
| | - Mahender Aileni
- Department of Biotechnology, Telangana University, Dichpally, Nizamabad 503322, India;
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA;
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Liaqat A, Salisu IB, Bakhsh A, Ali Q, Imran A, Ali MA, Farooq AM, Rao AQ, Shahid AA. A sub-chronic feeding study of dual toxin insect-resistant transgenic maize (CEMB-413) on Wistar rats. PLoS One 2023; 18:e0285090. [PMID: 37556453 PMCID: PMC10411795 DOI: 10.1371/journal.pone.0285090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/14/2023] [Indexed: 08/11/2023] Open
Abstract
Genetically modified (GM) crops expressing insecticidal crystal proteins are widely accepted worldwide, but their commercial utilization demands comprehensive risk assessment studies. A 90-day risk assessment study was conducted on Wistar rats fed with GM maize (CEMB-413) expressing binary insect-resistant genes (cry1Ac and cry2Ab) at low (30%) and high (50%) dose along with a control diet group. The study used fifty Wistar rats randomly distributed in five treatment groups. Our study revealed that compared to controls, GM diet had no adverse effects on animal's health, including body weight, food consumption, clinical pathological parameters, serum hormone levels and histological parameters of testes and ovaries of rats. Differences were observed in transcripts levels of fertility related genes, but these were independent of treatment with GM diet.
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Affiliation(s)
- Ayesha Liaqat
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ibrahim Bala Salisu
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Department of Animal Science, Faculty of Agriculture, Federal University Dutse, Dutse, Jigawa State, Nigeria
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qasim Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ayesha Imran
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Azam Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Abdul Munim Farooq
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Qayyum Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Loureiro I, Escorial MC, Chueca MC. Natural hybridization between wheat (Triticum aestivum L.) and its wild relatives Aegilops geniculata Roth and Aegilops triuncialis L. PEST MANAGEMENT SCIENCE 2023; 79:2247-2254. [PMID: 36785882 DOI: 10.1002/ps.7406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Cultivated bread wheat (Triticum aestivum L.) spontaneously hybridizes with wild/weedy related Aegilops populations, but little is known about the actual rates at which this hybridization occurs under field conditions. It is very important to provide reliable empirical data on this phenomenon in order to assess the potential crop-wild introgression, especially in the context of conducting risk assessments for the commercialization of genetically modified (GM) wheat, as gene flow from wheat to Aegilops species could transfer into the wild species genes coding for traits such as resistance to herbicides, insects, diseases or environmental stresses. RESULTS The spontaneous hybridization rates between wheat and A. geniculata and A. triuncialis, which are very abundant in the Mediterranean area, have been estimated for the first time in the northern part of the Meseta Central, the great central plateau which includes the largest area of wheat cultivation in Spain. Hybridization rates averaged 0.12% and 0.008% for A. geniculata and A. triuncialis, respectively. Hybrids were found in 26% of A. geniculata and 5% of A. triuncialis populations, at rates that can be ≤3.6% for A. geniculata and 0.24% for A. triuncialis. CONCLUSION The detection of Aegilops spp.-wheat hybrids in Aegilops populations indicates that gene flow can occur, although wheat is considered a crop with a low-to-medium risk for transgene escape. These data on field hybridization rates are essential for GM wheat risk assessment purposes. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Iñigo Loureiro
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - María Concepción Escorial
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - María Cristina Chueca
- Plant Protection Department, Weed Science Group, Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
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Residual Effects of Transgenic Cotton on the Intestinal Microbiota of Dysdercus concinnus. Microorganisms 2023; 11:microorganisms11020261. [PMID: 36838225 PMCID: PMC9967337 DOI: 10.3390/microorganisms11020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The interaction among plants, insects, and microbes (PIM) is a determinant factor for the assembly and functioning of natural and anthropic ecosystems. In agroecosystems, the relationships among PIM are based on the interacting taxa, environmental conditions, and agricultural management, including genetically modified (GM) organisms. Although evidence for the unintended effects of GM plants on non-target insects is increasingly robust, our knowledge remains limited regarding their impact on gut microbes and their repercussions on the host's ecology, especially in the wild. In this study, we compared the gut microbial community of Dysdercus concinnus bugs collected on wild cotton (Gossypium hirsutum), with and without insecticidal transgenes (cry1ab/ac), in its center of origin and diversity. By sequencing the V4-V5 region of 16S rRNA, we show differences in the diversity, structure, and topology of D. concinnus gut microbial interactions between specimens foraging cotton plants with and without transgenes. Identifying unintended residual effects of genetic engineering in natural ecosystems will provide first-line knowledge for informed decision-making to manage genetic, ecological, and evolutionary resources. Thus, determining which organisms interact with GM plants and how is the first step toward conserving natural ecosystems with evidence of transgenic introgression.
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Confirmation of 'Pollen- and Seed-Specific Gene Deletor' System Efficiency for Transgene Excision from Transgenic Nicotiana tabacum under Field Conditions. Int J Mol Sci 2023; 24:ijms24021160. [PMID: 36674672 PMCID: PMC9866632 DOI: 10.3390/ijms24021160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 01/10/2023] Open
Abstract
The commercial application of genetically modified plants has been seriously impeded by public concern surrounding the potential risks posed by such plants to the ecosystem and human health. Previously, we have developed a 'pollen- and seed-specific Gene Deletor' system that automatically excised all transgenes from the pollen and seeds of greenhouse-grown transgenic Nicotiana tabacum. In this study, we conducted seven field experiments over three consecutive years to evaluate the stability of transgene excision under field conditions. Our results showed that transgenes were stably excised from transgenic Nicotiana tabacum under field conditions with 100% efficiency. The stability of transgene excision was confirmed based on PCR, as well as the GUS staining patterns of various organs (roots, leaves, petiole, stem, flower, fruit, and seeds) from transgenic N. tabacum. In six transgenic lines (D4, D10, D31, D56, and D43), the transgenes were stably deleted in the T0 and T1 generations. Thus, the 'Gene Deletor' system is an efficient and reliable method to reduce pollen- and seed-mediated unintentional gene flow. This system might help to alleviate the food safety concerns associated with transgenic crops.
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10
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
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Liu L, Zhang L, Fu J, Shen W, Fang Z, Dai Y, Jia R, Liu B, Liang J. Fitness and Ecological Risk of Hybrid Progenies of Wild and Herbicide-Tolerant Soybeans With EPSPS Gene. FRONTIERS IN PLANT SCIENCE 2022; 13:922215. [PMID: 35755711 PMCID: PMC9224928 DOI: 10.3389/fpls.2022.922215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/24/2022] [Indexed: 05/11/2023]
Abstract
Exogenous genes of transgenic crops are usually transferred to their wild-type relatives through pollen-mediated gene flow, which may change the ecological fitness and ability to invade wild populations, resulting in the weeding of wild plants and other unpredictable environmental impacts. In this study, the F1 generation of herbicide-resistant soybeans and wild soybeans was obtained by artificial pollination, F2 generation seeds were obtained by self-crossing, and the fitness of the parents and their F1 and F2 generations were tested. The foreign protein EPSPS was expressed normally in the hybrid between transgenic and wild soybeans; however, the protein expression was significantly lower than that in transgenic soybeans. The fitness of the F1 hybrid between transgenic and wild soybeans was significantly lower than that of its parent. Compared with those of the wild soybeans, the F2 generation soybeans improved in some fitness indices, while the emergence rate, pollen germination rate, and number of full seeds per pod, pods per plant, and full seeds per plant did not significantly differ. The aboveground biomass and 100-seed weight of the F2 generation were higher than those of wild soybeans. Fitness among the F2-negative plants, homozygous, and heterozygous positive plants did not significantly vary. Improved fitness and presence of foreign genes in the F2 soybean were not significantly correlated. As the F2 generation of transgenic and wild soybeans had no fitness cost and the flowering stage were overlapped, the foreign gene might still spread in the wild soybean population.
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Affiliation(s)
- Laipan Liu
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Li Zhang
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Jianmei Fu
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Wenjing Shen
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Zhixiang Fang
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Ying Dai
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya, China
| | - Biao Liu
- Key Laboratory on Biosafety of Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
- State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
- *Correspondence: Biao Liu,
| | - Jingang Liang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
- Jingang Liang,
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12
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Incorporating the field border effect to reduce the predicted uncertainty of pollen dispersal model in Asia. Sci Rep 2021; 11:22187. [PMID: 34772995 PMCID: PMC8589847 DOI: 10.1038/s41598-021-01583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
The presence of the field border (FB), such as roadways or unplanted areas, between two fields is common in Asian farming system. This study evaluated the effect of the FB on the cross-pollination (CP) and predicted the CP rate in the field considering and not considering FB. Three experiments including 0, 6.75, and 7.5 m width of the FB respectively were conducted to investigate the effect of distance and the FB on the CP rate. The dispersal models combined kernel and observation model by calculating the parameter of observation model from the output of kernel. These models were employed to predict the CP rate at different distances. The Bayesian method was used to estimate parameters and provided a good prediction with uncertainty. The highest average CP rates in the field with and without FB were 74.29% and 36.12%, respectively. It was found that two dispersal models with the FB effect displayed a higher ability to predict average CP rates. The correlation coefficients between actual CP rates and CP rates predicted by the dispersal model combined zero-inflated Poisson observation model with compound exponential kernel and modified Cauchy kernel were 0.834 and 0.833, respectively. Furthermore, the predictive uncertainty was reducing using the dispersal models with the FB effect.
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Salgotra RK, Thompson M, Chauhan BS. Unravelling the genetic potential of untapped crop wild genetic resources for crop improvement. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Aycan M, Baslam M, Asiloglu R, Mitsui T, Yildiz M. Development of new high-salt tolerant bread wheat (Triticum aestivum L.) genotypes and insight into the tolerance mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:314-327. [PMID: 34147724 DOI: 10.1016/j.plaphy.2021.05.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/24/2021] [Indexed: 05/24/2023]
Abstract
The loss of cropland soils, climate change, and population growth are directly affecting the food supply. Given the higher incidence of salinity and extreme events, the cereal performance and yield are substantially hampered. Wheat is forecast to decline over the coming years due to the salinization widespread as one of the oldest and most environmental severe constraints facing global cereal production. To increase salinity tolerance of wheat, in this study, we developed two new salt-tolerant bread wheats, named 'Maycan' and 'Yıldız'. The salinity tolerance of these lines, their parents, and a salt-sensitive cultivar has been tested from measurements of physiological, biochemical, and genes associated with osmotic adjustment/plant tolerance in cultures containing 0 and 150 mM NaCl at the seedling stage. Differential growth reductions to increased salinity were observed in the salt-sensitive cultivar, with those newly developed exhibiting significantly greater root length, growth of shoot and water content as salinity tolerances overall than their parents. 'Maycan' and 'Yıldız' had higher osmoregulator proline content and antioxidants enzyme activities under salinity than the other bread wheat tested. Notably, an important upregulation in the expression of genes related to cellular ion balance, osmolytes accumulation, and abscisic acid was observed in both new wheat germplasms, which may improve salt tolerance. These finding revealed that 'Maycan' and 'Yıldız' exhibit high-salt tolerance at the seedling stage and differing in their tolerance mechanisms to the other tested cultivars, thereby providing an opportunity for their exploitation as modern bread wheats.
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Affiliation(s)
- Murat Aycan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Rasit Asiloglu
- Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Mustafa Yildiz
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey.
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15
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Teferra TF. Should we still worry about the safety of GMO foods? Why and why not? A review. Food Sci Nutr 2021; 9:5324-5331. [PMID: 34532037 PMCID: PMC8441473 DOI: 10.1002/fsn3.2499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/17/2021] [Indexed: 11/08/2022] Open
Abstract
Global population is increasing at an alarming rate, posing a threat on the supplies of basic needs and services. However, population increase does not seem to be a common agendum of the global scientists and political leaders. People in the developed countries are more concerned about new technologies and their products. Pseudo-threats related to the uncertainties of genetic engineering of crops and their outputs present on consumers are more audible and controversial than the real difficulties the world is experiencing at the moment and in the future. This review presents brief summaries of the real reasons to worry about and the uncertainties about genetically modified organisms. This article also presents the real uncertainties shared by consumers and scientists with respect to the past, present, and future of genetically engineered organisms. Developments in the field of precision genetics in the recent years and the implications on regulatory, breeding, and socio-cultural dimensions of the global settings are included.
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Affiliation(s)
- Tadesse Fikre Teferra
- School of Nutrition, Food Science and TechnologyCollege of AgricultureHawassa UniversitySidamaEthiopia
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16
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Nam KH, Kim DY, Moon YS, Pack IS, Jeong SC, Kim HB, Kim CG. Performance of hybrids between abiotic stress-tolerant transgenic rice and its weedy relatives under water-stressed conditions. Sci Rep 2020; 10:9319. [PMID: 32518274 PMCID: PMC7283212 DOI: 10.1038/s41598-020-66206-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/04/2020] [Indexed: 11/16/2022] Open
Abstract
Gene transfer from transgenic crops to their weedy relatives may introduce undesired ecological consequences that can increase the fitness and invasiveness of weedy populations. Here, we examined the rate of gene flow from abiotic stress-tolerant transgenic rice that over-express AtCYP78A7, a gene encoding cytochrome P450 protein, to six weedy rice accessions and compared the phenotypic performance and drought tolerance of their hybrids over generations. The rate of transgene flow from AtCYP78A7-overexpressing transgenic to weedy rice varied between 0% and 0.0396%. F1 hybrids containing AtCYP78A7 were significantly taller and heavier, but the percentage of ripened grains, grain numbers and weight per plant were significantly lower than their transgenic and weedy parents. The homozygous and hemizygous F2 progeny showed higher tolerance to drought stress than the nullizygous F2 progeny, as indicated by leaf rolling scores. Shoot growth of nullizygous F3 progeny was significantly greater than weedy rice under water-deficient conditions in a rainout shelter, however, that of homozygous F3 progeny was similar to weedy rice, indicating the cost of continuous expression of transgene. Our findings imply that gene flow from AtCYP78A7-overexpressing transgenic to weedy rice might increase drought tolerance as shown in the pot experiment, however, increased fitness under stressed conditions in the field were not observed for hybrid progeny containing transgenes.
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Affiliation(s)
- Kyong-Hee Nam
- LMO research team, National Institute of Ecology, Seocheon, 33657, Republic of Korea
| | - Do Young Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - Ye Seul Moon
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - In Soon Pack
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - Ho Bang Kim
- Life Sciences Research Institute, Biomedic Co., Ltd., Bucheon, 14548, Republic of Korea
| | - Chang-Gi Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea.
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17
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Liu Y, Stewart CN. An exposure pathway-based risk assessment system for GM plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1859-1861. [PMID: 31055881 PMCID: PMC6736782 DOI: 10.1111/pbi.13146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk AssessmentChinese Research Academy of Environmental SciencesBeijingChina
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18
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Scholz GE, Popescu AA, Taylor MI, Moulton V, Huber KT. OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression. Syst Biol 2019; 68:717-729. [PMID: 30668824 DOI: 10.1093/sysbio/syz004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain "overlay" of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.
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Affiliation(s)
| | | | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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19
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Martin SL, Lujan‐Toro BE, Sauder CA, James T, Ohadi S, Hall LM. Hybridization rate and hybrid fitness for Camelina microcarpa Andrz. ex DC (♀) and Camelina sativa (L.) Crantz(Brassicaceae) (♂). Evol Appl 2019; 12:443-455. [PMID: 30828366 PMCID: PMC6383699 DOI: 10.1111/eva.12724] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/28/2018] [Accepted: 10/08/2018] [Indexed: 12/25/2022] Open
Abstract
Hybridization between crops and their wild relatives has the potential to introduce novel variation into wild populations. Camelina (Camelina sativa) is a promising oilseed and cultivars with modified seed characteristics and herbicide resistance are in development, prompting a need to evaluate the potential for novel trait introgression into weedy relatives. Little-podded false flax (littlepod; Camelina microcarpa) is a naturalized weed in Canada and the USA. Here we evaluated the hybridization rate between the three cytotypes of littlepod (♀) and camelina (♂), assessed characteristics of hybrids, and evaluated the fitness of hexaploid littlepod and camelina hybrids in the glasshouse and field. In total we conducted, 1,005 manual crosses with diploid littlepod, 1, 172 crosses with tetraploid littlepod, and 896 crosses with hexaploid littlepod. Hybrids were not produced by the diploids, but were produced by the tetraploids and hexaploids at rates of one hybrid for 2,000 ovules pollinated and 24 hybrids for 25 ovules pollinated, respectively. Hybrids between tetraploid littlepod and camelina showed low pollen fertility and produced a small number of seeds. In the glasshouse, hybrids between hexaploid littlepod and camelina also showed significantly lower pollen fertility and seed production than parental lines, but their seeds showed high viability. A similar pattern was observed in field trials, with hybrids showing earlier flowering, reduced biomass, seed production and seed weight. However, seed produced by the hybrids showed greater viability than that produced by hexaploid littlepod and is potentially the result of a shortened lifecycle. The introgression of lifecycle traits into littlepod populations may facilitate range expansion and contribute to crop gene persistence. Consequently, future work should evaluate the hybridization rate in the field, the fitness of advanced generation backcrosses, and the role of time to maturity in limiting hexaploid littlepod's distribution.
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Affiliation(s)
- Sara L. Martin
- Ottawa Research and Development CentreAgriculture and Agri‐food CanadaOttawaOntario
| | | | - Connie A. Sauder
- Ottawa Research and Development CentreAgriculture and Agri‐food CanadaOttawaOntario
| | - Tracey James
- Ottawa Research and Development CentreAgriculture and Agri‐food CanadaOttawaOntario
| | - Sara Ohadi
- Agricultural Food and Nutritional ScienceUniversity of AlbertaEdmontonAlberta
| | - Linda M. Hall
- Agricultural Food and Nutritional ScienceUniversity of AlbertaEdmontonAlberta
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20
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Janzen GM, Wang L, Hufford MB. The extent of adaptive wild introgression in crops. THE NEW PHYTOLOGIST 2019; 221:1279-1288. [PMID: 30368812 DOI: 10.1111/nph.15457] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/24/2018] [Indexed: 05/05/2023]
Abstract
The study of crop evolution has focused primarily on the process of initial domestication. Post-domestication adaptation during the expansion of crops from their centers of origin has received considerably less attention. Recent research has revealed that, in at least some instances, crops have received introgression from their wild relatives that has facilitated adaptation to novel conditions encountered during expansion. Such adaptive introgression could have an important impact on the basic study of domestication, affecting estimates of several evolutionary processes of interest (e.g. the strength of the domestication bottleneck, the timing of domestication, the targets of selection during domestication). Identification of haplotypes introgressed from the wild may also help in the identification of alleles that are beneficial under particular environmental conditions. Here we review mounting evidence for substantial adaptive wild introgression in several crops and consider the implications of such gene flow to our understanding of crop histories.
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Affiliation(s)
- Garrett M Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Li Wang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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21
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Liu Y, Neal Stewart C, Li J, Wei W. One species to another: sympatric Bt transgene gene flow from Brassica napus alters the reproductive strategy of wild relative Brassica juncea under herbivore treatment. ANNALS OF BOTANY 2018; 122:617-625. [PMID: 29878055 PMCID: PMC6153478 DOI: 10.1093/aob/mcy096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/10/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Since pollen flow or seed dispersal can contribute to transgene persistence in the environment, the sympatric presence of transgenic crops with their wild relatives is an ecological concern. In this study, we tested the hypothesis that proximate growth of a herbivore-resistant Bt crop and wild relatives coupled with the presence of herbivores can increase relative frequency of crop-to-wild transgene flow persistence outside of cultivation. METHODS We conducted a field experiment using insect enclosures with and without herbivores with cultivated Bt-transgenic Brassica napus (Bt OSR) and wild brown mustard (Brassica juncea) in pure and mixed stands. Low-density diamondback moth (Plutella xylostella) caterpillar infestation treatments were applied and transgene flow and reproductive organs were measured. KEY RESULTS Bt-transgenic B. napus produced more ovules and pollen than wild mustard, but the pollen to ovule (P/O) ratio in the two species was not significantly different. Low-level herbivory had no effects on fitness parameters of Bt OSR or wild brown mustard or on the transgene flow frequency. All progeny from wild brown mustard containing the Bt transgene came from mixed stands, with a gene flow frequency of 0.66 %. In mixed stands, wild brown mustard produced less pollen and more ovules than in pure stands of brown mustard. This indicates a decreased P/O ratio in a mixed population scenario. CONCLUSIONS Since a lower P/O ratio indicates a shift in sex allocation towards relatively greater female investment and a higher pollen transfer efficiency, the presence of transgenic plants in wild populations may further increase the potential transgene flow by altering reproductive allocation of wild species.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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22
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Abstract
The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.
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23
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Velázquez-López R, Wegier A, Alavez V, Pérez-López J, Vázquez-Barrios V, Arroyo-Lambaer D, Ponce-Mendoza A, Kunin WE. The Mating System of the Wild-to-Domesticated Complex of Gossypium hirsutum L. Is Mixed. FRONTIERS IN PLANT SCIENCE 2018; 9:574. [PMID: 29868048 PMCID: PMC5954804 DOI: 10.3389/fpls.2018.00574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton's wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton's capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity.
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Affiliation(s)
- Rebeca Velázquez-López
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Alavez
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Javier Pérez-López
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Vázquez-Barrios
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Denise Arroyo-Lambaer
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - William E. Kunin
- Department of Ecology and Evolution, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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24
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Iriondo JM, Milla R, Volis S, Rubio de Casas R. Reproductive traits and evolutionary divergence between Mediterranean crops and their wild relatives. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:78-88. [PMID: 28976618 DOI: 10.1111/plb.12640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/27/2017] [Indexed: 05/12/2023]
Abstract
Changes in reproductive traits associated with domestication critically determine the evolutionary divergence between crops and their wild relatives, as well as the potential of crop plants to become feral. In this review, we examine the genetic mechanisms of plant domestication and the different types of selection involved, and describe the particularities of domestication of Mediterranean field crops with regard to their reproductive traits, showing illustrative examples. We also explore gene flow patterns between Mediterranean field crops and their wild relatives, along with their ecological, evolutionary and economic implications. Domestication entails multiple selective processes, including direct selection, environmental adaptation and developmental constraints. In contrast to clonal propagation in perennials, sexual reproduction and seed propagation in annuals and biennials have led to a distinct pathway of evolution of reproductive traits. Thus, the initial domestication and further breeding of Mediterranean field crops has brought about changes in reproductive traits, such as higher mean values and variance of seed and fruit sizes, reduced fruit and seed toxicity, non-shattering seeds and loss of seed dormancy. Evolution under domestication is not a linear process, and bi-directional gene flow between wild and crop taxa is a frequent phenomenon. Thus, hybridisation and introgression have played a very important role in determining the genetics of current cultivars. In turn, gene flow from crops to wild relatives can lead to introgression of crop genes into wild populations and potentially alter the characteristics of natural communities. In conclusion, plant evolution under domestication has not only changed the reproductive biology of cultivated taxa, its effects are multifaceted and have implications beyond agriculture.
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Affiliation(s)
- J M Iriondo
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - R Milla
- Área de Biodiversidad y Conservación, Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - S Volis
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - R Rubio de Casas
- Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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25
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Thomas E, Tovar E, Villafañe C, Bocanegra JL, Moreno R. Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia. RICE (NEW YORK, N.Y.) 2017; 10:13. [PMID: 28421550 PMCID: PMC5395511 DOI: 10.1186/s12284-017-0150-9] [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: 11/10/2016] [Accepted: 03/24/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Crop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs. RESULTS Our findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future. CONCLUSIONS Given (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian CWRs, effective in situ conservation might best be achieved through tailor-made management plans and exclusion of GM rice cultivation in areas holding the most genetically diverse CWR populations. This may be combined with assisted migration of populations to suitable areas where rice is unlikely to be cultivated under current and future climate conditions.
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Affiliation(s)
| | - Eduardo Tovar
- The Alexander von Humboldt Biological Resources Research Institute, Laboratory of Conservation Genetics, Bogota, Colombia
| | - Carolina Villafañe
- Ministry of Environment and Sustainable Development, Genetic Resources Group, Bogota, Colombia
| | - José Leonardo Bocanegra
- The Alexander von Humboldt Biological Resources Research Institute, International Affairs, Policy and Cooperation Office, Bogota, Colombia
| | - Rodrigo Moreno
- The Alexander von Humboldt Biological Resources Research Institute, International Affairs, Policy and Cooperation Office, Bogota, Colombia
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26
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Wang Z, Wang L, Wang Z, Lu BR. Non-random transmission of parental alleles into crop-wild and crop-weed hybrid lineages separated by a transgene and neutral identifiers in rice. Sci Rep 2017; 7:10436. [PMID: 28874702 PMCID: PMC5585250 DOI: 10.1038/s41598-017-10596-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
It is essential to assess environmental impact of transgene flow from genetically engineered crops to their wild or weedy relatives before commercialization. Measuring comparative trials of fitness in the transgene-flow-resulted hybrids plays the key role in the assessment, where the segregated isogenic hybrid lineages/subpopulations with or without a transgene of the same genomic background are involved. Here, we report substantial genomic differentiation between transgene-present and -absent lineages (F2-F3) divided by a glyphosate-resistance transgene from a crop-wild/weed hybrid population in rice. We further confirmed that such differentiation is attributed to increased frequencies of crop-parent alleles in transgenic hybrid lineages at multiple loci across the genome, as estimated by SSR (simple sequence repeat) markers. Such preferential transmission of parental alleles was also found in equally divided crop-wild/weed hybrid lineages with or without a particular neutral SSR identifier. We conclude that selecting either a transgene or neutral marker as an identifier to create hybrid lineages will result in different genomic background of the lineages due to non-random transmission of parental alleles. Non-random allele transmission may misrepresent the outcomes of fitness effects. We therefore propose seeking other means to evaluate fitness effects of transgenes for assessing environmental impact caused by crop-to-wild/weed gene flow.
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Affiliation(s)
- Zhe Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Lei Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Zhi Wang
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for biodiversity science and Ecological Engineering, Department of Ecology and Evolutionary Biology, Fudan University, Shanghai, 200433, China.
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27
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Genetic manipulations in crops: Challenges and opportunities. Genomics 2017; 109:494-505. [PMID: 28778540 DOI: 10.1016/j.ygeno.2017.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants could better adapt to adverse environmental conditions in a changing climate. The emergence of new tools for the introduction of foreign genes into plants has increased both our knowledge and the capacity to develop transgenic plants. In addition, a better understanding of genetic modifications has allowed us to study the impact that genetically modified crop plants may have on the environment. This article discusses different techniques routinely used to carry out genetic modifications in plants while highlighting challenges with them, which future research must address to increase acceptance of GM crops for meeting food security challenges effectively.
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Corbi J, Baack EJ, Dechaine JM, Seiler G, Burke JM. Genome-wide analysis of allele frequency change in sunflower crop-wild hybrid populations evolving under natural conditions. Mol Ecol 2017; 27:233-247. [PMID: 28612961 DOI: 10.1111/mec.14202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 05/20/2017] [Accepted: 05/24/2017] [Indexed: 01/20/2023]
Abstract
Crop-wild hybridization occurs in numerous plant species and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop-derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop-wild hybridization has generally been examined via short-term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop-derived alleles over multiple generations, particularly at a genome-wide scale. Here, we documented patterns of natural selection in an experimental crop × wild sunflower population that was allowed to evolve under natural conditions for two generations at two locations. Allele frequencies at a genome-wide collection of SNPs were tracked across generations, and a common garden experiment was conducted to compare trait means between generations. These data allowed us to identify instances of selection on crop-derived alleles/traits and, in concert with QTL mapping results, test for congruence between our genotypic and phenotypic results. We found that natural selection overwhelmingly favours wild alleles and phenotypes. However, crop alleles in certain genomic regions can be favoured, and these changes often occurred in parallel across locations. We did not, however, consistently observe close agreement between our genotypic and phenotypic results. For example, when a trait evolved towards the wild phenotype, wild QTL alleles associated with that trait did not consistently increase in frequency. We discuss these results in the context of crop allele introgression into wild populations and implications for the management of GM crops.
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Affiliation(s)
- Jonathan Corbi
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, USA.,CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Univ Lyon, Université Lyon 1, Villeurbanne, France
| | - Eric J Baack
- Department of Biology, Luther College, Decorah, IA, USA
| | - Jennifer M Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, WA, USA
| | - Gerald Seiler
- USDA-ARS, Northern Crop Science Lab., Fargo, ND, USA
| | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, GA, USA
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Tsatsakis AM, Nawaz MA, Kouretas D, Balias G, Savolainen K, Tutelyan VA, Golokhvast KS, Lee JD, Yang SH, Chung G. Environmental impacts of genetically modified plants: A review. ENVIRONMENTAL RESEARCH 2017; 156:818-833. [PMID: 28347490 DOI: 10.1016/j.envres.2017.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 06/06/2023]
Abstract
Powerful scientific techniques have caused dramatic expansion of genetically modified crops leading to altered agricultural practices posing direct and indirect environmental implications. Despite the enhanced yield potential, risks and biosafety concerns associated with such GM crops are the fundamental issues to be addressed. An increasing interest can be noted among the researchers and policy makers in exploring unintended effects of transgenes associated with gene flow, flow of naked DNA, weediness and chemical toxicity. The current state of knowledge reveals that GM crops impart damaging impacts on the environment such as modification in crop pervasiveness or invasiveness, the emergence of herbicide and insecticide tolerance, transgene stacking and disturbed biodiversity, but these impacts require a more in-depth view and critical research so as to unveil further facts. Most of the reviewed scientific resources provide similar conclusions and currently there is an insufficient amount of data available and up until today, the consumption of GM plant products are safe for consumption to a greater extent with few exceptions. This paper updates the undesirable impacts of GM crops and their products on target and non-target species and attempts to shed light on the emerging challenges and threats associated with it. Underpinning research also realizes the influence of GM crops on a disturbance in biodiversity, development of resistance and evolution slightly resembles with the effects of non-GM cultivation. Future prospects are also discussed.
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Affiliation(s)
- Aristidis M Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion, Crete, Greece; Educational Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok 690950, Russian Federation
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea
| | - Demetrios Kouretas
- Department of Biochemistry-Biotechnology, University of Thessaly, Larisa, Greece
| | | | - Kai Savolainen
- Finnish Institute of Occupational Health, POB 40 Helsinki, Finland
| | - Victor A Tutelyan
- Federal Research Centre of Nutrition, Biotechnology and Food Safety, Moscow, Russian Federation
| | - Kirill S Golokhvast
- Educational Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok 690950, Russian Federation; Pacific Institute of Geography, FEB RAS, Vladivostok 690041, Russian Federation
| | - Jeong Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626, Republic of Korea.
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Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus- Raphanus raphanistrum Model. Genetics 2017; 206:1361-1372. [PMID: 28533439 DOI: 10.1534/genetics.117.201715] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/07/2017] [Indexed: 11/18/2022] Open
Abstract
The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties (Brassica napus, AACC, 2n = 38) by a local population of wild radish (Raphanus raphanistrum, RrRr, 2n = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0-28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow.
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31
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Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes. Transgenic Res 2017; 26:465-475. [PMID: 28526984 DOI: 10.1007/s11248-017-0016-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 04/01/2017] [Indexed: 10/19/2022]
Abstract
Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced seed shattering in crop-weed hybrid descendants by partially silenced expression of the seed-shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence seed-shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.
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Wu M, Lewis J, Moore RC. A wild origin of the loss-of-function lycopene beta cyclase (CYC-b) allele in cultivated, red-fleshed papaya (Carica papaya). AMERICAN JOURNAL OF BOTANY 2017; 104:116-126. [PMID: 28082282 DOI: 10.3732/ajb.1600301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The red flesh of some papaya cultivars is caused by a recessive loss-of-function mutation in the coding region of the chromoplast-specific lycopene beta cyclase gene (CYC-b). We performed an evolutionary genetic analysis of the CYC-b locus in wild and cultivated papaya to uncover the origin of this loss-of-function allele in cultivated papaya. METHODS We analyzed the levels and patterns of genetic diversity at the CYC-b locus and six loci in a 100-kb region flanking CYC-b and compared these to genetic diversity levels at neutral autosomal loci. The evolutionary relationships of CYC-b haplotypes were assessed using haplotype network analysis of the CYC-b locus and the 100-kb CYC-b region. KEY RESULTS Genetic diversity at the recessive CYC-b allele (y) was much lower relative to the dominant Y allele found in yellow-fleshed wild and cultivated papaya due to a strong selective sweep. Haplotype network analyses suggest the y allele most likely arose in the wild and was introduced into domesticated varieties after the first papaya domestication event. The shared haplotype structure between some wild, feral, and cultivated haplotypes around the y allele supports subsequent escape of this allele from red cultivars back into wild populations through feral intermediates. CONCLUSIONS Our study supports a protracted domestication process of papaya through the introgression of wild-derived traits and gene flow from cultivars to wild populations. Evidence of gene flow from cultivars to wild populations through feral intermediates has implications for the introduction of transgenic papaya into Central American countries.
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Affiliation(s)
- Meng Wu
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Jamicia Lewis
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104 USA
| | - Richard C Moore
- Miami University, Department of Biology, 212 Pearson Hall, Oxford, Ohio 45056 USA
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Pace BA, Alexander HM, Emry DJ, Mercer KL. Reliable Method for Assessing Seed Germination, Dormancy, and Mortality under Field Conditions. J Vis Exp 2016. [PMID: 27842344 DOI: 10.3791/54663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We describe techniques for approximating seed bank dynamics over time using Helianthus annuus as an example study species. Strips of permeable polyester fabric and glue can be folded and glued to construct a strip of compartments that house seeds and identifying information, while allowing contact with soil leachate, water, microorganisms, and ambient temperature. Strips may be constructed with a wide range of compartment numbers and sizes and allow the researcher to house a variety of genotypes within a single species, different species, or seeds that have experienced different treatments. As opposed to individual seed packets, strips are more easily retrieved as a unit. While replicate packets can be included within a strip, different strips can act as blocks or can be retrieved at different times for observation of seed behavior over time. We used a high temperature glue gun to delineate compartments and sealed the strips once the seed and tags identifying block and removal times were inserted. The seed strips were then buried in the field at the desired depth, with the location marked for later removal. Burrowing animal predators were effectively excluded by use of a covering of metal mesh hardware cloth on the soil surface. After the selected time interval for burial, strips were dug up and seeds were assessed for germination, dormancy and mortality. While clearly dead seeds can often be distinguished from ungerminated living ones by eye, dormant seeds were conclusively identified using a standard Tetrazolium chloride colorimetric test for seed viability.
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Affiliation(s)
- Brian A Pace
- Department of Horticulture and Crop Science, Ohio State University;
| | - Helen M Alexander
- Department of Ecology and Evolutionary Biology, University of Kansas
| | | | - Kristin L Mercer
- Department of Horticulture and Crop Science, Ohio State University
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34
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Ahmad N, Michoux F, Lössl AG, Nixon PJ. Challenges and perspectives in commercializing plastid transformation technology. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5945-5960. [PMID: 27697788 DOI: 10.1093/jxb/erw360] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Plastid transformation has emerged as an alternative platform to generate transgenic plants. Attractive features of this technology include specific integration of transgenes-either individually or as operons-into the plastid genome through homologous recombination, the potential for high-level protein expression, and transgene containment because of the maternal inheritance of plastids. Several issues associated with nuclear transformation such as gene silencing, variable gene expression due to the Mendelian laws of inheritance, and epigenetic regulation have not been observed in the plastid genome. Plastid transformation has been successfully used for the production of therapeutics, vaccines, antigens, and commercial enzymes, and for engineering various agronomic traits including resistance to biotic and abiotic stresses. However, these demonstrations have usually focused on model systems such as tobacco, and the technology per se has not yet reached the market. Technical factors limiting this technology include the lack of efficient protocols for the transformation of cereals, poor transgene expression in non-green plastids, a limited number of selection markers, and the lengthy procedures required to recover fully segregated plants. This article discusses the technology of transforming the plastid genome, the positive and negative features compared with nuclear transformation, and the current challenges that need to be addressed for successful commercialization.
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Affiliation(s)
- Niaz Ahmad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Jhang Road, Faisalabad, Pakistan
| | - Franck Michoux
- Alkion Biopharma SAS, 4 rue Pierre Fontaine, 91058 Evry, France
| | - Andreas G Lössl
- Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College, South Kensington Campus, London SW7 2AZ, UK
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35
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Mandel JR, Ramsey AJ, Iorizzo M, Simon PW. Patterns of Gene Flow between Crop and Wild Carrot, Daucus carota (Apiaceae) in the United States. PLoS One 2016; 11:e0161971. [PMID: 27603516 PMCID: PMC5014312 DOI: 10.1371/journal.pone.0161971] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Studies of gene flow between crops and their wild relatives have implications for both management practices for cultivation and understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene flow for wild relatives of crop species. Moreover, the comparison of genetic markers with different modes of inheritance, or transmission, such as those of the nuclear and chloroplast genomes, can inform the relative risk of transgene escape via pollen versus seed. Here we investigate patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in two regions of the United States. We employed 15 nuclear simple sequence repeat (SSR) markers and one polymorphic chloroplast marker. Further, we utilized both conventional population genetic metrics along with Shannon diversity indices as the latter have been proposed to be more sensitive to allele frequency changes and differentiation. We found that populations in both regions that were proximal to crop fields showed lower levels of differentiation to the crops than populations that were located farther away. We also found that Shannon measures were more sensitive to differences in both genetic diversity and differentiation in our study. Finally, we found indirect evidence of paternal transmission of chloroplast DNA and accompanying lower than expected levels of chloroplast genetic structure amongst populations as might be expected if chloroplast DNA genes flow through both seed and pollen. Our findings of substantial gene flow for both nuclear and chloroplast markers demonstrate the efficiency of both pollen and seed to transfer genetic information amongst populations of carrot.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
- W. Harry Feinstone Center for Genomic Research, The University of Memphis, Memphis, Tennessee, United States of America
- * E-mail:
| | - Adam J. Ramsey
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
| | - Massimo Iorizzo
- Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, Kannapolis, North Carolina, United States of America
| | - Philipp W. Simon
- USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, Wisconsin, United States of America
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36
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Li L, Yang X, Wang L, Yan H, Su J, Wang F, Lu BR. Limited ecological risk of insect-resistance transgene flow from cultivated rice to its wild ancestor based on life-cycle fitness assessment. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1152-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Gompert Z, Buerkle CA. What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow. Evol Appl 2016; 9:909-23. [PMID: 27468308 PMCID: PMC4947152 DOI: 10.1111/eva.12380] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/27/2016] [Indexed: 01/17/2023] Open
Abstract
Hybridization is a potent evolutionary process that can affect the origin, maintenance, and loss of biodiversity. Because of its ecological and evolutionary consequences, an understanding of hybridization is important for basic and applied sciences, including conservation biology and agriculture. Herein, we review and discuss ideas that are relevant to the recognition of hybrids and hybridization. We supplement this discussion with simulations. The ideas we present have a long history, particularly in botany, and clarifying them should have practical consequences for managing hybridization and gene flow in plants. One of our primary goals is to illustrate what we can and cannot infer about hybrids and hybridization from molecular data; in other words, we ask when genetic analyses commonly used to study hybridization might mislead us about the history or nature of gene flow and selection. We focus on patterns of variation when hybridization is recent and populations are polymorphic, which are particularly informative for applied issues, such as contemporary hybridization following recent ecological change. We show that hybridization is not a singular process, but instead a collection of related processes with variable outcomes and consequences. Thus, it will often be inappropriate to generalize about the threats or benefits of hybridization from individual studies, and at minimum, it will be important to avoid categorical thinking about what hybridization and hybrids are. We recommend potential sampling and analytical approaches that should help us confront these complexities of hybridization.
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Xia H, Zhang H, Wang W, Yang X, Wang F, Su J, Xia H, Xu K, Cai X, Lu B. Ambient insect pressure and recipient genotypes determine fecundity of transgenic crop-weed rice hybrid progeny: Implications for environmental biosafety assessment. Evol Appl 2016; 9:847-56. [PMID: 27468303 PMCID: PMC4947147 DOI: 10.1111/eva.12369] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/22/2016] [Indexed: 11/27/2022] Open
Abstract
Transgene introgression into crop weedy/wild relatives can provide natural selective advantages, probably causing undesirable environmental impact. The advantages are likely associated with factors such as transgenes, selective pressure, and genetic background of transgene recipients. To explore the role of the environment and background of transgene recipients in affecting the advantages, we estimated the fitness of crop-weed hybrid lineages derived from crosses between marker-free insect-resistant transgenic (Bt/CpTI) rice with five weedy rice populations under varied insect pressure. Multiway anova indicated the significant effect of both transgenes and weedy rice genotypes on the performance of crop-weed hybrid lineages in the high-insect environment. Increased fecundity was detected in most transgene-present F1 and F2 hybrid lineages under high-insect pressure, but varied among crop-weed hybrid lineages with different weedy rice parents. Increased fecundity of transgenic crop-weed hybrid lineages was associated with the environmental insect pressure and genotypes of their weedy rice parents. The findings suggest that the fitness effects of an insect-resistant transgene introgressed into weedy populations are not uniform across different environments and genotypes of the recipient plants that have acquired the transgene. Therefore, these factors should be considered when assessing the environmental impact of transgene flow to weedy or wild rice relatives.
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Affiliation(s)
- Hui Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
- Shanghai Agrobiological Gene CenterShanghaiChina
| | - Hongbin Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Wei Wang
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Xiao Yang
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Feng Wang
- Fujian Province Key Laboratory of Genetic Engineering for AgricultureFujian Academy of Agricultural SciencesFuzhouChina
| | - Jun Su
- Fujian Province Key Laboratory of Genetic Engineering for AgricultureFujian Academy of Agricultural SciencesFuzhouChina
| | - Hanbing Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Kai Xu
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
| | - Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological EngineeringFudan UniversityShanghaiChina
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Khan A, Belfield EJ, Harberd NP, Mithani A. HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data. Sci Rep 2016; 6:29234. [PMID: 27378447 PMCID: PMC4932600 DOI: 10.1038/srep29234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/14/2016] [Indexed: 12/22/2022] Open
Abstract
Characterization of homoeallelic base-identity in allopolyploids is difficult since homeologous subgenomes are closely related and becomes further challenging if diploid-progenitor data is missing. We present HANDS2, a next-generation sequencing-based tool that enables highly accurate (>90%) genome-wide discovery of homeolog-specific base-identity in allopolyploids even in the absence of a diploid-progenitor. We applied HANDS2 to the transcriptomes of various cruciferous plants belonging to genus Brassica. Our results suggest that the three C genomes in Brassica are more similar to each other than the three A genomes, and provide important insights into the relationships between various Brassica tetraploids and their diploid-progenitors at a single-base resolution.
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Affiliation(s)
- Amina Khan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), D.H.A., Lahore 54792, Pakistan
| | - Eric J. Belfield
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Nicholas P. Harberd
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Aziz Mithani
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), D.H.A., Lahore 54792, Pakistan
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40
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Hu L, Li H, Qin R, Xu R, Li J, Li L, Wei P, Yang J. Plant phosphomannose isomerase as a selectable marker for rice transformation. Sci Rep 2016; 6:25921. [PMID: 27174847 PMCID: PMC4865823 DOI: 10.1038/srep25921] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/25/2016] [Indexed: 01/14/2023] Open
Abstract
The E. coli phosphomannose isomerase (EcPMI) gene is widely used as a selectable marker gene (SMG) in mannose (Man) selection-based plant transformation. Although some plant species exhibit significant PMI activity and active PMIs were even identified in Man-sensitive plants, whether plant PMIs can be used as SMGs remains unclear. In this study, we isolated four novel PMI genes from Chlorella variabilis and Oryza sativa. Their isoenzymatic activities were examined in vitro and compared with that of EcPMI. The active plant PMIs were separately constructed into binary vectors as SMGs and then transformed into rice via Agrobacterium. In both Indica and Japonica subspecies, our results indicated that the plant PMIs could select and produce transgenic plants in a pattern similar to that of EcPMI. The transgenic plants exhibited an accumulation of plant PMI transcripts and enhancement of the in vivo PMI activity. Furthermore, a gene of interest was successfully transformed into rice using the plant PMIs as SMGs. Thus, novel SMGs for Man selection were isolated from plants, and our analysis suggested that PMIs encoding active enzymes might be common in plants and could potentially be used as appropriate genetic elements in cisgenesis engineering.
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Affiliation(s)
- Lei Hu
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Hao Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Rongfang Xu
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Li Li
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Pengcheng Wei
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jianbo Yang
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
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41
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Millwood RJ, Moon HS, Poovaiah CR, Muthukumar B, Rice JH, Abercrombie JM, Abercrombie LL, Green WD, Stewart CN. Engineered selective plant male sterility through pollen-specific expression of the EcoRI restriction endonuclease. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1281-90. [PMID: 26503160 DOI: 10.1111/pbi.12493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/05/2015] [Accepted: 09/22/2015] [Indexed: 05/08/2023]
Abstract
Unintended gene flow from transgenic plants via pollen, seed and vegetative propagation is a regulatory concern because of potential admixture in food and crop systems, as well as hybridization and introgression to wild and weedy relatives. Bioconfinement of transgenic pollen would help address some of these concerns and enable transgenic plant production for several crops where gene flow is an issue. Here, we demonstrate the expression of the restriction endonuclease EcoRI under the control of the tomato pollen-specific LAT52 promoter is an effective method for generating selective male sterility in Nicotiana tabacum (tobacco). Of nine transgenic events recovered, four events had very high bioconfinement with tightly controlled EcoRI expression in pollen and negligible-to-no expression other plant tissues. Transgenic plants had normal morphology wherein vegetative growth and reproductivity were similar to nontransgenic controls. In glasshouse experiments, transgenic lines were hand-crossed to both male-sterile and emasculated nontransgenic tobacco varieties. Progeny analysis of 16 000-40 000 seeds per transgenic line demonstrated five lines approached (>99.7%) or attained 100% bioconfinement for one or more generations. Bioconfinement was again demonstrated at or near 100% under field conditions where four transgenic lines were grown in close proximity to male-sterile tobacco, and 900-2100 seeds per male-sterile line were analysed for transgenes. Based upon these results, we conclude EcoRI-driven selective male sterility holds practical potential as a safe and reliable transgene bioconfinement strategy. Given the mechanism of male sterility, this method could be applicable to any plant species.
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Affiliation(s)
| | - Hong S Moon
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | | | | | - John Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
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Lu B, Yang X, Ellstrand NC. Fitness correlates of crop transgene flow into weedy populations: a case study of weedy rice in China and other examples. Evol Appl 2016; 9:857-70. [PMID: 27468304 PMCID: PMC4947148 DOI: 10.1111/eva.12377] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/02/2016] [Indexed: 02/04/2023] Open
Abstract
Whether transgene flow from crops to cross‐compatible weedy relatives will result in negative environmental consequences has been the topic of discussion for decades. An important component of environmental risk assessment depends on whether an introgressed transgene is associated with a fitness change in weedy populations. Several crop‐weed pairs have received experimental attention. Perhaps, the most worrisome example is transgene flow from genetically engineered cultivated rice, a staple for billions globally, to its conspecific weed, weedy rice. China's cultivated/weedy rice system is one of the best experimentally studied systems under field conditions for assessing how the presence of transgenes alters the weed's fitness and the likely impacts of that fitness change. Here, we present the cultivated/weedy rice system as a case study on the consequences of introgressed transgenes in unmanaged populations. The experimental work on this system reveals considerable variation in fitness outcomes ‐ increased, decreased, and none ‐ based on the transgenic trait, its introgressed genomic background, and the environment. A review of similar research from a sample of other crop‐wild pairs suggests such variation is the rule. We conclude such variation in fitness correlates supports the case‐by‐case method of biosafety regulation is sound.
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Affiliation(s)
- Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering Department of Ecology and Evolutionary Biology Fudan University Shanghai China
| | - Xiao Yang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering Department of Ecology and Evolutionary Biology Fudan University Shanghai China
| | - Norman C. Ellstrand
- Department of Botany and Plant Sciences Center for Conservation Biology University of California Riverside CA USA
- Center for Invasive Species Research University of California Riverside CA USA
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Zhang W, Dasmahapatra KK, Mallet J, Moreira GRP, Kronforst MR. Genome-wide introgression among distantly related Heliconius butterfly species. Genome Biol 2016; 17:25. [PMID: 26921238 PMCID: PMC4769579 DOI: 10.1186/s13059-016-0889-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/28/2016] [Indexed: 12/30/2022] Open
Abstract
Background Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Zhang
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
| | | | - James Mallet
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, University of Chicago, Chicago, IL, 60637, USA.
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Cruz-Reyes R, Ávila-Sakar G, Sánchez-Montoya G, Quesada M. Experimental assessment of gene flow between transgenic squash and a wild relative in the center of origin of cucurbits. Ecosphere 2015. [DOI: 10.1890/es15-00304.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Guan ZJ, Zhang PF, Wei W, Mi XC, Kang DM, Liu B. Performance of hybrid progeny formed between genetically modified herbicide-tolerant soybean and its wild ancestor. AOB PLANTS 2015; 7:plv121. [PMID: 26507568 PMCID: PMC4670487 DOI: 10.1093/aobpla/plv121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/11/2015] [Indexed: 05/25/2023]
Abstract
Gene flow from genetically modified (GM) crops to wild relatives might affect the evolutionary dynamics of weedy populations and result in the persistence of escaped genes. To examine the effects of this gene flow, the growth of F1 hybrids that were formed by pollinating wild soybean (Glycine soja) with glyphosate-tolerant GM soybean (G. max) or its non-GM counterpart was examined in a greenhouse. The wild soybean was collected from two geographical populations in China. The performance of the wild soybean and the F2 hybrids was further explored in a field trial. Performance was measured by several vegetative and reproductive growth parameters, including the vegetative growth period, pod number, seed number, above-ground biomass and 100-seed weight. The pod setting percentage was very low in the hybrid plants. Genetically modified hybrid F1 plants had a significantly longer period of vegetative growth, higher biomass and lower 100-seed weight than the non-GM ones. The 100-seed weight of both F1 and F2 hybrids was significantly higher than that of wild soybean in both the greenhouse and the field trial. No difference in plant growth was found between GM and non-GM F2 hybrids in the field trial. The herbicide-resistant gene appeared not to adversely affect the growth of introgressed wild soybeans, suggesting that the escaped transgene could persist in nature in the absence of herbicide use.
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Affiliation(s)
- Zheng-Jun Guan
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China Department of Life Sciences, Yuncheng University, Yuncheng, Shanxi 044000, China
| | - Peng-Fei Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ding-Ming Kang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing, Jiangsu 210042, China
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46
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Liu Y, Zhang YX, Song SQ, Li J, Neal Stewart C, Wei W, Zhao Y, Wang WQ. A proteomic analysis of seeds from Bt-transgenic Brassica napus and hybrids with wild B. juncea. Sci Rep 2015; 5:15480. [PMID: 26486652 PMCID: PMC4614387 DOI: 10.1038/srep15480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Transgene insertions might have unintended side effects on the transgenic host, both crop and hybrids with wild relatives that harbor transgenes. We employed proteomic approaches to assess protein abundance changes in seeds from Bt-transgenic oilseed rape (Brassica napus) and its hybrids with wild mustard (B. juncea). A total of 24, 15 and 34 protein spots matching to 23, 13 and 31 unique genes were identified that changed at least 1.5 fold (p < 0.05, Student’s t-test) in abundance between transgenic (tBN) and non-transgenic (BN) oilseed rape, between hybrids of B. juncea (BJ) × tBN (BJtBN) and BJ × BN (BJBN) and between BJBN and BJ, respectively. Eight proteins had higher abundance in tBN than in BN. None of these proteins was toxic or nutritionally harmful to human health, which is not surprising since the seeds are not known to produce toxic proteins. Protein spots varying in abundance between BJtBN and BJBN seeds were the same or homologous to those in the respective parents. None of the differentially-accumulated proteins between BJtBN and BJBN were identical to those between tBN and BN. Results indicated that unintended effects resulted from transgene flow fell within the range of natural variability of hybridization and those found in the native host proteomes.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Ying-Xue Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475001, China
| | - Song-Quan Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Wei Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yujie Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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47
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Liu Y, Li J, Neal Stewart C, Luo Z, Xiao N. The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 530-531:263-270. [PMID: 26047860 DOI: 10.1016/j.scitotenv.2015.05.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 05/26/2023]
Abstract
The adventitious presence of transgenic crops in wild plant populations is of ecological and regulatory concern. In this context, their effects on non-target, below-ground organisms are not well understood. Here, we introduced, at various frequencies, Bt-transgenic oilseed rape (OSR, Brassica napus) into wild mustard (Brassica juncea) populations in the presence and absence of the target herbivore (Plutella xylostella). The impacts on soil nematode and microbial communities were assessed in this system. There were no significant changes on the number of nematode genera and abundance in proportions of OSR with mustard. Nonetheless, the Shannon-Wiener and Pielou evenness index was lowest in plant stands containing 50% of Bt-transgenic OSR. Among treatments, there was no significant variation for culturable soil microbes. There was a positive association between foliar herbivory and the abundance of plant parasitic (PP) and cp-3 nematodes, whereas there was no association between herbivory and soil microbial populations. There was no direct effects of the presence of Bt-transgenic OSR in wild mustard populations on the rhizosphere nematode and microbial communities, whereas its indirect effects via aboveground herbivory might be important to consider for biosafety assessments.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN 37996-4561, USA
| | - Zunlan Luo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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48
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Abstract
Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.
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Abstract
Convincing evidence has accumulated that unintended transgene escape occurs in oilseed rape, maize, cotton and creeping bentgrass. The escaped transgenes are found in variant cultivars, in wild type plants as well as in hybrids of sexually compatible species. The fact that in some cases stacked events are present that have not been planted commercially, implies unintended recombination of transgenic traits. As the consequences of this continuous transgene escape for the ecosystem cannot be reliably predicted, I propose to use more sophisticated approaches of gene technology in future. If possible GM plants should be constructed using either site-directed mutagenesis or cisgenic strategies to avoid the problem of transgene escape. In cases where a transgenic trait is needed, efficient containment should be the standard approach. Various strategies available or in development are discussed. Such a cautious approach in developing novel types of GM crops will enhance the sustainable potential of GM crops and thus increase the public trust in green gene technology.
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Affiliation(s)
- Gerhart U Ryffel
- a Institut für Zellbiologie (Tumorforschung); Universitätsklinikum Essen ; Essen , Germany
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50
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Liu Y, Stewart CN, Li J, Huang H, Zhang X. The presence of Bt-transgenic oilseed rape in wild mustard populations affects plant growth. Transgenic Res 2015; 24:1043-53. [PMID: 26338267 DOI: 10.1007/s11248-015-9903-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/28/2015] [Indexed: 12/21/2022]
Abstract
The adventitious presence of transgenic plants in wild plant populations is of ecological and regulatory concern, but the consequences of adventitious presence are not well understood. Here, we introduced Bacillus thuringiensis Cry1Ac (Bt)-transgenic oilseed rape (Bt OSR, Brassica napus) with various frequencies into wild mustard (Brassica juncea) populations. We sought to better understand the adventitious presence of this transgenic insecticidal crop in a wild-relative plant population. We assessed the factors of competition, resource availability and diamondback moth (Plutella xylostella) infestation on plant population dynamics. As expected, Bt OSR performed better than wild mustard in mixed populations under herbivore attack in habitats with enough resources, whereas wild mustard had higher fitness when Bt OSR was rarer in habitats with limited resources. Results suggest that the presence of insect-resistant transgenic plants could decrease the growth of wild mustard and Bt OSR plants and their populations, especially under high herbivore pressure.
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Affiliation(s)
- Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996-4561, USA
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Hai Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Xitao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
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