scholarly journals Bootstrap simulations for evaluating the model estimation of the extent of cross-pollination in maize at the field-scale level

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0249700
Author(s):  
Bo-Jein Kuo ◽  
Yun-Syuan Jhong ◽  
Tien-Joung Yiu ◽  
Yuan-Chih Su ◽  
Wen-Shin Lin
Keyword(s):  
Gene Flow ◽  
Genetic Material ◽  
Farming Systems ◽  
Gm Crops ◽  
Interval Length ◽  
Small Scale ◽  
Field Scale ◽  
Maize Pollen ◽  
Cross Pollination ◽  
Gm Maize

With the recent advent of genetic engineering, numerous genetically modified (GM) crops have been developed, and field planting has been initiated. In open-environment cultivation, the cross-pollination (CP) of GM crops with wild relatives, conventional crops, and organic crops can occur. This exchange of genetic material results in the gene flow phenomenon. Consequently, studies of gene flow among GM crops have primarily focused on the extent of CP between the pollen source plot and the adjacent recipient field. In the present study, Black Pearl Waxy Corn (a variety of purple glutinous maize) was used to simulate a GM-maize pollen source. The pollen recipient was Tainan No. 23 Corn (a variety of white glutinous maize). The CP rate (%) was calculated according to the xenia effect on kernel color. We assessed the suitability of common empirical models of pollen-mediated gene flow (PMGF) for GM maize, and the field border (FB) effect of the model was considered for small-scale farming systems in Asia. Field-scale data were used to construct an optimal model for maize PMGF in the maize-producing areas of Chiayi County, southern Taiwan (R.O.C). Moreover, each model was verified through simulation and by using the 95% percentile bootstrap confidence interval length. According to the results, a model incorporating both the distance from the source and the FB can have optimal fitting and predictive abilities.

scholarly journals A new isolation device for shortening gene flow distance in small-scale transgenic maize breeding

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lili Zhang ◽  
Shanshan Huo ◽  
Yang Cao ◽  
Xiang Xie ◽  
Yanhua Tan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Flow Rate ◽  
Small Scale ◽  
Maize Breeding ◽  
Maize Pollen ◽  
Gm Maize ◽  
Isolation Distance ◽  
Isolation Device ◽  
And Control ◽  
Labeling System

Abstract The transmission of pollen is the main cause of maize gene flow. Under the compulsory labeling system for genetically modified (GM) products in China, isolation measures are crucial. At present, there is no effective isolation device for preventing and controlling the short-range flow of GM maize pollen. The purposes of the present experiments were to overcome the deficiencies of existing technology and to demonstrate a new isolation device for decreasing the gene flow distance of GM maize. The isolation device we invented was shown to be more robust than traditional isolation methods, and it can be disassembled and repeatedly reused. The most important point was that the frequency of gene flow could be greatly reduced using this device. When the distance from the isolation device was more than 1 m, the gene flow rate could be decreased to less than 1%, and when the distance from the isolation device was more than 10 m, the gene flow rate could be reduced to less than 0.1%. When the isolation device was adopted to isolate GM maize in conjunction with bagging the tassels of GM maize at the pollination stage, the gene flow could be controlled to less than 0.1% when the distance from the isolation device was more than 1 m. This device was, however, only applicable for small plots and can shorten the isolation distance of GM maize planting and improve the purity of seeds, all while meeting the needs of close isolation breeding. The use of this device represents a feasible method for risk prevention and control of GM crops.

ASSESSMENT OF NITROGEN FIXATION POTENTIAL IN AHIPA (Pachyrhizus ahipa) AND ITS EFFECT ON ROOT AND SEED YIELD

2009 ◽  
Vol 45 (2) ◽  
pp. 177-188 ◽  
Author(s):  
D. N. RODRÍGUEZ-NAVARRO ◽  
M. CAMACHO ◽  
F. TEMPRANO ◽  
C. SANTAMARÍA ◽  
E. O. LEIDI
Keyword(s):  
Raw Materials ◽  
Farming Systems ◽  
Yield Potential ◽  
Small Scale ◽  
South American ◽  
Field Inoculation ◽  
Promising Alternative ◽  
Yield Increase ◽  
Alternative Crop ◽  
Attractive Option

SUMMARYAhipa is a legume of great interest for the production of raw materials (starch, sugar, oil and proteins) for industrial use. Its yield potential and ability to fix atmospheric N2 in association with rhizobia makes it an attractive option for low input agriculture systems. At present, it is cultivated on a very small scale as a food crop in a few South American countries. Little information is available on symbiotic N2 fixation in ahipa and no work has been performed on strain selection for inoculant production. Soils in southwest Europe are devoid of specific rhizobia able to nodulate on ahipa. Selecting rhizobia for symbiotic effectiveness from a collection led to the isolation of strains which provided greater shoot growth and N content under controlled conditions. In the field, inoculation at sowing with the selected strains increased significantly seed and tuberous root yield and seed protein content. The amount of N2 fixed, estimated by 15N natural abundance, reached 160–260 kg N ha−1. In previous work, ahipa appeared to be a promising alternative crop for the production of industrial raw materials. The results of the present study showed a yield increase in tuberous roots and seeds when applying effective rhizobia inoculants. Furthermore, a positive soil N balance was left after its cultivation making ahipa even more interesting for sustainable farming systems.

Coexistence Between GM and Non-GM Maize Crops ? Tested in 2004 at the Field Scale Level (Erprobungsanbau 2004)

2007 ◽  
Vol 193 (2) ◽  
pp. 79-92 ◽  
Author(s):  
W. E. Weber ◽  
T. Bringezu ◽  
I. Broer ◽  
J. Eder ◽  
F. Holz
Keyword(s):  
Field Scale ◽  
Scale Level ◽  
Gm Maize

Persistence in the desert: ephemeral waterways and small-scale gene flow in the desert spring amphipod,Wangiannachiltonia guzikae

2014 ◽  
Vol 59 (4) ◽  
pp. 653-665 ◽  
Author(s):  
Hannah L. Robertson ◽  
Michelle T. Guzik ◽  
Nicholas P. Murphy
Keyword(s):  
Gene Flow ◽  
Small Scale ◽  
Desert Spring

Erosion and sediment transport models with reference to the needs of small scale

2021 ◽  
Author(s):  
Ahsan Raza ◽  
Thomas Gaiser ◽  
Muhammad Habib-Ur-Rahman ◽  
Hella Ahrends
Keyword(s):  
Soil Erosion ◽  
Overland Flow ◽  
Model Development ◽  
Agroforestry Systems ◽  
Specific Model ◽  
Small Scale ◽  
Field Scale ◽  
Erosion Prediction ◽  
Dynamic Components ◽  
Output Information

<p>Information on field scale soil erosion and related sedimentation process is very important for natural resource management and sustainable farming. Plenty of models are available for study of these processes but only a few are suitable for dynamic small scale soil erosion assessments. The available models vary greatly in terms of their input requirements, analysis capabilities, process [t1] complexities, spatial and temporal scale of their intended use, practicality, the manner they represent the processes, and the type of output information they provide. The study aims in examining, theoretically, 51 models classified as physical, conceptual, and empirical based on their representation of the processes of soil erosion. The literature review shows that there is no specific model available for soil erosion prediction under agroforestry systems.   It is further suggested that models like EPIC, PERFECT, GUEST, EPM, TCRP, SLEMSA, APSIM, RillGrow, and CREAMS can be potentially used for soil erosion assessment at plot/field scale at daily time steps. Most of these models are capable to simulate the soil erosion process at small scale; further model development is needed regarding their limitations with respect to components interaction i.e., rainfall intensity, overland flow, crop cover, and their difficulties in upscaling. The research suggested that SIMPLACE network can provide modules with LintulBiomass, HillFlow, Runoff to develop new dynamic components to simulate overland flow and soil erosion incorporating improved upscaling capabilities</p>

Modeling gene flow from genetically modified plants.

2021 ◽  
pp. 103-117
Author(s):  
Wei Wei ◽  
Jun-Ming Wang ◽  
Xiang-Cheng Mi ◽  
Yan-Da Li ◽  
Yan-Ming Zhu
Keyword(s):  
Gene Flow ◽  
Genetically Modified ◽  
Predictive Ability ◽  
Crop Wild Relatives ◽  
Gm Crops ◽  
Wild Plants ◽  
Experimental Conditions ◽  
Flow Models ◽  
Herbicide Resistant ◽  
Gm Plants

Abstract Gene flow from genetically modified (GM) plants is concerning because of its ecological risks. In modeling studies, these risks may be reduced by altering crop management while taking environmental conditions into account. Gene flow modeling should consider many field aspects, both biological and physical. For example, empirical statistical models deduced from experimental data simulate gene flow well only under limited conditions (similar to experimental conditions). Mechanistic models, however, offer a potentially greater predictive ability. Gene flow models from GM crops to non-GM crops are used to simulate field conditions and minimize the adventitious presence of transgenes to meet certain threshold levels. These models can be adapted to simulate gene flow from GM crops to crop wild relatives using parameters of sexual compatibility and growth characteristics of the wild plants. Currently, modeling gene flow from herbicide-resistant weeds has become very important in light of the increased application of herbicides and widely evolved resistance in weeds.

scholarly journals Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 ◽  
Vol 69 (5) ◽  
pp. 848-862 ◽  
Author(s):  
Melisa Olave ◽  
Axel Meyer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Flow ◽  
Genetic Material ◽  
Cichlid Fish ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Nucleotide Polymorphism ◽  
Rapid Radiation ◽  
Data Set ◽  
Single Nucleotide

Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]

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