Agricolae - Ten years of an open source statistical tool for experiments in breeding, agriculture and biology

Mendiburu, Felipe De; Simon, Reinhard

doi:10.7287/peerj.preprints.1404v1

Cited by 644 publications

(642 citation statements)

References 16 publications

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“…Images were collected using the Slidebook software package (Intelligent Imaging Innovations, Denver, CO) at exposure times ranging from 0.1 to 1 s. Spindle measurements were collected using the Line tool in the Slidebook software. Statistical significance was determined through an ANOVA using the R package “agricolae” (de Mendiburu, 2015). …”

Section: Methodsmentioning

confidence: 99%

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The Maize Divergent spindle-1 (dv1) Gene Encodes a Kinesin-14A Motor Protein Required for Meiotic Spindle Pole Organization

2016

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The classic maize mutant divergent spindle-1 (dv1) causes failures in meiotic spindle assembly and a decrease in pollen viability. By analyzing two independent dv1 alleles we demonstrate that this phenotype is caused by mutations in a member of the kinesin-14A subfamily, a class of C-terminal, minus-end directed microtubule motors. Further analysis demonstrates that defects in early spindle assembly are rare, but that later stages of spindle organization promoting the formation of finely focused spindle poles are strongly dependent on Dv1. Anaphase is error-prone in dv1 lines but not severely so, and the majority of cells show normal chromosome segregation. Live-cell imaging of wild type and mutant plants carrying CFP-tagged β-tubulin confirm that meiosis in dv1 lines fails primarily at the pole-sharpening phase of spindle assembly. These data indicate that plant kinesin-14A proteins help to enforce bipolarity by focusing spindle poles and that this stage of spindle assembly is not required for transition through the spindle checkpoint but improves the accuracy of chromosome segregation.

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Section: Methodsmentioning

confidence: 99%

“…A total of 500 pollen grains from each plant were scored for viability based on color. Statistical significance was determined through an ANOVA using the R package “agricolae” (de Mendiburu, 2015). …”

Section: Methodsmentioning

confidence: 99%

The Maize Divergent spindle-1 (dv1) Gene Encodes a Kinesin-14A Motor Protein Required for Meiotic Spindle Pole Organization

2016

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“…To compare each trait between host plants, data were analyzed using one-way analysis of variance (ANOVA) followed by mean separation with Tukey HSD test ( P ≤ 0.05) contingent on a significant effect using R Studio (Racome, 2011) and R Statistical software (R Development Core Team, 2009). The following R packages were used for the data analysis: Plotrix (Lemon, 2006), Agricolae (de Mendiburu, 2015), Reshape (Wickham, 2007), Lattice (Sarkar, 2008), and Vegan (Oksanen et al, 2015). Ordination of the data using principal components analysis was used to determine which traits contributed the most variability.…”

Section: Methodsmentioning

confidence: 99%

Host plant affects morphometric variation ofDiaphorina citri(Hemiptera: Liviidae)

Paris

Allan

Hall

et al. 2016

PeerJ

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The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is one of the most serious citrus pests worldwide due to its role as vector of huanglongbing or citrus greening disease. While some optimal plant species for ACP oviposition and development have been identified, little is known of the influence of host plants on ACP size and shape. Our goal was to determine how size and shape of ACP wing and body size varies when development occurs on different host plants in a controlled rearing environment. ACP were reared on six different rutaceous species; Bergera koenigii, Citrus aurantifolia, Citrus macrophylla, Citrus maxima, Citrus taiwanica and Murraya paniculata. Adults were examined for morphometric variation using traditional and geometric analysis based on 12 traits or landmarks. ACP reared on C. taiwanica were consistently smaller than those reared on the other plant species. Wing aspect ratio also differed between C. maxima and C. taiwanica. Significant differences in shape were detected with those reared on M. paniculata having narrower wings than those reared on C. macrophylla. This study provides evidence of wing size and shape differences of ACP based on host plant species which potentially may impact dispersal. Further study is needed to determine if behavioral and physiological differences are associated with the observed phenotypic differences.

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“…Multiple comparison tests between groups after Kruskal–Wallis tests were done with the Kruskalmc function while the Student–Newman–Keuls test was used to compare means after the general linear model procedure. The Kruskal–Wallis and Student–Newman–Keuls tests used were those available in the R “agricolae” (version 1.1-8) package (De Mendiburu, 2014), all other tests were done using the R “Stats” (version 2.15.3) package. All the data were used in a first analysis based on a model with one factor (gene).…”

Section: Methodsmentioning

confidence: 99%

Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits

et al. 2014

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The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.

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Agricolae - Ten years of an open source statistical tool for experiments in breeding, agriculture and biology

Cited by 644 publications

References 16 publications

The Maize Divergent spindle-1 (dv1) Gene Encodes a Kinesin-14A Motor Protein Required for Meiotic Spindle Pole Organization

The Maize Divergent spindle-1 (dv1) Gene Encodes a Kinesin-14A Motor Protein Required for Meiotic Spindle Pole Organization

Host plant affects morphometric variation ofDiaphorina citri(Hemiptera: Liviidae)

Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits

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