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apretencao.Rmd
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apretencao.Rmd
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---
title: "Genetic architecture of tropical maize for interaction with plant growth-promoting bacteria via high-throughput phenotyping"
subtitle: " "
author: "PhD Student: Rafael M. Yassue <br> Advisor: Roberto Fritsche Neto"
institute: "Genetics and Plant Breeding Program"
date: "02/11/2020"
output:
xaringan::moon_reader:
lib_dir: libs
nature:
highlightStyle: github
highlightLines: true
countIncrementalSlides: false
---
#Rafael Massahiro Yassue
<br> <br> <br> <br>
---
# Summary
+ Introduction
- Maize
- Nitrogen
- Holobiont
- Plant Growth-Promoting Bacteria
- “Breeding pillars” and Phenomics
- Components of electromagnetic spectrum
- Plant Growth-Promoting Bacteria and HTTP
+ Goals
+ Material and methods
- Pilot trial
+ Results
- Orthomosaic
- Genotyping-by-sequencing
- Population structure
- Population parameters
+ Outlook
---
#Maize
---
#Nitrogen
- Average maize crop removes 160 kg/ha of nitrogen <br>
--
- BNF by PGPB has been reported to contribute up to 12–33% of total N uptake in maize (Montañez et al., 2009)<br>
--
- PGPR may be a good alternative to more sustainable production
--
- 300 maize-associated endophytes (mostly bacteria) <br>
--
- Based on the genomes currently in NCBI, bacteria and fungi contain an average of <b> 3,800 and 9,600 genes </b> , respectively. If we assume <b> 35 unique fungi and 175 </b> unique bacteria per plant (see Sect. 14.2.4), it implies that the maize endosphere contains <b> 858,000–1.14 million genes </b> , over twenty times that of the maize plant itself (Hardoim et al., 2015). <br>
---
#Holobiont
--
---
#Plant Growth-Promoting Bacteria
---
#Plant Growth-Promoting Bacteria
---
#Plant Growth-Promoting Bacteria
<img src="effects.png" width="1000" height="350" />
---
#Plant Growth-Promoting Bacteria
<img src="effects2.png" width="1000" height="350" />
---
#Plant Growth-Promoting Bacteria
<img src="effects3.png" width="1000" height="350" />
---
#Plant Growth-Promoting Bacteria
- Type of Soil (Oliveira et al., 2006) <br>
--
- Genotype x PGPB (Montañez et al., 2009) <br>
--
- Environment interaction (Rouphael et al., 2018) <br>
--
- Nitrogen disponibility (Egamberdiyeva, 2007) <br>
--
- Microbiome x microbiome interaction (Van Der Heijden et al., 2008)
--
- Heterosis (Vidotti et al. 2019, preprint Wagner et al. 2020)
---
# “Breeding pillars” and Phenomics
---
# “Breeding pillars” and Phenomics
---
#Components of electromagnetic spectrum
--
<img src="table1.png" style="width: 60%" />
---
#Plant Growth-Promoting Bacteria
<img src="microbioma.png" style="width: 100%" />
---
#Plant Growth-Promoting Bacteria
<img src="microb.png" style="width: 100%" />
---
#Plant Growth-Promoting Bacteria and HTTP
<img src="HTTP2.png" style="width: 100%" />
---
#Plant Growth-Promoting Bacteria and HTTP
<img src="HTTP.png" style="width: 100%" />
---
#Goal
- Genetic and phenotypic characterization of maize inbred lines for response to plant growth-promoting bacteria
--
- Implementation of a High-Throughput Phenotyping platform in the greenhouse
--
- Prospecting new traits that may be associated with a positive response to plant x PGPB interaction
---
#Material and methods
- Greenhouse condition
--
- 360 inbred lines, with and without PGPB
--
- V2, V4, and V6
| Classic phenotyping | High-throughput phenotyping |
| ------------- | ------------- |
| Plant height (3x) | NDVI (3x) |
| Stalk diameter | NDVIred (3x) |
| Number of leaves (3x) | NDVIgreen (3x) |
| Chlorophyll content (3x) | Chlorophyll indices (3x) |
| Canopy mass | Canopy temperature (3x) |
| Dry mass of canopy and root | Plant height (3x) |
| | WinRHIZO |
---
# Material and methods
Table. Blend of Bacterias
|Bacteria |Mechanism|
|------|-------|
|<i>Bacillus </i>sp. RZ2MZ9 | P solubilization, ACC deaminase activity and ammonia and IAA production|
|<i> Azospirillum brasilense </i> Ab-v5 |Fixing N2 and synthesis of phytohormones|
|<i> Pantoea agglomerans </i> 33.1 |Synthesize indoleacetic acid and solubilize phosphate|
|<i> Delftia </i> sp. 93A. |High nitrogen-fixing activity and acetylene reduction|
---
# Material and methods
- Augmented blocks (Federer), 6 blocks with 60 lines and 3 checks with and without PGPB (I)
\begin{aligned}
y=X 1 \boldsymbol{g}+X 2 \boldsymbol{b}+X 3 \boldsymbol{c}+X 4 \boldsymbol{p}+X 5 \boldsymbol{i}+\boldsymbol{\varepsilon}
\end{aligned}
--
- Sown three times (II)
\begin{aligned}
y=x 1 g+X 2 e+X 3 p+X 4 i+\varepsilon
\end{aligned}
g effects of genotype <br>
b effects of blocks <br>
c effects of checks <br>
p effect of inoculation with PGPB <br>
e effect experiment effect of <br>
i effect of interaction genotype x inoculation with the PGPB <br>
𝜺 ~𝑁(0, 𝑹).
---
# Pilot trial
- Type of soil
--
- Microbiome
--
- Fertilization – Hoagland without Nitrogen
--
- Data collection pipeline and image processing – Metashape and QGIS
---
# Pilot trial
<br>
.pull-left[]
.pull-right[]
<br> <br>
.middle[Figure. Collection of thermal (left) and multispectral (right) images]
---
# Orthomosaic
.pull-bottom[.center[]]
Figure. Orthomosaic using multispectral camera
---
# Genotyping-by-sequencing
.pull-left[ - SNP: 14639 <br> - Two enzymes approach - Pst1-MSE1 (Poland, 2011) <br> - SNPCalling: TASSEL 5.0 <br> - Aligner: Bowtie 2 <br> - Imputation: Beagle 5.0
<br> <br> <br> <br> <br> <br> <br> <br> <br> <br> <br> <br> <br> <br> ]
--
.pull-right[ <img src="omics.png" style="width: 250%" /> ]
.bottom[ <font size="3"> Figure. Raw data coverage (A), and depth (B), Filtered data coverage (C), and depth (D) </font> ]
---
# Population structure
.pull-left[]
.pull-right[]
<br>
.middle[Figure. Proportion of variation accumulated (A) and Cumulative proportion of variance explained by the principal components (1, 2 and 3, B)]
---
# Population structure
<img src="STRUTpng.png" style="width: 100%" /> <br>
Figure. Genotypes sorted by origin (A) and group (K) (B)
---
# Population structure
Figure. Additive (Ga), and dominance (Gd) relationship matrix
---
# Population parameters
|Parameter |Esalq |Iapar |All |
| ------------- | ------|----- |-----|
|Ne |101.50 |98.82 |199.83|
|Va |4385.2 |4422.9 |4493.14|
|Vd |1635.88 |1635.27 |1644.02|
|Number of fixed alleles |30 |80 |..|
|GD |0.3 |0.3 |0.31|
|PIC |0.24 |0.25 |0.25|
|MAF |0.21 |0.22 |0.22|
|Ho |0.03 |0.03 |0.03|
|F |0.89 |0.91 |0.9|
--
#### F-statistics
|Pop |Fis |Fst| Fit|
|-----|----|------|-------|
|Esalq x Iapar| 0.901| 0.021| 0.902|
---
#Outlook
- Hyperspectral camera
--
- Random regression from high-throughput phenotyping data with Association Weight Matrix
---
<br> <br> <br> <br> <br> <br> <br> <br> <br> <br>
# .center[Thank you]
###.right[ Rafael Massahiro Yassue ]
.right[]