**BSc Botany 3rd Year Genetic Plant Breeding Notes 2023**.Plant breeding, application of genetic principles to produce plants that are more useful to humans. Plant breeding dates to the very beginnings. BSc Botany or Bachelor of Science in Botany is a 3-year undergraduate degree .Cell Biology, Genetics, Plant Anatomy, Plant Embryology,**BSc Botany 3rd Year Genetic Plant Breeding & Statistics Notes 2023**.

plant breeding, application **of genetic principles to produce plants** that are more useful to humans. This is accomplished by selecting plants found to be economically or aesthetically desirable, first by controlling the mating of selected individuals, and then by selecting certain individuals among the progeny.

## Genetic Basis of Plant Breeding

His investigation used self-pollinating (autogamous) plants and he assessed **simply- inherited, qualitative traits in a controlled environment**. Plant breeders seldom have such luxury, as most agronomically significant traits are determined by complex gene interactions.

## What is the importance of genetics in plant breeding?

Advancements in plant genetics and genomics, when used in breeding, **help support higher production and cultivation of crops resistant to pests, pathogens, and drought**.

# Statistical Analysis in Plant Biology

## Introduction.

This is a statistical tutorial for Plant Biology. It will provide you with the basics of various common statistical methods and examples of how to perform these tests using SPSS statistical software available in York’s computer labs and accessible from home using York’s remote Web-based File Access System.

## Outline

- Hypothesis Building
- Null hypothesis/alternate hypothesis

- Hypothesis Testing
- Visual summary

- Common Statistical tests and how to run them
- Summary statistics
- T-test

- Setting Up a T-test
- Paired versus independent t-tests
- 1-tailed versus 2-tailed t-tests

- Running a T-test in SPSS
- Importing the data and analysis in SPSS
- Reporting t-test results

- Graphing
- How to present your findings
- Types of graphs and usage
- Formatting

- Correlations

## 1. Hypothesis Building

- Creating a testable hypothesis is central to scientific method

### 1a. Null hypothesis/alternate hypothesis

**Null (H**– ‘no effect’ or ‘no difference’ between samples or treatments_{0}) hypothesis**Alternative (H**– experimental treatment has a certain statistically significant effect_{A}) hypothesis- A claim for which we are trying to find evidence

Some Examples

**H**“Different light spectra have no effect on photosynthetic activity” (_{0}:**H**: x_{0}_{2}=x_{1}or x_{2}-x_{1}=0)**H**“Pollen treated with chloramphenicol grow faster than untreated pollen” (_{A}:**H**: x_{A}_{2}>x_{1}or x_{2}-x_{1}>0)

## 2. Hypothesis Testing

- Either reject or fail to reject the
**H**based on statistical testing_{0} - Statistical testing compares the p-value of observed data to an assigned significance level (α —
*alpha*)- p-value – the frequency or probability with which the observed event would occur
- α = the probability that the outcome did not occur by chance
- Popular levels of significance are 5% (0.05), 1% (0.01), and 0.1% (0.001)

- If the p-value is SMALLER than α, reject the null hypothesis (
**H**)_{0}

### 2a. Visual Summary

## 3. Common Statistical Tests

### 3a. Summary statistics

You should already be aware of the basic summary statistics. Usually, scientific data are summarized by reporting the mean, the standard deviation and the sample size.

### 3b. T tests

For this course you are expected to understand and use t-tests

**T-tests** are used to determine if two sets of data (2 means) are significantly different from each other. It assumes that the data are normally distributed and samples are equal.

Two decisions must be made when selecting a t-test:

- Are the samples paired or independent?
- Is the comparison 1-tailed or 2-tailed?

## 4. Setting Up a T-Test

### 4a. Paired versus independent t-tests

- A
**One-sample (paired) t-test**compares two samples in cases where each value in one sample has a natural partner in the other (data are not independent). It can be used during pre- or post- data analysis. It is also used to compare a sample mean to a specified value.One example of paired t-test analysis is comparing patient performance before and after the application of a drug. The data are paired because the same patuent is compared before and after treatment. - A
**two-sample (independent) t-test**compares the means for two groups of cases.An example of independent t-test analysis is comparing patient performance in a group receiving a drug versus a separate group receiving a trial drug.

### 4b. 1-tailed versus 2-tailed t-tests

- A
**One-tailed/sided t-test**expects the effect to be in a certain direction. - Is the sample mean greater than μ? (μ is the population mean, the greek letter ‘
*mu*‘) - Is the sample mean less than μ?
- A
**Two-tailed/sided t-test**tests for different means regardless of whether it is greater or smaller. - Is there a significant difference?

- A carefully state experimental hypothesis will indicate the type of effect you are looking For example, the hypothesis that “Coffee improves memory” suggests paire, one tail because you will repeatedly measure the same participants and expect an improvement”Men weigh a different amount from women” suggests an independent two taile test as no direction is implie.
**So remember, don’t be vague with your hypothesis if you are looking for a specific effect! Be careful with the null hypothesis too – avoid “A does not affect B” if you really mean “A does not improve B”.**

## 5. Running a T-test in SPSS

**Question:** Do two photosynthetic organisms have the same oxygen evolution capability?

**Null Hypothesis:** **H _{A}:** μ

_{1}= μ

_{2}(Both photosynthetic organisms produce the same amount of oxygen)

An independent 2-tailed t-test!

**Alternative Hypothesis:** **H _{A}:** μ

_{1}≠ μ

_{2}(the two photosynthetic organisms DO NOT produce equal amounts of oxygen)

### 5a. Importing the data and analysis in SPSS

In your browser, ‘viewing image’ should enlarge the screenshots

- Make sure your spreadsheet is save on the C: drive of your computer
- Make sure excel file types are select

- Click ‘Data view’ tab rather than ‘Variable view’

- Notice the variable names in the column headers
- All raw data is list (SPSS will calculate means for you)
- Data is list in one column (all with the same units) with the first column indicating the grouping

- Select Analyze –> compare means –> independent samples t testO2evo is the test variable, species is the grouping variable
- Click on define groups, then
- type the two names used in the data view

- We first check Levene’s test –which assesses if variances are equalif p > 0.05, then the variances are equal and you can interpret the t results
- The t-test result is p = 0.014so we can reject the null hypothesis, thus the two photosynthetic organsims DO NOT produce equal amounts of oxygen.

### 5b. Reporting t-test results

- All perform statistics MUST be referr to in the text of your report
- You must indicate:
- The type of test performed
- The data the test was performe on
- The α (–
*alpha*) level used (0.05 is the default) - The p-value outcome of your t-test
- Whether you accept or reject the null hypothesis

For purposes of this course you are require to take a print screen of your SPSS output (as in the previous slide) and attach this in your report.

## 6. Graphing

### Choosing Graphs

- Some tests are related to specific figuresFor example, correlations and scatter plots
- The following examples outline the basic use of several common graphsScatter plotsLine GraphsBar graphsHistograms

### Scatter plots

- Displays 2 variables for a set of data
- Dependent vs. independent — one variable is under the control of the other variable

### Line graphs

- Shows relationship between values plotted on each axis (dependent vs. independent)
- Used on continuous variables

### Bar graphs

- Used for discrete quantitative variables which are similar but not necessarily related
- Often used to display t-test results

### Histograms

- Used exclusively for showing the distribution of data that are continuous.

## 7. Correlations

Correlation analysis measures the strength and direction of a linear relationship between two random variables. But be careful! Two random variables may be strongly correlated, but that does not mean the relationship is *causal* (as explained by Randall Munroe –xkcd.com).

- Pearson’s Correlation Coefficient (r) measures the relationship between two variables
- Positive r-values means that the two variables increase with each other. Negative r-values mean they decrease with each other. When the r-value is close to zero, the variables have no relationship, while r-values close to either -1 or 1 mean the relationship is strong.
- R
^{2}(coefficient of determination) is used to assess how well a regression line fits the data: 0 means no fit, 1 means a perfect fit.