Lab 1: Genotyping & Phenotyping Flashcards
To improve fruit quality
What is the primary objective of fruit breeding programs?
Fruit quality
Driven by consumer demand
Outline the scientific process of developing new fruit varieties with improved traits.
Done by selecting and cross-breeding existing varieties
What is a molecular marker?
A molecular marker (DNA marker) is a fragment of DNA that is associated with a certain location within the genome.
Describe the mapping process.
Marker development process
Define: phenotype
Consequence of the interaction between the plant genetic background (i.e., genotype) and the biotic and abiotic conditions experienced by the plant in its growing environment.
Define: phenotyping.
The process of characterizing traits in detail.
Define: genotype
The plant genetic background. Also used to refer to individuals with distinct genetic background.
Define: genotyping
The analysis of variations in genomes between individual organisms
Describe the evolution of molecular markers. [5]
- Restriction fragment length polymorphism
- Random amplified polymorphic DNA
- Amplified fragment length polymorphism
- Simple sequence repeat (a.k.a. microsatellites)
- Single nucleotide polymorphism
What is a SNP marker?
- A single nucleotide polymorphism
- A variation at a single position in a DNA sequence among individuals
- Occurs in more than one percent of the general population
Describe the process from DNA extraction to SNP calling.
Define: genetic mapping
Statistical methods that link certain complex phenotypes to specific regions of chromosomes.
Using genome-wide association mapping.
Describe how to interpret a Manhattan plot for a genome-wide association study. [5]
- Scatter plot
- The dots are SNPs
- x axis shows chromosomes
- y axis shows negative log of p value
- Green line is the threshold for significance
Provide the background for raspberries as a crop to focus on for improvement.
- Red raspberry is a high value crop
- Diploid, 2n = 14
- Native to North America and Eurasia
- Mexico, California, and the Pacific Northwest are leading producers worldwide
- In Canada, BC accounts for over half of the marketed production, with a farm-gate value of ~$14 million per year
Raspberries display a broad range of colours (red-yellow) and intensities (dark-light).
What do the requirements of fruit colour depend on, and what are the major pigments found in raspberries?
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Colour requirements:
- Fresh: bright medium red
- Processing: dark red
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Major pigments:
- Anthocyanins (red)
- Carotenoids (yellow)
Describe the structure of anthocyanins.
Anthocyanins are glycosylated anthocyanidins