# *Genome 2 Phenome 4 Non-Biologists Workshop*: Overview, March 18 2021

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## Overview of Workshop Series
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### Learning Objectives:

* Understand how to interact with this HackMD notepad
* Overview of genotypes → phenotypes
* Know case study examples: genotype → phenotype
* [Hack MD Tutorial](https://hackmd.io/s/tutorials)
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### Question 1, Name a simple trait and a complex trait:

* Breakout Room 1:
* Complex trait: Height
* Simple trait: Coat color

* Breakout Room 2:

* Complex trait: Yield
* Complex trait: Intelligence
* Simple trait: Eye / skin colour

* Breakout Room 3:
* Simple trait: Eye & flower colour, hemophelia
* Complex trait: Human Height, longevity

* Breakout Room 4:
* Simple trait: Polled phenotype
* Complex trait: Milk yield
* Breakout Room 5:
* complex trait: milk composition and yield, cancer
* simple trait: hair color

* Breakout Room 6:
* complex trait - Height
* simple trait - eye color
* Breakout Room 7:
* Simple trait: Coat color, coat hair length and thickness
* Complex trait: Milk production

* Breakout Room 8:

* Question 1: Simple = Coat or feather color; Complex = height, weight, skin color, crop yield.

* Breakout Room 9:
* Simple Trait: Auricular hypertrichosis (Hairy Earlobes)

* Breakout Room 10:
* simple traits - pea color, coat color
* complext trait - weight, intelligence,
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* Breakout Room 11:
* Simple traits - plumage color,
* Complex traits - weight, yield

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### Question 2, What are the differences between traits with “simple” genetics from those with “complex” genetics?:

* Breakout Room 1:
* Traits with simple genetics are mendelian traits whereas the traits with complex genetics are quantitative traits.
* Breakout Room 2:

* Simple genetics have few SNPs while complex traits have many.

* Breakout Room 3:
* Simple: One or few genes controlling traits
* Complex: Many genes controlling traits

* Breakout Room 4:

* Simple traits very low environmental effects and highly impacted by a single locus
* e.g. Myostatin and double muscling

* Breakout Room 5:
* traits with simple genetics refer to a few of genes, traits in complex genetics refer to great number of genes
* Breakout Room 6:
* number of genes so many geens for complex traits and few genes for simple.

* Breakout Room 7:
* Simple = 1 gene
* Complex = more than 1 gene
* Breakout Room 8:
* complex = hard to breed; simple = easier to breed and select; environment doesn't impact simple traits (as much)
* Question 2: Simple genetics relies only on one allele, complex genetics are reliant on more than one allele. Complex traits are more affected by the environment.
* Breakout Room 9:
* Simple genetics has direct corrolated genotype to phenotype affects that only inlcude a small number of genes, whereas the complex genetic involves many genetic and epigenetic interactions

* Breakout Room 10:
* interaction between multiple genes for complex traits; for simple traits - one gene, one trait; easy to predict expression in simple traits; complex traits are hard to predict
* Breakout Room 11:
* Simple traits are controlled by only 1 o few genes. complex traits are affected by many genes. and env. factors

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### Question 3, How can we use genetics to predict a future phenotype in a plant or animal?:

* Breakout Room 1:
* Using statistical association.
* Breakout Room 2:
* Correlation of certain genes with certain phenotypes, mechanistic understanding of genes to phenotypes.

* Breakout Room 3:
* Identify simple or complex and then change the genetics through mutation or remove the phenotype.
* Knowledge is power

* Breakout Room 4:
* Genomic selection process and breeding

* Breakout Room 5:
* with the actual performance we can create records that can be correlated with genomics to predict future phenotype
* Improving the genome annotation to identify regulatory regions that involved in each specific phenotypes
* Breakout Room 6:

* Breakout Room 7:
* Find the genes that are responsible for a phenotype and search for those alleles
* Breakout Room 8:
* affects the way we have to breed for a crop; QTL, GWAS, RNAseq, SNPs to understand the underlying genetics.
* Question 3: Using SNPs, we can predict the simple or complex trait that an organism will express.

* Breakout Room 9:
* By doing a genomic analysis that includes multiple individuals which are expressing varing phenotypes, comparing their genetic differences to draw corrolations between genotype and phenotype.

* Breakout Room 10:
* breeding values (phenotype) can be collected for individual cattles (for example weight), so can use to predict outcome of breeding two individuals.
* If you know which alleles give any specific phenotype, then you can predict breeding outcome.

* Breakout Room 11:

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### Question 4, How can we change phenotypes?:

* Breakout Room 1:
*
* Breakout Room 2:

* Environmental effects can change the expression of genes as phenotypes, while not changing the genes directly, G X E expressions. Additionally, changing the genes can change phenotypes.

* Breakout Room 3:
* Mutation

* Breakout Room 4:
* Editing the Genotype responsible for the trait followed by management of the environment necessary.

* Breakout Room 5:
* first improving enviromental effects, second having offspring from the superior individual for an specific trait
* Using CRISPR-Cas9 system
* Breakout Room 6:

* Breakout Room 7:
* By changing the environment or selecting or introducing new alleles

* Breakout Room 8:
* Epigenetics if we change the environment; use biotechnology such as gene editing to change the genetic code; intermating and random segregation;
* Question 4: Epigenetic expression can be changed if we change our environment. Or, we can use biotechnology like genetic editing to change our genetic code. Or, we can use genetic selection to choose individuals with the genetic traits we want.
* Breakout Room 9:
* By controlling the envorimental factors that can cause varying epigenetic expressions; selective breeding of individuals who express desirable traits; and through application of germcell/other tissue editing.

* Breakout Room 10:

* Breakout Room 11:

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**Glossary/Jargon** (for terminolgy you don't know)

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**Resources for Further Learning:**

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