Animal Genetics Exam 2

How do we decide if the results meet our hypothesis about the mode of inheritance and expression of genotypes? What is the critical chi value? F its higher or less than, we?

Ex: In the Sweet Pea trial we expect a 9 C: 7 c ratio, we observe 50 C : 30 c out of 80 plants

Experiment 1: observe 50 C : 30 c out of 80 plants

• Test statistic; 𝜒2 = (50−45)²/45 + (30-35)²/ 35 = 1.27

Compare the calculated Chi-square value with the Chi-square critical value from Table of Chi-square at particular significance threshold (e.g. P<0.05) and 1 degree of freedom. The critical Chi-square value is 3.841

Why we use 1 degree of freedom?

 If calculated 𝜒 2 value is less than 3.841, Accept (fail to reject) the null hypothesis (i.e. H 0 )

 If calculated 𝜒 2 value is higher than 3.841, Reject the null hypothesis

What are alleles?

Alleles are different forms (versions) of mutation, genetic variant, or genes possible in a physical position on the genome

Allele Frequency: Beta casein

What is Beta casein? It’s two forms? Which breed has highest A2A2?

• is a protein that makes up around 30% of all milk proteins

• BTA6

• There are two main versions of beta casein: A1 and A2.

• Codominance mode of action

We need to know genotype frequency and then breed A2A2 x A1A1 → A2A2 X A2A1 → 50% A2A2 replacement and 50% A1A2 (cull)

What is Allele Frequency?

Refers to how frequently a particular allele detected (i.e., observed) in a population.

Why do we care about Allele and Genotype Frequency? Overall idea and 4 specific uses?

They underpin practical breeding decisions:

=> Genomic prediction (GEBVs) relies on allele frequencies at markers across the genome to estimate breeding values and compute genomic relationship matrices.

=> Estimating heterozygosity and inbreeding depression risk in a herd requires genotype frequency data. Inbreeding depression risk = reduction in the animal performance

=> Frequency of a deleterious or favorable allele (e.g., a fertility-linked variant) tells you how much genetic potential exists to select for or against it, and how fast you could move that frequency through selection.

=> Carrier frequency for recessive genetic defects (important in dairy cattle, where several recessive lethals are tracked) is calculated directly from genotype/allele frequencies, which is critical for mating decisions to avoid carrier × carrier matings.

Calculating Allele Frequencies: assumptions, two methods

Assumptions: We are dealing with a single locus in a large and random mating

population. we are dealing with diploid species.

What are the frequencies of A1 and A2 alleles?

We can calculate allele frequency by two methods:

▪ Counting

▪ Proportion

Calculating Allele Frequencies by Counting: fill in blanks

Dominant vs minor allele? What does p and q mean?

Dominant/major allele is the most commonly frequent allele in this population (p)

Minor allele is the less common or frequent allele in this population (MAF) (q)

2. Calculating Allele Frequencies by Proportion: q + p = 1