Inbreeding

Question 1

Identity by descent

Answer 1

inbreeding is the inheritance of identical chromosome segments (chunk of chromosome same between individuals); if mutation in one chromosome it will also be in other;

Question 2

inbreeding affects all

Answer 2

finite population to some degree; particularly strong in small populations and populations (of any size) where matings between close relatives occur

Question 3

inbreeding measured by

Answer 3

inbreeding coefficient (f); can be estimated from a pedigree or calculated from genetic data

Question 4

inbreeding increases

Answer 4

homozygosity so it can increase expression of homozygous recessive alleles which may be deleterous

Question 5

inbreeding depression

Answer 5

caused by increase of deleterious recessive alleles

Question 6

coefficient of relatedness

Answer 6

r (how related are two individuals)
identical twins 1
parent-offspring: .5
full siblings: .5
grandparent-grandchildren: .25
half siblings: .25
First cousins: .125
Second cousins: .0325

Question 7

why are you approximately 25% related to grandma?

Answer 7

because you are 50% related to each parent but because of recombination could have little more or a little less from grandma or grandpa

Question 8

coefficient of relatedness and coefficient of inbreeding

Answer 8

coefficient of inbreeding is half of coefficient of relatedness

Question 9

outbred identical twins selfing inbreeding coefficient

Answer 9

Have coefficient of relatedness of 1 with self the offspring are going to have f=.5 because recombination

Question 10

inbred identical twins selfin

Answer 10

f=1; for inbred parents the coefficient of relatedness is the same as coefficient of inbreeding

Question 11

if parents are related inbreeding coefficient in relation to coefficient of relatendess

Answer 11

will be half plus more if parents are related

Question 12

if parents are unrelated offspring will be

Answer 12

outbred (f=0) even if parents are inbred

Question 13

if parents are related (COR=x) offspring will be

Answer 13

inbred (f=x/2 or more if parents are inbred)

Question 14

Drawbacks to pedigree based estimates of relatedness and inbreeding

Answer 14

• they’re just estimates; amount of genomic sharing btwn to individuals depends on actual chromosomal segments transmitted (ie can have distant ancestors who made no genetic contribution if far enough back)
• might be wrong if pedigree is wrong (paternity?)
• only capture IBD as far back as pedigree is recorded (usually 5-10 generations max)

Question 15

far back pedigree

Answer 15

starting with only a few ancestors contributing same hapolotypes differences appear with recombination events

Question 16

run of homozygosity

Answer 16

look for this when calculating relatedness and inbreeding; run of homozygosity is continuous length of homozygous genotype present in genome that is shared
- looking at this generally captures inbreeding tracts inherited in last ~100 generations

Question 17

f with subscript ROH

Answer 17

proportion of genome that is shared; chunk of chromosome that is shared btwn related individuals with no mutations

Question 18

Inbreeding and Hardy-Weinberg

Answer 18

• effect of inbreeding is a loss of heterozygosity (locus can’t be heterozygous if it occurs in inbreeding tract)
• inbreeding tracts can’t contain heterozygosity so f determines amount of loss in heterozygosity
• inbreeding is violation of random mating assumption of hardy-weinberg equilibrium

Question 19

expected heterozygosity under hardy-weinberg equilibrium

Answer 19

Ho=2pq

Question 20

observed heterozygosity

Answer 20

=H

Inbreeding coefficient f=(Ho-H)/Ho

Question 21

inbreeding hardy-weinbrg frequencies

Answer 21

AA p^2 + fpq
AB 2pq(1-f)
BB q^2 + fpq

Question 22

f=(Ho-H)/ Ho same as

Answer 22

H=Ho(1-f)

Question 23

when allele frequency is low and there is inbreeding

Answer 23

it increases number of homozygous genotypes by a large factor if inbreeding is .2 then frequency of recessive allele is now 20x higher than it was before this is why we see more recessive alleles in purebred animals (more inbreeding)

Question 24

is inbreeding harmful?

Answer 24

Goldens with inbreeding loops in last 10 generations did not live as long and had smaller litter size but there are organisms that have evolved to live in highly inbred populations which works because if inbreeding/ selfing has occurred for many many generations the most deleterious recessive alleles have been exposed to selection and lost
INBREEDING IS NOT HARMFUL IT IS ONLY HARMFUL WHEN IT UNMASKS HARMFUL RECESSIVE VARIANTS

Question 25

inbreedign in domestic animals

Answer 25

causes inbreedng depression because it unmasks deleterious recessive variants (inbreeding occurs in all domestic animals and is almost always associated with decreased fitness bc it unmasks deleterious recessive alleles)

Question 26

warnings re genomic testing

Answer 26

1. don’t try to use inbreeding to purge deleterious alleles, use genetic testing
2. don’t blindly use genomic tools to pedigrees to simply maximize outcrossing; small differences in relatedness/ inbreeding may not be meaningful need to consider other things such as are both parents health and conforming to breed standards (a poor poodle crossed with a poor lab doesn’t make good little or labradoodles)

Question 27

labradoodles

Answer 27

many are inbred because only if its a lab x poodle vs labradoodle x labradoodle can you say its not inbred and even lab x poodle can make crappy dog if crappy genes

Question 28

conservation genomics and outcrossing

Answer 28

distant relatives/ lines may be adapted to different purpose/ environment and outcrossing them may make something adapted to neither which is not good in conservation genomics

Question 29

inbreeding is ___ the relatedness of parents in outbred population

Answer 29

half; can be more in inbred populations

Question 30

inbreeding (and relatedness) can be accurately calculated from

Answer 30

genome-wide data (dense genotyping arrays or sequencing)

Question 31

how to estimate inbreeding and relatedness without genomic data

Answer 31

use a pedigree, if no pedigree use molecular markers