1.3: Genetic Diversity in Agricultural Systems

Question 1

which 3 species account for 60% of food energy intake by humans

Answer 1

rice, maize, wheat

Question 2

t/f the localities with variation is the likely place of domestication

Answer 2

true

Question 3

name the common names
1. hordeum vulgare
2. triticum spp.
3. vitis vinifera
4. lens culinaris
5. pisum vativum
6. olea europaea
7. phoenix dactylifera
8. cicer arietinum
9. linum usitatissimum

Answer 3

1. barley/beer
2. wheat/beer
3. grapes/wine
4. lentils
5. peas
6. olives
7. dates
8. chickpeas/garbanzos
9. flax

Question 4

define severe bottleneck

Answer 4

only a tiny subset of individuals of the wild population are chosen to be cultivated
(only a small fraction of individuals contributing genes to next gen)

Question 5

define strong artificial selection

Answer 5

a deterministic process where humans breed and retain the best performing crop plants – low genetic variation, selection on germination timing, seed size, nutrition (features beneficial for humans)

Question 6

what happens during domestication of crops (2)

Answer 6

severe bottleneck, strong artificial selection

Question 7

how to measure the reduced genetic variation (consequences of domestication)

Answer 7

H: average freq of heterozygous indiv per gene locus
P: proportion of gene loci that are polymorphic
π: avg number of nucleotide differences per site, for any randomly sampled pair of nucleotides

Question 8

why do we care about genetic variation in crops (3)

Answer 8

1. clues to past artificial selection – on what traits did our ancestors select and clue agriculture products are the way they are
2. pest and pathogen management - can we reduce crop loss to pests
3. future improvement to crops – is it possible to keep breeding better crops without genetic engineering

Question 9

domestication of teosinte to maize led to a ___________ of variation

Answer 9

dramatic loss

Question 10

genetic diff in maize/genetic diff in teo = ???

Answer 10

0.57

Question 11

if the genetic diff in maize/genetic diff in teo = 0.57, what is the % loss of variation

Answer 11

43%

Question 12

What is Ne

Answer 12

the effective population size - the size of an idealized population with the same properties with respect to genetic drift and allele freq as the observed populations
(genetic drift equals the observed rate in the real population)

Question 13

describe an idealized population

Answer 13

all indiv with equal opportunity to pass on their genes and do so equally

Question 14

what do both bottlenecks and selection do?

Answer 14

reduce effective population size (Ne)

Question 15

which is more important for evolutionary analysis, Ne or N

• what is N?

Answer 15

Ne

N is the census size = total number of adults in a population

Question 16

why does N not equal Ne

Answer 16

• variation in num of progeny among individuals - stochastic differences in the genetic contribution of individuals
• unequal sex ratio (ie 50m:50f)
• overlapping generations - mating between offpsring and parents leading to fewer unique copies of genes to next gen
• fluctuations in pop size: pop bottlenecks, Ne is a harmonic mean across generations

consequently the number of individuals making genetic contributions to the next gen is almost always lower than the total census of number of indiv and natural or artificial selection reduces Ne even further

Question 17

how can Ne be measured (2)

Answer 17

as a species average across the genome, also be measured for each gene separately (selection on a given gene will lower its Ne)

Question 18

describe the two views of domestication

Answer 18

1. Ne-T1 > Ne-Te – bottleneck affects the entire genome (lowers), all loci are affected
2. Ne-T1 > Ne-T2 –> Ne-T1&raquo_space;> Ne-T2 where the bottleneck produces genome-wide reduction in Ne for all loci and then selected loci show even greater reduction in Ne compared to the rest of the genome

Question 19

fill in the blanks
1. purely demographic consequences of _____________ have genome wide effects of reducing Ne
2. artificial selection should lead to additional _________ in Ne that are _____ specific
3. describe the test for this

Answer 19

1. purely demographic consequences of bottleneck have genome wide effects of reducing Ne
2. artificial selection should lead to additional reduction in Ne that are locus specific – for loci affecting the traits under artificial selection
3. test: look for genes that show evidence of a more severe reduction in Ne than is typical of the rest of the genome

Question 20

for the 1:1 line in the graph, is genome wide reduction in Ne above or below it

Answer 20

below

Question 21

t/f bottlenecks CANNOT explain the full loss of variation

Answer 21

no pts in grey on x axis

Question 22

_ to _% of the teosinte genome experienced strong artificial selection during domestication

Answer 22

2-4%
detectable imprint in the genome evidence in population genetic patterns

Question 23

how many genes were extrapolated to genome? and some state some expected/unexpectated

Answer 23

extrapolated to genome: 1200 genes
expected: genes eat production, growth, morphological traits
unexpected: 5 of top 30 genes are genes of unknown function

Question 24

what was the genetic issue of the irish potato famine

Answer 24

potato was the sole food source for ~1/3 of the irish population
only 1-3 genotypes of potato were cultivated and they were clonally propagated
- the phytophthora infestans (potato blight), an oomycete, fungus-like eukaryote but distinct from fungi and it can disperse by spores in the wind

Question 25

describe what happened to potatoes upon pathogen attack and what the superior approach may be

Answer 25

upon pathogen attack: natural and artificial selection are impotent without genetic variation, no improved resistance possible

the superior approach is genetically diverse potatoes so the resistant genotypes persist after the blight

Question 26

describe the general implications in the societal and biological from the irish potato famine

Answer 26

societal
- failure to apply general principles of mendelian genetics & darwinian evolution can have profound social and human health effects
- ignoring evolution because it is inconvenient is likely to have adverse effects on: agriculture, medicine, covid management, many other socially important issues

biological
- we can use evolutionary genetic principles to: discover regions of the genome under past artificial selection, improve future agricultural crops, design sensible planting schemes to reduce risks of monoculture devastation

Question 27

what is the implications of reversal lines

Answer 27

shows upon selective pressures, there is still genetic variation bc it was able to change

Question 28

what are the challenges/limitations from the corn oil and protein experiment

Answer 28

• the limits to artificial selection have not been reached
• simplest explanation: there are many genes affecting these traits, each of small effect and the combined effect of slight changes in allele freq of many genes of small effect leads to the response
  challenges
• what about crops like potato and banana (sterile triploids) that don’t flower easily/reproduce in a way for outcrossing and artificial selection
• what to do if crops, like papaya, lacks genetic variation for the challenges (invasive spec, novel pathogens)
• artificial selection targets genetically variable genes. how is this diff than knowing the genes and using mol bio