Lecture 3 - genetic diversity in agricultural systems

what happens during domestication of crops?

severe bottleneck and strong artificial selection

severe bottleneck

only a tiny subset of individuals in the wild population are chosen to be cultivated

strong artificial selection

humans breed and retain the best performing crop plants by selecting on germination timing, seed size and nutrition

what is the consequence of domestication

reduced genetic variation (no genetic drift_

H

average frequency of heterozygous individuals per gene locus

P

proportion of gene loci that are polymorphic

π

average number of nucleotide differences per site for any randomly sampled pair of nucleotides

why is genetic variation in crops important?

• clues to past artificial selection

• pest and pathogen management

• future improvement of crop

domestication of maize from teosinte

what does a bottleneck combined with selection do to the population?

it reduces the effective population size

census size (N)

total number of adults in a population

effective size (Ne)

number of adults that breed

• most important factor for evolutionary analysis

what is the relationship between effective size and census size

effective size is usually smaller than census size because not every single individual in the population is gonna reproduce

why is effective size and census size not equivalent to eachother?

• variation in number of progeny among individuals

• unequal sex ratio (male to female ratio in the population is not 1:1

• overlapping generations caused by mating between offspring and parents

• fluctuations in population size due to population bottleneck, Ne is a mean across generations

what factors can cause further reductions in Ne?

natural or artificial selection

how can Ne be measured?

as a species average across the genome or separately for each gene

first view of domestication

the bottleneck affects the entire genome and all loci are affected

second view of domestication

bottleneck produces genome wide reduction in Ne for all loci and it is further reduced in natural or artificially selected loci compared to the rest of the genome

artificial selection

should lead to additional reduction in Ne that are locus specific

locus specific reduction

for loci affecting the traits under artificial selection

how can selection affects on bottlenecks be tested?

by looking for genes that show evidence of amore severe bottle neck than is typical for the rest of the genome

what were the results when selection effects were tested in maize and teosinte?

• 2 to 4% of the teosinte genome experienced strong artificial selection during domestication

what genes were targeted by artificial selection

• expected: those for ear production, growth and morphological traits

• unexpected: 5 whose function is unknown

irish potato famine

caused death of 1 million Irish people, 1-2 million emigrated, population of Ireland declined by 25%, immigrants settled in Britain, the US and Canada

how do potatoes grow?

sprout easily for the underground tuber leading to clonal propagation

lumper variety of potatoes

large yield of potatoes with lots of carbs and calories that most Irish people ate

clonal propagation

asexual reproduction generating identical progeny ensuring no mixing of genetic variation

oomycete

fugus-like eukaryotes that can disperse by spores in the wind causing potatoes to root in the ground which started the famine

what happened to Ireland in the first year of the pathogen attack in the potato famine>

dramatic drop in potatoes because there were only 1 to 3 genotypes of the potatoes (monoculture) so natural and artificial selection was useless because of the lack of genetic variation so there was no improvement in resistance to the pathogen in the potatoes

societal implications

• no application of mendelian genetics and Darwinian evolution can have deep social and human health effects

• ignoring evolution has negative effects on agriculture, medicine, covid management etc

biological implications

we can use evolutionary genetic principle to discover regions of the genome with past artificial selection, improve future agricultural crops and design sensible schemes to reduce risks of monoculture consequences

long term selection experiment on corn kernels for protein and oil content

starting content of protein was 10% and oil was 5 % and investigators measured protein content and allowed the ones who produced the most to mate with eachother to start the next generation, same with the least producing ones and same for oil content

how much was maize reduced as a consequence of artificial selection, bottleneck and domestication in relation to teosinte?

by 43%

oil content results

steady artifical selection for the most oil producing generations and the least oil production lines

protein content results

steady artificial selection for the most protein producing generations and the least protein production lines

reversal lines

at gen 40 or 45 there is a plateau but why?

• variation in the genome has been fixed so there may be no more genetic variation

• or any of the variation altering protein content may have pleiotropic effects on the plant slowing its growth (tradeoff somewhere in the life cycle)

this is therefore done to distinguish between the two possibilities

what happens after the reversal lines are applied?

selection resumes and there is continued increase in the production of oil and protein content