Crop Evolution

Question 1

what are the stages of crop domestication?

Answer 1

onset of domestication
in situ increase in frequency of desirable alleles
formation of cultivated populations that are adapted to enviornments and local preferences
deliberate breeding

Question 2

how is selection used?

Answer 2

domestication can bottleneck
selection directly fixes genetic loci responsible for domestication traits
artificial selection reduces genetic diversity in cultivars

Question 3

what happened in 1960s and 2006?

Answer 3

1960s - green revolution - high yielding crop varieties introduced
2006 - rice genome published

Question 4

what does applied selection do?

Answer 4

improve yield
improve resource efficiency
increase disease resistance
operate on phenotypic traits - heritable changes

Question 5

what does artificial selection do?

Answer 5

selection can’t distinguish between hetero/homo
selection for recessive alleles - favoured alleles fixed in single gen
selection for dom allele - selection less efficient as allele approaches fixation

Question 6

what works better than artificial selection?

Answer 6

genetic markers

Question 7

what is the infinitisimal polygenic model?

Answer 7

quantitative traits are assumed to be under the control of an infinite number of gene, each contributing small effect on phenotype - random sampling gives a normal distributed phenotype

Question 8

what is phenotypic variance?

Answer 8

the sum of all genetic and environmental variance

Question 9

what are the genotype effects?

Answer 9

they’re defined relative to their mid point
the genotypic value is composed of;
A - additive effects - sum of the effects of individual alleles
D - dominance effects - interactions between alleles at a single locus
I - epistatic effects - interactions between genes at two or more loci

Question 10

what is genotypic variation?

Answer 10

Vg = Va + Vd + Vi
Va is the variation caused by additive effects passed from parent to offspring
the others are the dominance/interaction effects that are specific to individuals

Question 11

what does narrow sense heritibility tell us?

Answer 11

the relative contribution of genetic effects that can be passed from parent to offspring
the proportion of phenotypic variance caused by additive genetic variance

Question 12

what is the selection differential (S)?

Answer 12

the difference between mean of base pop and the mean of selected individuals

Question 13

when does S increase?

Answer 13

when selection intensity increases

Question 14

what is the response to selection?

Answer 14

a change in the mean phenotype of offspring of pop

Question 15

what does response to selection depend on?

Answer 15

S and narrow sense heritability

the intensity of selection and contribution of additive and enviro effects

Question 16

what happens if trait heritability is low?

Answer 16

breeding progress is low

Question 17

why are crop genomes hard to sequence?

Answer 17

large genome size and repetitive

Question 18

why are single genome sequences bad?

Answer 18

tell us nothing about genetic variation

Question 19

what do reference genomes do?

Answer 19

allow cost effective genome wide resequencing across multiple individuals

Question 20

what are SNPs?

Answer 20

single nucleotide polymorphisms

they are used to generate large numbers of genetic markers

Question 21

what are QTLs?

Answer 21

markers linked to quantitative traits can be substituted for phenotypic selection
many influenced by single genes of large effect
predict quantitative phenotypes after new route to genetic gain

Question 22

how does QTL mapping work?

Answer 22

make a cross between contrasting phenotypes
cross within F1 to get segregating F2 pops
genotype with genome-wide genetic markers
genetic markers tested for association with traits of interest

Question 23

how does QTL mapping work in disease resistant barley?

Answer 23

resistant crossed with susceptible 
segregated F2 pop produced
genotyped at 348 SNP loci
field trials for disease resistance 
markers tested for association with disease

Question 24

how does marker assisted selection work?

Answer 24

crosses made between contrasting parents
segregating pop genotyped for linked marker
initial selection based on marker genotypes
selected individuals taken forward for phenotypic investment

Question 25

advantages of MAS

Answer 25

quick - seedling level, reduced gen time so faster genetic gain
cheap
response to selection doesn’t depend on environmental variation - effective when trait heritability low