Notes 20100326.115550 Special Genome Fluidity

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Genome fluidity in soybeans, plant adaptation

Susana Goggi
follows up the arabidposis work presented earlier this semester
adaptation: allows survival of an organism; feeding, breeding; an organism can move
self pollinated plants used
must have a means to adapt without mobility
aside: NSF http://www.nsf.gov
evolution change a lot faster than we had previously thought (Phil. Trans. R. Soc. B., 2010)
example fish: able to adapt in its environment in four weeks
fish under different stresses-- able to switch from algae eating to insect and worm eating
working with self pollinated soy beans
cross pollination of soybean plants < 3%
capable of adaptation in only a single generation
in one generation, a plant can mature later than its peers

everything between the time that a seed is formed until the time that it is planted
why do seeds go dormant?
even under ideal circumstances-- reabsorption of water, germination
seed science center at Iowa State University
improve production, quality, marketing, utilization, regulatory environment for moving seeds
largest public seed laboratories
administered USDA National Seed Health System: testing for seed pathogens, development, deployment, education of tests
regulations deployed in 54 countries
harmonization of regulations to allow for fast movement of qualified seeds internationally
especially useful for droughts
allows fighting famine since seeds are of the same regulation when drought ends
theme: effect of environment on seed
nested in the corn and soybean belt of the United States

non-Mendellian genetic changes and inheritance
stresses previously applied to full plants
current experiments stress seeds, not full plants
do the genes switch back after the stress is removed
biotic stresses: disease, animal
abiotic: temperature, hail, salt, drought, flood, heavy metals, high winds, soil pH, etc.
honeycomb configuration -- low plant population density
this low density configuration is actually a stress -- over expression of many traits due to extra sunlight, water, space
hail
plants were bombarded (incidentally), seeds are harvested
all of the seeds of each plant are assigned to an 'entry'.
grafting experiments done: roots and shoots of seeds mixed and matched
accelerated aging: keeping a plant in the worse possible environment while keeping them alive
relative humidity is 100%, but there is no liquid water available; unable to germinate
the seeds were actually 'primed' instead of stressed; were better off and faster to germinate
all seeds germinated as soon as they were planted
genetic variation seen
priming: increase seed performance by hydration after redrying
'priming' also refers to the biological changes that occur during that time

seed water uptake is triphasic-- (1) slow uptake to start (2) plateau in absorption, physiological readying (3) fast absorption push toward germination
aside: Cloud Gate, British, Anish Kapoor: www.millenniumpark.org/artandarchitecture/cloud_gate.html
aconitase in Kreb's cycle -- Aco2, Aco4 are studied here (there are four)
low-level stressed plants (transplants, cross-polination): low level of genome changes
high-stress: honeycomb hail graft-- high frequency of genetic changes
genotype mirrors the phenotype-- non-Mendellian
parts of the plant are switching back to the wildtype
where in the process did the variation come from? (honeycomb, hail, grafting, combination)
where in specific?
how robust is this switching; how robust is switch induction (i.e. can we stress a plant out so much, it just stops switching)
grafting experiment: maturity difference between plants
when a soybean plant produces seeds, a given genetic change is then heritable
most of the changes are reversion to ancestral forms
pod colour becomes black; seed colour becomes black; sharp pubescent tips, leaflets; vine-like growth
extra-genomic cache: genomic sequence information disappears for one or more generations; reappears in later generations

the cache mechanism is hypothesized to be segments of DNA that's been annotated with unknown function
the switch is one-way (no mention of which enzymes are players)
there is no restoration-- so the cache is a revision history rather than concurrent version tracking
evidence collected that some loci are hotspots