AgriGenomics Flashcards
what are the trends in crop production and yield?
both increase each year - due to better crop varieties through breeding and better crop management - fertiliser, pesticides, irrigation.
however, starting to plateau and unsure why, also, in the last 15 years or so, area used is increasing.
current gains in yield are insufficient to reach demands by 2050.
is population growth the real problem?
yes, although technically we can manage it.
a greater problem is increasing affluence which means more people will want access to meat and more luxurious foods
which countries are stressing their groundwater supplies?
Middle East, central/west US, Central Asia
not stressed: northern europe, Russia, Australia, much of Africa, South America
basically- how are forward and reverse genetics used in agriculture
Reverse: Use genomic tools to understand how crops evolved after domestication.
Forward: Use genomics to actively assist breeding.
reverse will provide us with the basic knowledge needed to improve forward (eg neo-domestication).
what causes the gap between actual yield and potential yield?
biotic stress: microbes, nematodes, insects, weeds, fungi
abiotic stress: nutrient availability soil salinity water availability air pollution temperature
how can the yield be increased
1) increase yield potential. - remove limits of pests, nutrient limitation, effective control
2) decrease yield gap - increase disease resistance, abiotic stress tolerance etc
what is the record and average wheat yield?
2017 - 16.8t/ha
average in 2017 - 3.5t/ha
how long ago did the agricultural revolution start?
10000 ya people gave up hunter gatherer lifestyle and chose to settle.
domestication gradually occurred as farmers kept and replanted rare variants with useful traits.
when agri rev started, 5m people on earth. 5000 years later - Egyptian dynasty, approx 100m
common features of domestication
Synchronisation of germination and ripening apical dominance loss of seed shattering enlargements of fruit or seed improved flavour/nutrition
these changes would be terrible for NS of the plant in the wild. Shows that engineered plants wouldn’t be able to survive in the wild anyway, we should not worry about this.
what is the undomesticated ancestor of maize?
teosinte
has long tassels branches
few large kernels with rough exterior (modern corn grains would be digested by animals and not dispersed.)
maize is dependent on humans for sowing seed.
how different are domestic plant genomes from wild progenitors?
little difference, because 10,000 years is a short time in evolutionary perspective.
dramatic changes in appearance are due to mutations in only a few domestication genes.
eg 50 genes contribute to domestication in maize
sites of selection show loss of genetic diversity, caused by selective sweep.
what does tb1 gene do
teosinte branched 1
protein is a TF suppresses lateral shoot formation (apical dominance)
how does tb1 diversity differ in maize and teosinte?
Dom maize has only 30% diversity in protein coding region of tb1 compared to teosinte - this reflects background diversity changes.
2% diversity in region 5’ to Tb1 gene.
selection has been applied to a regulatory region, not coding region.
maize tb1 carries retrotransposon in reg region and maize has higher mRNA levels of tb1 than teosinte.
what types of genes are often targeted in domestication?
genes encoding TFs
what does the hopscotch transposon do in teosinte?
hopscotch insertion into tb1 variant teosinte swept to high frequency yielding plants with few branches (gives apical dominance)
example of orthologue of tb1
in wheat
regulates spike architecture
gives ‘hb’ - highly branched, phenotype.
extra pair of chr 4D = increased expression of tb1 gene.
negative consequences of genetic sweep
loss of diversity - higher chance of getting wiped out in stressful conditions.
what does a co-expression network show?
TF as ‘hubs’
many connections to other transcripts.
due to ability of TFs to bind to promoters of many genes and influence expression.
so a change in a TF can affect many genes = big phenotypic change, so often targeted.
another gene which has been altered from teosinte to maize
tga1 - teosinte glume architecture 1. glume is surrounding seed, in teosinte it is a hard seed case. in maize, allele reduces to a soft membrane. tga1 similar expression levels in maize and teosinte, but SNP in one exon (lysine -> asparagine in maize)
this allele not found in teosinte, suggesting evolved after domestication.
gene targeted for domestication of wheat.
Q gene - in domesticated wheat is responsible for cultivation of wheat, confers free thrashing trait (seeds separate easily from glumes).
also pleiotropically influences other domestication related traits.
encodes AP2 TF.
what is de-domestication?
unique evolutionary process by which domesticated crops re-acquire wild-like traits to survive and persist in agricultural fields without the need for human cultivation.
