Transcript Domestication genes in plants

Crop domestication
Centres of Plant Domestication
• Concept first devised by Vavilov in 1919
• Archaeological evidence suggests that hunter-gatherers independently
began cultivating food plants in 24 regions,….” (Purugannan and Fuller,
2009)
Domestication
‘Domestication is the process by which humans
actively interfere with and direct crop evolution.’
• It involves a genetic bottleneck:
• Often only few genes are actively selected and account
for large shifts in phenotype.
• Crops exhibit various levels of domestication.
What is a domestication syndrome?
A domestication syndrome describes the properties
that distinguish a certain crop from it’s wild progenitor.
Typically such characteristics are:
• larger fruits or grains
• more robust plants
• more determinate growth / increased apical
dominance
• loss of natural seed disperal
• fewer fruits or grains
• decrease in bitter substances in edible structures
• changes in photoperiod sensitivity
• synchronized flowering
Tomato - Fewer and Larger Fruits
Sunflowers - reduced branching, larger seeds,
increased seed set per head
Wheat - reduced seed shattering, increased seed size
Squash – larger, fleshier fruits
Corn – reduced fruitcase, softer glume, more kernels
per cob, no dispersal, reduced branching, apical
dominance
Lettuce – leaf size/shape, fewer secondary compounds
Rice – no shattering,
larger grains
Domestication is a process
• The distinction ‘domesticated’ or ‘not domesticated’ is an oversimplification
• Some crops have moved further along this process further than
others.
• We can recognize different levels of domestication
• How can we decide which level?
• Different domestication traits were selected for progressively
•Distinction between selection under domestication vs. crop
diversification  more targeted, ‘conscious’ selection during
diversification
• ‘Slow’ rate of evolution of different domestication traits
despite faster rates suggested by models
• Artificial selection can be “similar across different taxa,
geographical origins and time periods”
• Parallel evolution for “sticky glutinous varieties” in rice and
foxtail millets, all through selection at the waxy locus
• Most QTL studies suggest that many domestication traits are
controlled by a few genes of large effect – not though in
sunflower
• Population genomic studies in maize suggest 2 – 4% of genes
show evidence of artificial selection
Domestication of Maize
How often has maize been domesticated?
– Sampling (Matsuoka et al, 2002)
How often has maize been domesticated?
– Once. (Matsuoka et al, 2002)
Tracking footprints of maize domestication and evidence for a
massive selective sweep on chromosome 10
(Tian et al., 2009 PNAS)
Teosinte branched 1 (tb1)
• was identified as a major QTL controlling the difference in apical
dominance between maize and its progenitor, teosinte (Doebley et al.,
1997; Doebley, 2004)
• is a member of the TCP family of transcriptional regulators, a class of
genes involved in the transcriptional regulation of cell-cycle genes.
•Differences in tb1 expression patterns between maize and teosinte indicate
that human selection was targeted at regulatory differences that produced a
higher level of tb1 message in maize.
• Lack of any fixed amino acid differences between maize and teosinte in
the TB1 protein supports this hypothesis.
“For maize tb1 … [the selection coefficient] is in the range 0.05
to 0.2, comparable to cases of natural selection.” (Purugannan
and Fuller, 2009)
Teosinte glume architecture1 (tga1)
• was identified as a QTL controlling the formation of the casing that
surrounds the kernels of the maize ancestor, teosinte (Wang et al., 2005)
• is a member of the squamosa-promoter binding protein (SBP) family of
transcriptional regulators.
• tga1 has phenotypic effects on diverse traits including cell lignification,
silica deposition in cells, three-dimensional organ growth, and organ size
•The difference in function between the maize and teosinte alleles of tga1
appears to be the result of a single amino acid change. The fact that there
are no discernable differences in gene expression supports this
interpretation.
Domestication genes in plants
Crop Diversification genes in plants
The evolution of non-shattering
in the archaeological record
The genetic basis of the evolution of non-shattering
Non-shattering is often regarded as the hallmark of
domestication in most seed crops because it renders a
plant species primarily dependent on humans for survival
and propagation:
• rice gene sh4 (similar to the genes encoding MYBlike transcription factors in maize)
• rice quantitative trait locus (QTL) qSH1, which
encodes a homeobox-containing protein
• the wheat gene Q, which is similar to genes of the
AP2 family in other plants
• In sunflower likely controlled by multiple genes
Domestication genes in plants
• Maize and rice domestication seem to suggest few loci of
large effect are important
• Sunflower domestication seems to suggest many loci of small
to intermediate effect are important
• 9 domestication genes in plants so far, as well as 26 other loci
known to underlie crop diversity
• Of the 9 domestication loci, 8 encode transcriptional
activators.
•
More than half of crop diversification genes encode enzymes.
 Domestication seems to be associated with changes in
transcriptional regulatory networks, whereas crop
diversification involves a larger proportion of enzymeencoding loci (lots of them loss-of-function alleles).
The role of polyploidy in domestication
Towards resolving the genetic
basis of domestication in the
Compositae
Artificial selection
through
domestication
but HOW ?
Some fundamental questions in domestication genetics
 Which genes show strong signs of selection in
crops?
different
Can we see common patterns in taxa that have been
domesticated for similar purposes?
 Can we see dissimilar categories of genes under
selection in different crop types despite their close
phylogenetic relationship (e.g. sunflower and
jerusalem artichoke)?
Methodological ‘bottom-up’ approach
Bioinformatics pipeline:
1.) Input: EST libraries of crop, progenitor
and outgroup
2.) Genes that are orthologous in all taxa
are identified
3.) These genes are scanned for signs of
strong positive selection
4.) Such genes are compared to all known
proteins in Arabidopsis
5.) Functional characteristics of best fits in Arabidopsis genomic
database (TAIR) are annotated
Some preliminary results
Preliminary results from candidate domestication gene search
in Compositae crops:
• Several stress response genes are under selection in leaf
and oil seed crops
• Other interesting candidate domestication genes:
 safflower: fatty acid metabolism
 sunflower: nitrate assimilation
 Jerusalem artichoke: lateral root formation
What to do with candidate genes?
Confirm their role underlying traits
- functional analysis (introgression/transgenes)
- expression
- population genetic work
confirm associations with fitness
association mapping with traits of interest
What to do with candidate genes?
Applications:
breeding / improvement
conservation of genetic diversity
identification of taxon boundaries
understanding adaptation/domestication
comparative analysis – other taxa
Crop improvement
• Phenotype – based selection
– Slow, ineficient but can be effective
• Using genetics to inform breeding
– Marker-assisted selection
– Marker-assisted introgression
• Transformation
– Efficient (if you have the gene) but controversial
Transgenics controversy
• Advantages:
– Targeted to specific gene
– Any gene can be changed / introduced from any species
– Fast and efficient
• Disadvantages:
– Safety issues
– Regulations / legal issues
– Requires expertise and technology
Transgenics controversy
• Advantages:
– Huge improvements in phenotype of interest possible
– Yield improvements
– Health / nutrition benefits
– Reduce herbicide / pesticide / fertilizer use
– New products – pharmaceuticals, chemicals, etc.
• Disadvantages:
– Little regulation for health/environmental safety
– Loss of genetic diversity
– Reliance on big seed companies