Polyploids and domesticated species

1
Polyploids and domesticated species

• Natalia Alvarez
• UW Madison
• March 20th, 2007

2
Polyploidy and its effects

• It is estimated that 70 of the flowering plants
  has polyploidy in their history (Masterson,1994).
• Increased cell size and gigas effect in some
  organs.
• Changes in shape and texture of organs.
• Greater ability to colonize new habitats than
  diploid ancestors.
• Reduction in fertility and seed production

(Stebbins,1971)
3
The role of polyploidy in crop improvement

• Gene buffering Slower response to selection but
  more adaptive potential.
• Dosage effect additive effect of the alleles
  increases the number of phenotypes.
• Increased allele diversity and heterozygosis
  more possible allele combinations and
  opportunities for breeding.
• Novel phenotypic variation genome interactions
  and changes in gene expression in new synthesized
  allopolyploids.

4
Did polyploidy confer advantages for plant
domestication..?

• Survey of 244 crops species belonging to 11
  monocot and 48 dicot families. Chromosome number
  obtained from literature
• Neopolyploids determined by comparing with the
  smallest chromosome number in its respective
  genus.
• Determination of Paleopolyploids. Two criteria
  (Goldblatt,1980), n 11 and (Grant,1963), n
  13.
• The frequency of polyploids in crops was compared
  with estimates for angiosperms, monocots and
  dicots.

(Hilu,1993)
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Did polyploidy confer advantages for plant
domestication..?
If yes, polyploids frequency should be higher for
crops than for angiosperms.
of species counted Polyploidy n 13 (Grant, 1963) Polyploidy n 11 (Goldblatt,1980 Lewis, 1980b)
Angiosperms estim. - 47 75
Total crops 244 55 75
Not significant difference was found. Therefore,
domestication would not favored polyploids over
diploids.
6
Comparing at the family level
Polyploids frequency was not statistically
different in 5 of the selected families, except
in Dioscoreaceae.
(Hilu,1993)
7
Are polyploids more frequent in perennial plants?
of species counted Polyploidy n 13 (Grant, 1963) Polyploidy n 11 (Goldblatt,1980 Lewis, 1980b)
Angiosperms estim. - 47 75
Total crop annuals 76 46 68
Total crop perennials 146 60 76
The frequencies of annual vs. perennial polyploid
crops were statistically similar, contrasting
with the proposed idea that perennial polyploids
have a selection advantage.
(Hilu,1993)
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What happens after polyploid formation?

• In autopolyploids
• Genomes act independently
• Gene expression
• Dosage effect (linear relationship between gene
  expression and number of gene copies).
• Non-dosage regulation (over/under-regulation).

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What happens after polyploid formation?

• In allopolyploids
• Genomic changes
• Diploidization and structural evolution
• Intergenomic colonization.
• Nuclear-cytoplasmic interactions.
• Rapid genome changes
• Gene changes
• Divergence
• Silencing
• Intergenomic gene conversion
• Differential rate of evolution

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Bringing the story to the cotton

• Parental genomes from different continents
• Maternal A-genome from Africa
• Paternal D-genome from the New World
• Polyploidization 1.5 Mya
• Origin of 5 Allopolyploid species

http//www.athenapub.com/nwdom1.htm
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New World
Africa
The progenitors 2n 2x 26
G. arboreum G. herbaceum
G. raimondii
G. darwinii G. tomentosum G. mustelinum G.
hirsutum G. barbadense
The descendants 2n 4x 52
G. hirsutum G. barbadense
G. arboreum G. herbaceum
The domesticated species
http//www.eeob.iastate.edu/faculty/WendelJ/fibere
volution.htm
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Domestication in the New World

• Archaeological reports of cotton fabrics found in
  prehistoric ruins in Arizona.
• Gossypium hirsutum evolved in Mexico. The oldest
  archaeological specimens were found in Tehuacan,
  and are tentatively dated at 3400 to 2300 B.C.
• Gossypium barbadense, is the second species of
  New World cotton. Peruvian archaeological
  excavations found cotton textiles of 2500 B.C.

http//www.mayanindians.com/mayan-weavers.html
http//www.hno.harvard.edu/gazette/2002/01.24/09-t
extile.html
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What happens in the nucleus of the polyploid
cotton?
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Gene and genome evolution hypothesis
Adams and Wendel, 2004
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Genomic interactions

• Intergenomic colonization
• Repetitive sequences specific from A-genome
  are found in the D-genome in Gossypium
  polyploids. Transposable elements might be
  related.

(Zhao et al. 1998)
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Genomic interactions

• Rapid genomic changes and silencing
• Immediate consequences of allopolyploidization
  seem to occur in evolutionary timescale.
• Near-complete genomic stasis across
  generations of synthetic allopolyploids is
  observed. It contrast with evidence from other
  synthetic allopolyploids.
• Similar gene silencing within synthetic
  allopolyploids and respect to the natural
  allotetraploid of G. hirsutum. (Adams et
  al.,2003)

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Evolution of duplicated genes

• Biased expression toward one homeologue or the
  other .
• Some genes show organ-specific, reciprocal
  silencing.

adhA gene in G. hirsutum
Transcript level ()
Adams et al. 2003)
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Evolution of duplicated genes

• Interlocus concerted evolution
• Sequences of ITS regions and 5.8S ribosomal
  gene in the AD-genome species and their diploid
  progenitors show homogeneity. Four of the 5
  allopolyploids homogenized the 4 loci to the
  D-like form and one to the A-like form.

Gene tree
Wendel et al.(1995)
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Evolution of duplicated genes

• Differential rate of evolution
• Nucleotide diversity at homeologous locus of adhA
  and gene in G. hirsutum and G. barbadense was
  higher in the D-genome than in the A-genome of
  the allopolyploids. The results were observed
  also for adhC gene (Small et al.,1999 Small and
  Wendel,2002).

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References

• Adams,K and Wendel, J. (2004) Exploring the
  genomic mysteries of polyploidy. Biol. Journal of
  the Linnean Society 82 573-581.
• Hilu, K. (1993) Polyploidy and the evolution of
  domesticated plants. Amer. Journal of Botany
  80(12) 1494-1499.
• Stebbins, G. (1971) Chromosomal evolution in
  higher plants. Ch. 5. Edward Arnold, London
• Udall, J. and Wendel, J. (2006) Polyploidy en
  crop improvement. The Plant Genome (A supplement
  to Crop Science), Nov. 2006, No. 1.
• Wendel, J. (2000) Genome evolution in polyploids.
  Plant Molecular Biology 42 225-249.