Polyploids and domesticated species

Natalia Alvarez

UW Madison

March 20th, 2007

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)

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.

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)

# of species counted

% Polyploidyn = 13

(Grant, 1963)

% Polyploidyn = 11

(Goldblatt,1980; Lewis, 1980b)

Angiosperms estim.

- 47 75

Total crops 244 55 75

Did polyploidy confer advantages for plant domestication..?

If yes, polyploids frequency should be higher for crops than for angiosperms.

Not significant difference was found. Therefore, domestication would not favored polyploids over diploids.

Comparing at the family level

Polyploids frequency was not statistically different in 5 of the selected families, except in Dioscoreaceae.

(Hilu,1993)

# of species counted

% Polyploidyn = 13

(Grant, 1963)

% Polyploidyn = 11

(Goldblatt,1980; Lewis, 1980b)

Angiosperms estim. - 47 75

Total crop annuals 76 46 68

Total crop perennials 146 60 76

Are polyploids more frequent in perennial plants?

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)

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).

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

What happens after polyploid formation?

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

G. arboreumG. herbaceum

The progenitors

2n= 2x = 26

New World

G. raimondii

Africa

The descendants

2n = 4x = 52

The domesticatedspecies

http://www.eeob.iastate.edu/faculty/WendelJ/fiberevolution.htm

G. darwiniiG. tomentosumG. mustelinumG. hirsutumG. barbadense

G. hirsutumG. barbadense

G. arboreumG. herbaceum

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-textile.html

What happens in the nucleus of the polyploid cotton…?

Gene and genome evolution hypothesis

Adams and Wendel, 2004

• Intergenomic colonization

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

Genomic interactions

(Zhao et al. 1998)

• 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)

Genomic interactions

• Biased expression toward one homeologue or the other .

• Some genes show organ-specific, reciprocal silencing.

Transcript level (%)

Adams et al. 2003)

adhA gene in G. hirsutum

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.

Evolution of duplicated genes

Gene tree

Wendel et al.(1995)

• Differential rate of evolutionNucleotide 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).

Evolution of duplicated genes

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.