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)

5. 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.

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? 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)

8. 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).

9. 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

10. 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

11. New World Africa The progenitors 2n= 2x = 26 G. raimondii G. arboreum G. herbaceum 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/fiberevolution.htm

12. 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

13. What happens in the nucleus of the polyploid cotton…?

14. Gene and genome evolution hypothesis Adams and Wendel, 2004

15. 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)

16. 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)

17. 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)

18. 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)

19. Evolution of duplicated genes • Differential rate of evolution Nucleotide diversity at homeologous locus of adhA andgenein 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).

20. 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.