Polyploidy as an evolutionary event in rice

Polyploidy as an evolutionary event in rice

Sadaf  Saleem

Department of Plant Breeding and Genetics, University of Agriculture Faisalabad.

Introduction

The organism with multiple sets of its haploid chromosome no. (x) is termed as polyploid and the phenomena lead to the situation is polyploidy. The individual with two sets of chromosomes is diploid “2x”, with three sets it would be triploid “3x”, with four sets tetraploid “4x”, pentaploid “5x” and so on.  In animals the occurrence of polyploidy individuals is rare but in plants it is very common.

Polyploidy in evolution

In diversification of many plants and animals polyploidy found to play creative role in evolution. Polyploidy incidence in flowering plants is 2-4% and 7% in ferns for change. Even in sympatric mode of speciation polyploidy has been predominant to all other forces of diversification as it provides the ingredients for diversification include morphological changes, reproductive isolated barriers and ecological tolerance on its own by effecting developmental processes and gene regulations as well. Even polyploidy lineages have better adaptability than others. Although polyploidy do not always results in evolution but has the potential for greater diversification which lead to evolution. As estimate suggests 40% to 70% flowering plants are of polyploidy origin. The polyploidy origin was studied in 14 model plant species, the 9 (Triticum aestivum, Zea mays, Gossypium hirsutum, Gossypium arboreum, Lycopersicon esculentum, Glycine max, Arabidopsis thaliana, Solanum tuberosum and Medicago truncatula) are suspected strongly to involve large scale duplications in evolutionary periods.

Diploidization in rice

Gramineae family is believed to have some common ancestor which further diverge and give rise to distinctly characterized groups as wheat, maize rice etc. Evidences are comparative mapping analysis of related species which show co-linearity and similarity in their genomes and presence of some shared blocks in genomes which uncover the strong presence of duplication events in common ancestor followed by rearrangements.

The chromosome no of rice is 12, and the whole genome has sequenced in ‘’The international rice genome sequencing project’’. In Oryza sativa (indica group) the 12 chromosomes carry the whole genome 370 Mb in size, and all these chromosomes have 10 duplicated blocks which contain 47% of the total predicted genes in rice.

Earlier it was thought rice has aneuploidy origin as in the findings of scientists working on the basis of draft sequences in japonica rice group and found that 59% of DNA markers have 2 or more copies, suggested the duplication events in rice at 40-50 million years ahead and a 2nd duplication event in chromosomes 11 & 12 about 25 million years ago. Later on to find the exact date and amount of duplication they analyze 2897 (BAC) rice sequences by The international rice genome sequencing project and found 15% of the genes are from duplicated regions in rice and more share from chromosome 2, as major fraction of duplication is from chromosome 2, on the basis of findings proposed the aneuploidy origin of rice with duplication event at 70 million years ago.

But working with same group (japonica), another group of scientists found  a large amount (61%) of sequences are from duplicated regions, hence suggest the polyploidy instead of aneuploidy origin of rice with duplication event 70 million years ago but the event was proposed to occur before the divergence of cereal crops.

Further Studies based on the phylogenetic analyses support the polyploidy origin of rice, reveal large scale duplications have occurred in rice about 70 million years ago as well as another duplication event involving chromosome 11 and 12 was occurred 5 million years ago. The time of the events are understood by phylogenetic analysis but there is a contradiction about extent or amount of duplication among different researchers. However the first duplication was before the divergence of rice and maize, and 2nd, after the divergence.

Further large scale deletion events and chromosomal rearrangements occur shortly after the duplications tend to loss 30 to 60% of these diploid genes which lead to rapid diploidization in rice.

References

1. Sarah P Otto, Jeannette Whitton. 2000. POLYPLOID INCIDENCE AND EVOLUTION. Annual Review of Genetics, Vol 34.
2. Paterson AH, Bowers JE, Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, USA 101: 9903–9908. Blackwell Publishing, Ltd.
3. Xiyin Wang, Xiaoli Shi, Bailin Hao, Song Ge and Jingchu Luo. 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization .New Phytologist, 165.
4. Yang , XU Guo-hua , GUO Xing-yi , FAN Long-jiang , Zhang et al.2005. Two ancient rounds of polyploidy in rice genome. Zhejiang Univ SCI 2005 6B(2):87-90

5.Avraham A. Levy and Moshe Feldman. 2002.The impact of polyploidy on grass genome evolution. Plant Physiology, Vol. 130.

6. Thomas G. Ranney.2006. Polyploidy: From Evolution to New Plant Development .Combined Proceedings International Plant Propagators’ Society, 138 Volume 56.
7. Guillaume Blanca, Kenneth H. Wolfea.2004. Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes. The Plant Cell, Vol 16.