Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome

Krishna S., Gopala, Waters, Daniel L. E. and Henry, Robert J. (2014) Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome. PLoS One, 9 6: e98843.1-e98843.6. doi:10.1371/journal.pone.0098843

Author Krishna S., Gopala
Waters, Daniel L. E.
Henry, Robert J.
Title Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2014-06-06
Sub-type Article (original research)
DOI 10.1371/journal.pone.0098843
Open Access Status DOI
Volume 9
Issue 6
Start page e98843.1
End page e98843.6
Total pages 6
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Collection year 2015
Language eng
Formatted abstract
Background: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia.

Results: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection.

Conclusions: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2015 Collection
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 10 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 6 times in Scopus Article | Citations
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Created: Wed, 26 Mar 2014, 14:31:20 EST by Professor Robert Henry on behalf of Qld Alliance for Agriculture and Food Innovation