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

Krishnan S G, Waters DL, Henry RJ - PLoS ONE (2014)

Bottom Line: 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 4.58 Mbp 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.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.

View Article: PubMed Central - PubMed

Affiliation: Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia; Division of Genetics, Indian Agricultural Research Institute, New Delhi, India.

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 4.58 Mbp 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.

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Related in: MedlinePlus

Predomestication bottleneck prior to domestication and crop improvement resulting in ‘Polymorphism deserts’ in cultivated rice.Different classes of genes are represented by different shapes; dice shape (♦) indicates genes for adaptive traits, circles (•) indicates domestication genes, star shape (*) indicates genes for crop improvement. The allelic forms of genes are represented in different colors. A predomestication bottleneck possibly induced by environmental stress resulted in loss of polymorphisms in the adaptive genes in case of wild rice. Additional selection pressure during domestication and crop improvement resulted in further depauperating the polymorphisms resulting in the ‘polymorphism deserts’ as in the case of chromosome 5 of rice. Artificial selection during rice domestication in genes such as sh4, PROG1 resulted in reduced diversity in the adjoining genomic regions due to selection sweeps associated with the genes. Further selection during crop improvement in genes such as GS3, Bh4, qSW5, wx and Rc also reduced the polymorphisms in the regions associated with these genes. While the selections during domestication and crop improvement helped in retaining favourable alleles at these loci, an additional pre-domestication bottleneck has resulted in loss of variation in the genes providing adaptive traits in the ‘polymorphism desert’ of Chromosome 5.
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pone-0098843-g002: Predomestication bottleneck prior to domestication and crop improvement resulting in ‘Polymorphism deserts’ in cultivated rice.Different classes of genes are represented by different shapes; dice shape (♦) indicates genes for adaptive traits, circles (•) indicates domestication genes, star shape (*) indicates genes for crop improvement. The allelic forms of genes are represented in different colors. A predomestication bottleneck possibly induced by environmental stress resulted in loss of polymorphisms in the adaptive genes in case of wild rice. Additional selection pressure during domestication and crop improvement resulted in further depauperating the polymorphisms resulting in the ‘polymorphism deserts’ as in the case of chromosome 5 of rice. Artificial selection during rice domestication in genes such as sh4, PROG1 resulted in reduced diversity in the adjoining genomic regions due to selection sweeps associated with the genes. Further selection during crop improvement in genes such as GS3, Bh4, qSW5, wx and Rc also reduced the polymorphisms in the regions associated with these genes. While the selections during domestication and crop improvement helped in retaining favourable alleles at these loci, an additional pre-domestication bottleneck has resulted in loss of variation in the genes providing adaptive traits in the ‘polymorphism desert’ of Chromosome 5.

Mentions: The present study shows that the Asian cultivated rice has lost variability as a result of selection during domestication and crop improvement, and the diversity within Australian wild rice is of immense value for rice improvement and adaptation to environmental changes especially in the face of climate change. The reduction in variation in certain genomic regions of wild rice populations indicate bottlenecks induced by natural selection prior to domestication has also contributed to reduction in diversity in the rice genome (Figure 2). Biotic or abiotic stress in the environment of wild rice in tandem with reduced recombination [34] associated with the physical distribution of mutations [35] may explain loss of diversity in specific chromosome areas encoding genes contributing to adaptation to these environmental factors. This adaptation may have been important in the evolution of essential features of modern rice such as adaptation to an aquatic environment. Whole genome re-sequencing has enabled the identification of novel polymorphisms preserved in Australian A genome wild rices which would be useful in diversifying the ‘polymorphism deserts’ of cultivated rice [36].


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

Krishnan S G, Waters DL, Henry RJ - PLoS ONE (2014)

Predomestication bottleneck prior to domestication and crop improvement resulting in ‘Polymorphism deserts’ in cultivated rice.Different classes of genes are represented by different shapes; dice shape (♦) indicates genes for adaptive traits, circles (•) indicates domestication genes, star shape (*) indicates genes for crop improvement. The allelic forms of genes are represented in different colors. A predomestication bottleneck possibly induced by environmental stress resulted in loss of polymorphisms in the adaptive genes in case of wild rice. Additional selection pressure during domestication and crop improvement resulted in further depauperating the polymorphisms resulting in the ‘polymorphism deserts’ as in the case of chromosome 5 of rice. Artificial selection during rice domestication in genes such as sh4, PROG1 resulted in reduced diversity in the adjoining genomic regions due to selection sweeps associated with the genes. Further selection during crop improvement in genes such as GS3, Bh4, qSW5, wx and Rc also reduced the polymorphisms in the regions associated with these genes. While the selections during domestication and crop improvement helped in retaining favourable alleles at these loci, an additional pre-domestication bottleneck has resulted in loss of variation in the genes providing adaptive traits in the ‘polymorphism desert’ of Chromosome 5.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4048307&req=5

pone-0098843-g002: Predomestication bottleneck prior to domestication and crop improvement resulting in ‘Polymorphism deserts’ in cultivated rice.Different classes of genes are represented by different shapes; dice shape (♦) indicates genes for adaptive traits, circles (•) indicates domestication genes, star shape (*) indicates genes for crop improvement. The allelic forms of genes are represented in different colors. A predomestication bottleneck possibly induced by environmental stress resulted in loss of polymorphisms in the adaptive genes in case of wild rice. Additional selection pressure during domestication and crop improvement resulted in further depauperating the polymorphisms resulting in the ‘polymorphism deserts’ as in the case of chromosome 5 of rice. Artificial selection during rice domestication in genes such as sh4, PROG1 resulted in reduced diversity in the adjoining genomic regions due to selection sweeps associated with the genes. Further selection during crop improvement in genes such as GS3, Bh4, qSW5, wx and Rc also reduced the polymorphisms in the regions associated with these genes. While the selections during domestication and crop improvement helped in retaining favourable alleles at these loci, an additional pre-domestication bottleneck has resulted in loss of variation in the genes providing adaptive traits in the ‘polymorphism desert’ of Chromosome 5.
Mentions: The present study shows that the Asian cultivated rice has lost variability as a result of selection during domestication and crop improvement, and the diversity within Australian wild rice is of immense value for rice improvement and adaptation to environmental changes especially in the face of climate change. The reduction in variation in certain genomic regions of wild rice populations indicate bottlenecks induced by natural selection prior to domestication has also contributed to reduction in diversity in the rice genome (Figure 2). Biotic or abiotic stress in the environment of wild rice in tandem with reduced recombination [34] associated with the physical distribution of mutations [35] may explain loss of diversity in specific chromosome areas encoding genes contributing to adaptation to these environmental factors. This adaptation may have been important in the evolution of essential features of modern rice such as adaptation to an aquatic environment. Whole genome re-sequencing has enabled the identification of novel polymorphisms preserved in Australian A genome wild rices which would be useful in diversifying the ‘polymorphism deserts’ of cultivated rice [36].

Bottom Line: 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 4.58 Mbp 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.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.

View Article: PubMed Central - PubMed

Affiliation: Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia; Division of Genetics, Indian Agricultural Research Institute, New Delhi, India.

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 4.58 Mbp 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.

Show MeSH
Related in: MedlinePlus