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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

SNP distribution across Chromosome 5.Numbers on vertical axis are SNP/kb. Numbers on vertical horizontal axis are Mb from origin. Vertical grey bar represents the centromere.
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pone-0098843-g001: SNP distribution across Chromosome 5.Numbers on vertical axis are SNP/kb. Numbers on vertical horizontal axis are Mb from origin. Vertical grey bar represents the centromere.

Mentions: Genome wide comparisons between O. sativa ssp. japonica and O. sativa ssp. indica cultivars have revealed a low diversity region also referred to as ‘polymorphism desert’ between 8.97 and 13.56 Mbp on chromosome 5 with less than 10 SNP per 100 kb while the mean SNP rate of Chromosome 5 is comparable to the mean SNP rate across other chromosomes [6]. A similar SNP distribution pattern has been observed in indica-japonica[25]–[27], indica-indica[6], and japonica-japonica[28] comparisons. Analysis of the equivalent region in Asian O. rufipogon and the Australian AA genome wild rice found divergence from cultivated rice to be reduced by more than 40% in these species relative to the chromosome as a whole. This was observed not only based upon comparisons with O. sativa ssp. japonica cv. Nipponbare (Table 1 and Figure 1) but also with the O. sativa ssp. indica (cv. 93-11) reference genome sequences (Figure S1).


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

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

SNP distribution across Chromosome 5.Numbers on vertical axis are SNP/kb. Numbers on vertical horizontal axis are Mb from origin. Vertical grey bar represents the centromere.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0098843-g001: SNP distribution across Chromosome 5.Numbers on vertical axis are SNP/kb. Numbers on vertical horizontal axis are Mb from origin. Vertical grey bar represents the centromere.
Mentions: Genome wide comparisons between O. sativa ssp. japonica and O. sativa ssp. indica cultivars have revealed a low diversity region also referred to as ‘polymorphism desert’ between 8.97 and 13.56 Mbp on chromosome 5 with less than 10 SNP per 100 kb while the mean SNP rate of Chromosome 5 is comparable to the mean SNP rate across other chromosomes [6]. A similar SNP distribution pattern has been observed in indica-japonica[25]–[27], indica-indica[6], and japonica-japonica[28] comparisons. Analysis of the equivalent region in Asian O. rufipogon and the Australian AA genome wild rice found divergence from cultivated rice to be reduced by more than 40% in these species relative to the chromosome as a whole. This was observed not only based upon comparisons with O. sativa ssp. japonica cv. Nipponbare (Table 1 and Figure 1) but also with the O. sativa ssp. indica (cv. 93-11) reference genome sequences (Figure S1).

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