Genetic Diversity in AA and CC Genome Oryza Species in Southern South Asia

Bautista, Nonnatus S.; Vaughan, Duncan A.; Jayasuriya, A. H. M.; Liyanage, Athula; Kaga, Akito; Tomooka, Norihiko

doi:10.1007/s10722-004-3227-4

Cited by 18 publications

(19 citation statements)

References 11 publications

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“…The relationships among the three diploid species with the C‐genome type have been investigated intensively using different genetic markers. Different results were produced, favoring either the relationship between O. officinalis and O. rhizomatis (Shcherban et al, 2000a, 2000b; Bao & Ge, 2004; Zou et al, 2008; Wang et al, 2009) or between O. eichingeri and O. rhizomatis (Bao et al, 2006; Bautista et al, 2006; Zhang & Ge, 2007). With a much larger dataset of 68 genes and the inclusion of additional samples of O. eichingeri from Africa, we obtained a fully resolved phylogeny of the C‐genome diploid species.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Zang

Zou

Zhang

et al. 2011

J of Sytematics Evolution

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The diploid Oryza species with C‐genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C‐genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C‐genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C‐genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single‐copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C‐genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.

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Section: Discussionmentioning

confidence: 99%

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Zang

Zou

Zhang

et al. 2011

J of Sytematics Evolution

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“…, 2006; Lin et al. , 2007), Rc gene governs the pericarp colour of seeds (Bautista et al. , 2006; Konishi et al.…”

Section: Introductionmentioning

confidence: 99%

SNP deserts of Asian cultivated rice: genomic regions under domestication

Wang

Hao

et al. 2009

J of Evolutionary Biology

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When performing a genome‐wide comparison between indica (93‐11) and japonica (Nipponbare), we find 8% of the genome, which have an extremely low SNP rate (< 1 SNP/kb). Inside these ‘SNP deserts’, experimentally confirmed genes show increased Ka/Ks that indicate adaptive selection. To further elucidate this connection, we survey the level and pattern of genetic variation in both cultivated and wild rice groups, using 155 noncoding regions located within SNP deserts. The results suggest that cultivated rice has greatly reduced genetic variation within SNP deserts as compared to either the nondesert or corresponding genomic regions in wild rice. Consistent with this reduction in genetic variation, we find a biased distribution of derived allele frequency in the cultivated group, indicative of positive selection. Furthermore, over half of the confirmed, domestication‐related genes are found within SNP deserts, also suggesting that SNP deserts are strongly related to domestication, and might be the key sites in the process of domestication.

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“…Our present result indicates that gene flow may exist between O. eichingeri and O. rhizomaits in Sri Lanka to some extent. The result consists with the study by Bautista et al (2006). Using RAPD and SSR markers, Bautista et al (2006) studied the genetic diversity of A-and C-genome species in southern South Asia and found that one O. rhizomatis accession clustered with the O. eichingeri accessions.…”

Section: Relationships Among Species and Speciation Of The Aiiotetrapmentioning

confidence: 89%

“…The result consists with the study by Bautista et al (2006). Using RAPD and SSR markers, Bautista et al (2006) studied the genetic diversity of A-and C-genome species in southern South Asia and found that one O. rhizomatis accession clustered with the O. eichingeri accessions. Nevertheless, further investigations using multiple approaches are needed to clarify the genetic relationships between the two species and verify the taxonomic status of the two races of O. eichingeri.…”

Section: Relationships Among Species and Speciation Of The Aiiotetrapmentioning

confidence: 89%

“…Recently, some authors (Bautista et al, 2006) screened 551 SSR primers derived from O. sativa on selected C-genome accessions and found 12 (2.2%) were useful for cross amplification. The low rate of successful cross-species amplification of microsatellite in these studies might reflect the genetic affinity between the target species and the species from which SSRs were developed.…”

Section: Transferability Of Microsatellite Markers In Wild Ricementioning

confidence: 99%

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Genetic diversity and evolutionary relationships ofOryza species with the B- and C-genomes as revealed by SSR markers

et al. 2006

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Genetic diversity and evolutionary relationships of 72 accessions representing six species with the B-, C-, and BC-genomes in the genus Oryza were investigated by seven microsatellite markers. Of four diploid species, Oryza officinalis maintained the highest diversity (P=71.4%, He=0.565), followed by Oryza eichingeri (P=57.1%, He=0.376), Oryza punctata (P=57.1%, He=0.272) and Oryza rhizomatis (P=42.9%, He=0.222). In comparison, a higher level of genetic diversity was revealed in the tetraploid (P=71.4%, He=0.461-0.637). UPGMA dendrograms based on genetic distance revealed an obvious genetic differentiation between Asian and African races of O. eichingeri. Three BBCC species clustered with different accessions of the diploid O. punctata, suggestive of their multiple origins. The results inferred from the dendrogram suggested that diploid species, O. officinalis and African O. eichingeri might be the C-genome donors for tetraploid species, Oryza minuta and O. punctata, respectively, while the C-genome ancestor of Oryza malampuzhaensis seemed to be either O. rhizomatis or the Sri Lankan O. eichingeri species. The genetic relationship among the CC and BBCC species further indicated that the tetraploid species with the BC-genome have originated independently, at least three times in history. In addition, we have demonstrated successful cross-species amplification of seven rice SSR loci across Oryza species with B-and C-genomes.

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Genetic Diversity in AA and CC Genome Oryza Species in Southern South Asia

Cited by 18 publications

References 11 publications

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

Phylogeny and species delimitation of the C‐genome diploid species in Oryza

SNP deserts of Asian cultivated rice: genomic regions under domestication

Genetic diversity and evolutionary relationships ofOryza species with the B- and C-genomes as revealed by SSR markers

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