Differentiation of perennial and annual types due to habitat conditions in the wild riceOryza perennis

Morishima, Hajime; Sano, Yoshio; Oka, Hiko-Ichi

doi:10.1007/bf00986670

Cited by 80 publications

(90 citation statements)

References 24 publications

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“…Among wild accessions the self-crossing rate is quite variable, although O. rufipogon tends to have lower rates than O. nivara: 50%-80% and 75%-95%, respectively (Morishima et al 1984;Oka 1988;Gao et al 2002;Phan et al 2012). As for the cultivated accessions, they are thought to be almost totally inbred with self-crossing rates close to 95%, although O. s. indica has been described as having slightly lower rates (Oka 1988 To assess the impact of explicitly assuming inbreeding on SFS estimation, we estimated it for each of the four rice species/ subspecies.…”

Section: Estimating Inbreeding Coefficients From Ngs Datamentioning

confidence: 99%

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

et al. 2013

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Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.

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Section: Estimating Inbreeding Coefficients From Ngs Datamentioning

confidence: 99%

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

et al. 2013

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“…The perennial wild rice has a reproductive system different from that of annual wild rice to adapt to the habitats of water conditions (Morishima et al 1984). The perennial ecotypes mainly grow in deepwater habitats and show partial outcrossing, a low seed productivity and high regenerating ability.…”

Section: Intraspecific Variations In Wild Ricementioning

confidence: 99%

Variations of Floral Traits in Asian Cultivated Rice (Oryza sativa L.) and its Wild Relatives (O. rufipogon Griff.)

et al. 2003

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To clarify the inter-and intraspecific variations of floral traits in rice, we investigated eleven traits related to pistil, stamen and glume using 128 Asian cultivated rice (Oryza sativa L.) accessions including 72 Indica and 56 Japonica type accessions, and 53 wild rice (O. rufipogon Griff.) accessions including 32 perennial and 21 annual ecotype accessions. We examined the results from three specific levels: intraspecific variation between perennial and annual ecotypes of wild rice, interspecific variation between cultivated rice and wild rice, and intraspecific variation between Indica and Japonica type cultivars. The annual wild rice accessions exhibited a shorter stigma and anther than the perennial wild rice ones. The cultivated rice accessions showed a lower stigma exsertion, shorter stigma, shorter anther, and thicker and wider lemma and palea than the wild rice accessions. These floral traits of cultivated rice are considered to play an important role in selfing and high seed production. None of the floral traits showed distinct differences between the Indica and Japonica type accessions in cultivated rice, although the Indica type accessions tended to display a slenderer stigma and glume than the Japonica type accessions. It is suggested that the varietal differentiation into the Indica and Japonica types is not likely to be related to genetic variations of floral traits. We clarified the differences in floral traits between annual and perennial ecotypes of wild rice, between cultivated rice and wild rice, and between the Indica and Japonica type cultivars, and discussed the relationship between genetic variations of floral traits and domestication and varietal differentiation in rice.

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“…Annual wild rice grows widely in tropical areas and occurs in shallow and temporary swamps as well as in disturbed habitats, while perennial wild rice grows in deeperwater fields and/or stable habitats (Morishima et al 1984, Oka 1988. Disturbance was defined as follows; mechanisms which limit the plant biomass by causing its partial or total destruction (Grime 1979).…”

Section: Introductionmentioning

confidence: 99%

“…Disturbance was defined as follows; mechanisms which limit the plant biomass by causing its partial or total destruction (Grime 1979). Annual wild rice can grow near paddy fields where the habitats are markedly disturbed due to trampling and/or grazing (Morishima et al 1984, Oka 1988. A conspicuous feature of an annual type of wild rice is represented by its adaptability to disturbed habitats, and its short stature with many tillers and a prostrate growth habit (Sano and Morishima 1982, Morishima et al 1984, Oka 1988.…”

Section: Introductionmentioning

confidence: 99%

“…Annual wild rice can grow near paddy fields where the habitats are markedly disturbed due to trampling and/or grazing (Morishima et al 1984, Oka 1988. A conspicuous feature of an annual type of wild rice is represented by its adaptability to disturbed habitats, and its short stature with many tillers and a prostrate growth habit (Sano and Morishima 1982, Morishima et al 1984, Oka 1988. The architecture of plants should display ecological significances for the gathering and allocation of resources, breeding systems, interactions with biotic and abiotic environmental factors, etc.…”

Section: Introductionmentioning

confidence: 99%

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A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice

et al. 2007

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The wild progenitor (Oryza rufipogon) of Asian rice (Oryza sativa) shows a wide range of variations in lifehistory traits, forming an annual-perennial continuum. A conspicuous feature of an annual type of wild rice is represented by its adaptability to disturbed habitats, and its short stature with many tillers and a prostrate growth habit. The present study was carried out to examine the genetic differentiation between wild annual and cultivated (Japonica type) rice strains by quantitative trait locus (QTL) analysis. In total, 20 adaptive and/ or domestication-related traits were evaluated in recombinant inbred lines (RILs). A total of 28 putative QTLs were detected across the genome. Six QTLs responsible for plant architecture were located on the short arm of chromosome 7. The near-isogenic line with the region containing the QTL cluster confirmed that the QTLs exerted a significant effect on the plant architecture in the genetic background of cultivated rice. A similar QTL cluster was also found in another annual strain of a different origin, suggesting that the QTL cluster might be predominant in annual wild rice. Furthermore, a QTL for tolerance to disturbance (simulated trampling) was detected within the region of the cluster on chromosome 7. These results are discussed in relation to their ecological significance in wild annuals of rice.

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Differentiation of perennial and annual types due to habitat conditions in the wild riceOryza perennis

Cited by 80 publications

References 24 publications

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

Variations of Floral Traits in Asian Cultivated Rice (Oryza sativa L.) and its Wild Relatives (O. rufipogon Griff.)

A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice

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