Assessing the genetic structure of Oryza glumaepatula populations with isozyme markers

Veasey, Elizabeth Ann; Cardin, Daruska; Silva, Rainério Meireles; Bressan, Eduardo de Andrade; Vencovsky, Roland

doi:10.1590/s1516-89132008000500001

Cited by 10 publications

(15 citation statements)

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“…The Colombian populations we studied did show some affiliation, but could nonetheless clearly be separated from each other in ordination space. Overall, our findings confirm the clear genetic differences in species pertaining to the CCDD genome observed by Aggarwal et al (Aggarwal et al 1996) and supported by others (Ge et al 1999; Zamora et al 2003; Veasey et al 2008a). …”

Section: Discussionsupporting

confidence: 91%

Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

Thomas

Tovar

Villafañe

et al. 2017

Rice

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BackgroundCrop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs.ResultsOur findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future.ConclusionsGiven (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian CWRs, effective in situ conservation might best be achieved through tailor-made management plans and exclusion of GM rice cultivation in areas holding the most genetically diverse CWR populations. This may be combined with assisted migration of populations to suitable areas where rice is unlikely to be cultivated under current and future climate conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0150-9) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 91%

Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

Thomas

Tovar

Villafañe

et al. 2017

Rice

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“…The higher interpopulational value found for the diploid populations (φ ST = 0.737) was indicative of a higher genetic structuring among populations, which could provide an explanation for the higher level of genetic spatial structure observed for O. glumaepatula populations. Comparable values of F ST were found for O. glumaepatula populations by other authors, such as F ST = 0.85 (Brondani et al, 2005) with SSR markers, F ST = 0.763 (Veasey et al, 2008a) with isozyme markers, although a lower F ST = 0.491 was reported by Karasawa et al (2007a) with SSR markers.…”

Section: Resultssupporting

confidence: 41%

“…The crude extract was then centrifuged at 18,000 x g for 20 min at 4ºC and 130 μL of the supernatant placed in 0.5 mL microtubes, diluted in 150 μL of a solution containing Tris-HCl pH 6.8 and Coomassie blue, the latter component indicating the protein migration in the gel. Electrophoresis was conducted according to Veasey et al (2008a).…”

Section: Methodsmentioning

confidence: 99%

“…To date, there are quite a few studies concerning the genetic structure of the diploid O. glumaepatula populations (Akimoto et al, 1998;Buso et al, 1998;Brondani et al, 2005;Karasawa et al, 2007a,b;Veasey et al, 2008a), but very little has yet been published on the genetic structure and variability of the tetraploid American species (Agrama and Eizenga, 2008;Arrieta-Espínoza et al, 2005;Quesada et al, 2002;Veasey et al, 2008b). The wild species represent an important genetic reservoir for rice plant breeding for the purpose of introgression of useful genes into the cultivated species O. sativa (Brondani et al, 2002;Eisenga et al, 2009;Multani et al, 2003;Yoon et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity of American wild rice species

Veasey¹,

Bressan²,

Zucchi³

et al. 2011

Sci. agric. (Piracicaba, Braz.)

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Studies on genetic diversity and genetic structure of natural populations are important in order to define strategies for in situ and ex situ conservation actions and for plant pre-breeding programs. Aiming to assess the genetic diversity and genetic structure of three wild American Oryza species with isozyme markers, 14 populations of the diploid O. glumaepatula (A gl A gl ), 11 populations of the tetraploid O. grandiglumis (CCDD) and five populations of the also tetraploid O. latifolia (CCDD) were studied. They were all originated from Rio Paraguay hydrographic basin and the Amazon. Four enzymes were used and they gave 40 polymorphic bands. The most polymorphic species was O. glumaepatula, followed by O. latifolia and O. grandiglumis. A cluster analysis with the Jaccard similarity coefficient separated the diploid from the two tetraploid species, and also the two tetraploid species. This separation was also evident on a scatter plot from a principal component analysis, suggesting that they should be treated as two separate species, although further studies are necessary to provide support for this affirmative. The AMOVA analyses showed a high intrapopulational variability for O. latifolia (67.6%) and O. grandiglumis (52.2%), when compared to their interpopulational variability (32.4% and 47.8%, respectively), which suggests the hypothesis of a higher degree of outcrossing events within these species. When studying the correlation between the Jaccard dissimilarity coefficient and geographic distances, a spatial genetic structure was observed for O. glumaepatula only. These results are important for defining strategies of both in situ and ex situ conservation.

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“…A população PG-3, originária da bacia hidrográfica do Rio Paraguai, em área do Pantanal Matogrossense, não foi classificada num grupo isolado das demais populações da Amazônia, como seria esperado pela maior distância geográfica e impossibilidade de haver fluxo gênico entre esta população e as da Amazônia, e pelas diferentes condições climáticas e ecológicas, o que também foi observado por Karasawa et al (2007). No entanto, esta separação foi nítida quando foram utilizados marcadores isoenzimáticos (Veasey et al 2008), tendo sido observadas freqüências alélicas diferenciadas em função dos dois biomas, com predominância de parte dos alelos no Pantanal e parte na Amazônia em dois locos isoenzimáticos.…”

Section: Discussionunclassified

Elevada diversidade genética interpopulacional em Oryza glumaepatula Steud. (Poaceae) avaliada com microssatélites

et al. 2007

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Microsatellite markers were used to characterize the genetic diversity within and among seven natural populations of Oryza glumaepaula. Six of these populations originated from the hydrographic basin of the Amazon and one from Rio Paraguay in the Pantanal Matogrossense. Using seven microsatellite loci, the following intrapopulation genetic diversity parameters were estimated on average: 1.98 alleles per locus, 56.2% polymorphic loci, H o = 0.026 and H e = 0.241. High interpopulational differentiation was noticed by examining Wright's fixation index and Slatkin's divergence parameter (F ST = 0.715 and R ST = 0.595, respectively), as well as a high level of total inbreeding (F IT = 0.963), greatly influenced by the mating system (F IS = 0.858). No population was in Hardy-Weinberg equilibrium, due to the prevailing autogamic mating behavior, as also indicated by the average apparent outcrossing rate observed: t a = 0.055. Consequently, among populations gene flow was practically absent, which has contributed to the high interpopulational genetic divergence. In general, very low or null outcrossing rates were found in the Amazonian populations. However, population PG-3 from Rio Paraguay, originated from Pantanal Matogrossense, showed a higher outcrossing rate (13.2%), indicating a mixed mating system with the predominance of self-fertilization. Since intrapopulation diversity was low, results indicate that sampling a large number of populations is the most appropriate strategy for the ex situ conservation of this species. For in situ conservation, taking in consideration the allelic richness, the following populations are indicated as priority: PG-3, TA-3, Marcadores microssatélites foram usados para caracterizar a diversidade genética entre e dentro de sete populações naturais de Oryza glumaepaula. Seis dessas populações são originárias da bacia hidrográfica da Amazônia e uma do rio Paraguai no Pantanal Matogrossense. Utilizando sete locos de microssatélites, observou-se diversidade genética intrapopulacional média de 1,98 alelos por loco, 56,2% de locos polimórficos, H o = 0,026 e H e = 0,241. Elevada diferenciação interpopulacional foi observada pelo índice de fixação de Wright e pelo parâmetro de divergência de Slatkin (F ST = 0,715 e R ST = 0,595, respectivamente), bem como elevado nível de endogamia total (F IT = 0,963), em grande parte influenciada pelo sistema reprodutivo (F IS = 0,858). Verificou-se que nenhuma população estava em equilíbrio de Hardy-Weinberg, devido ao predomínio da autofertilização, o que também pôde ser verificado pela taxa média aparente de cruzamentos: t a = 0,055. Consequentemente, o fluxo gênico entre populações foi praticamente nulo o que contribuiu para o elevado nível de divergência interpopulacional. De modo geral, as taxas de cruzamento foram muito baixas ou nulas nas populações da Amazônia. Entretanto, a população PG-3 do Rio Paraguai, originária do Pantanal Matogrossense, apresentou taxa de cruzamento mais elevada (13,2%), indicando sistema reprodutivo misto com predomínio de...

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Assessing the genetic structure of Oryza glumaepatula populations with isozyme markers

Abstract: ABSTRACT

Cited by 10 publications

References 26 publications

Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

Genetic diversity of American wild rice species

Elevada diversidade genética interpopulacional em Oryza glumaepatula Steud. (Poaceae) avaliada com microssatélites

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