Origins and population genetics of weedy red rice in the USA

Londo, Jason P.; Schaal, Barbara A.

doi:10.1111/j.1365-294x.2007.03489.x

Cited by 183 publications

(260 citation statements)

References 40 publications

(77 reference statements)

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“…Resistant Pi-ta was found only in indica, weedy rice, japonica cultivars carrying the indicaderived Pi-ta region and O. rufipogon, suggesting that resistant Pi-ta did not originate from japonica. The Pi-ta variants in H5 and H6 were found only in japonica accessions, while H2 and H3 were found only in indica (Figure 2), consistent with a previous study (Londo and Schaal 2007). The Pi-ta variant containing Ala-918 (PT1) separates the resistant Pi-ta variant from other variants in both O. sativa and O. rufipogon.…”

Section: Discussionsupporting

confidence: 90%

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Evolutionary Dynamics of the Genomic Region Around the Blast Resistance Gene Pi-ta in AA Genome Oryza Species

et al. 2009

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The race-specific resistance gene Pi-ta has been effectively used to control blast disease, one of the most destructive plant diseases worldwide. A single amino acid change at the 918 position of the Pi-ta protein was known to determine resistance specificity. To understand the evolutionary dynamics present, we examined sequences of the Pi-ta locus and its flanking regions in 159 accessions composed of seven AA genome Oryza species: O. sativa, O. rufipogon, O. nivara, O. meridionalis, O. glaberrima, O. barthii, and O. glumaepatula. A 3364-bp fragment encoding a predicted transposon was found in the proximity of the Pi-ta promoter region associated with the resistance phenotype. Haplotype network analysis with 33 newly identified Pi-ta haplotypes and 18 newly identified Pi-ta protein variants demonstrated the evolutionary relationships of Pi-ta haplotypes between O. sativa and O. rufipogon. In O. rufipogon, the recent directional selection was found in the Pi-ta region, while significant deviation from neutral evolution was not found in all O. sativa groups. Results of sequence variation in flanking regions around Pi-ta in O. sativa suggest that the size of the resistant Pi-ta introgressed block was at least 5.4 Mb in all elite resistant cultivars but not in the cultivars without Pi-ta. These findings demonstrate that the Pi-ta region with transposon and additional plant modifiers has evolved under an extensive selection pressure during crop breeding.

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Section: Discussionsupporting

confidence: 90%

“…The divergence of indica and japonica subgroups in O. sativa was predicted to be caused by two independent domestications from geographically divergent O. rufipogon populations (Londo and Schaal 2007). The Pi-ta haplotypes of indica or japonica origin were identified in this study (Figure 2).…”

Section: Discussionmentioning

confidence: 84%

Evolutionary Dynamics of the Genomic Region Around the Blast Resistance Gene Pi-ta in AA Genome Oryza Species

et al. 2009

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“…However, weedy rice is now common in rice growing regions in the United States and is one of the major weeds limiting rice production (Ziska et al 2015). Genetic analysis has shown that American weedy rice population arose independently from indica and aus varieties (Londo and Schaal 2007). These observations indicate that rice could frequently revert to the wild state in domestication traits.…”

Section: Discussionmentioning

confidence: 99%

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

et al. 2017

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The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice, O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen-and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow from aus, indica, and japonica varieties into colocated wild rice. We also show that admixture from aus and indica is more recent than gene flow from japonica, possibly consistent with an earlier spread of japonica varieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.

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“…Study aimed at characterizing phenotypically the different types of red rice in the State of Arkansas found that the blackhull showed higher H compared to strawhull (Shivrain et al, 2010). However, it is noteworthy that the blackhull has higher genetic diversity compared to strawhull due to the greater proximity with wild rice, which has less selection pressure imposed by man and therefore less reduction in genetic diversity (Londo & Schaal, 2007), which could partly explain the lowest H observed for blackhull plants in the experiment.…”

Section: Resultsmentioning

confidence: 89%

“…indica and O. rufipogon Griff., while blackhull comes from O. sativa indica var. Aus and O. rufipogon (Londo & Schaal, 2007).…”

Section: Introductionmentioning

confidence: 99%

Relative competitive ability of rice with strawhull and blackhull red rice biotypes

Nohatto¹,

Agostinetto²,

Gealy³

et al. 2016

Científica

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The weed interference varies on several factors, especially the composition of the weed community and the ability to compete with the culture. Thus, this study aimed at evaluating the competitive ability of rice and different populations of red rice (strawhull or blackhull). The experiments were conducted in greenhouse from January to August 2013, at United States Department of Agriculture, Dale Bumpers National Rice Research Center (USDA/DBNRRC) in the city of Stuttgart, Arkansas. The experimental design was completely randomized with four replications. Treatments consisted of rice or red rice plant ratios (100:0, 75:25, 50:50, 25:75 and 0:100%). Variables evaluated included: shoot dry weight, leaf area and plant height. Results show that strawhull or blackhull red rice biotypes have superior competitive ability than rice, CL 142 AR. Overall, the blackhull red rice biotype has superior competitive ability compared to strawhull one. For rice, the interspecific competition dominates, while for red rice biotypes the intraspecific competition was more harmful.Additional keywords: interference; Oryza sativa; replacement series. ResumoA interferência de plantas daninhas varia em função de vários fatores, destacando-se a composição da comunidade infestante e a capacidade dessa de competir com a cultura. Diante disso, o objetivo do trabalho foi avaliar a habilidade competitiva entre arroz e diferentes populações de arroz-vermelho (strawhull ou blackhull). Os experimentos foram conduzidos em casa de vegetação, no período de janeiro a agosto de 2013, no Departamento de Agricultura dos Estados Unidos, Dale Bumpers National Rice Research Center (USDA/DBNRRC), na cidade de Stuttgart, Arkansas. O delineamento experimental utilizado foi o completamente casualizado, com quatro repetições. Os tratamentos consistiram nas proporções de plantas de arroz ou arrozvermelho (100:0; 75:25; 50:50; 25:75 e 0:100%). As variáveis avaliadas foram: massa da matéria seca da parte aérea, área foliar e estatura de planta. Os resultados obtidos evidenciam que os biótipos de arroz-vermelho strawhull ou blackhull apresentam habilidade competitiva superior ao arroz, cultivar CL 142 AR, enquanto, o biótipo de arroz-vermelho blackhull, em geral, apresenta superioridade competitiva comparada ao strawhull. Para o arroz, a competição interespecífica predomina, enquanto para os biótipos de arroz-vermelho a competição intraespecífica foi mais prejudicial.Palavras-chave adicionais: interferência; Oryza sativa; série de substituição.

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Origins and population genetics of weedy red rice in the USA

Cited by 183 publications

References 40 publications

Evolutionary Dynamics of the Genomic Region Around the Blast Resistance Gene Pi-ta in AA Genome Oryza Species

Evolutionary Dynamics of the Genomic Region Around the Blast Resistance Gene Pi-ta in AA Genome Oryza Species

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

Relative competitive ability of rice with strawhull and blackhull red rice biotypes

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