Genetic diversity of weedy red rice (<i>Oryza sativa</i>) in Arkansas, USA

Shivrain, Vinod K.; Burgos, Nilda R.; Agrama, H. A.; Lawton‐Rauh, Amy; Lu, Bao‐Rong; Sales, M. A.; Boyett, V. A.; Gealy, David R.; Moldenhauer, K. A. K.

doi:10.1111/j.1365-3180.2010.00780.x

Cited by 67 publications

(89 citation statements)

References 37 publications

(63 reference statements)

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“…However, a number of valuable genes harboured in weedy rice lines such as disease resistance may seep into cultivated rice through natural hybridization and introgression (Chen et al 2004). In this study, weedy rice lines showed a relatively higher degree of GD value, similar to the results of Shivrain et al (2010). The introduced lines used here showed the highest level of GD, possibly due to their diverse geographic origins.…”

Section: Discussionsupporting

confidence: 86%

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

Wang¹,

Kwon²,

Park³

2013

Electron. J. Biotechnol.

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Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat markers. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the accessions. A total of 105 accessions (79.5%) showed a clear relationship to each cluster, while the remaining 27 accessions (20.5%) were categorized as admixtures. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide association mapping. The mean r 2 value for all intrachromosomal loci pairs was 0.1286. The LD between linked markers decreased with the genetic distance between pairs of linked loci. Conclusions: These results will provide an effective aid for future allele mining, association genetics, mapping and cloning gene(s), germplasm conservation, and improvement programs.

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Section: Discussionsupporting

confidence: 86%

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

Wang¹,

Kwon²,

Park³

2013

Electron. J. Biotechnol.

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“…Whereas hull color was among the morphological traits most strongly correlated with population structure in historical U.S. weedy rice Shivrain et al, 2010a), no clear correlation between hull color and the population structure of HR weedy rice was observed (Fig. 6).…”

Section: Correlations Between Population Structure and Phenotype In Hmentioning

confidence: 90%

The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice

et al. 2014

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The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

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“…The U.S. red rice populations are genetically diverse and can be divided phenotypically and evolutionarily into two major groups: strawhull (SH; awnless) and blackhull (BH; awned) (Gealy et al 2009(Gealy et al , 2012Londo and Schaal 2007;Reagon et al 2010;Shivrain et al 2010a).…”

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confidence: 99%

Outcrossing Potential between U.S. Blackhull Red Rice and Indica Rice Cultivars

et al. 2015

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Weedy red rice is a major weed pest of rice in the southern United States. Outcrossing between red rice and commercial tropical japonica rice cultivars has resulted in new weed biotypes that further hinder the effectiveness of weed management. In recent years, indica rice has been used increasingly as a germplasm source for breeding and for reduced-input systems in the United States, but little is known about its outcrossing potential with U.S. weedy red rice biotypes. In a 2-yr study, simple sequence repeat marker analysis was used to show that blackhull (BH) red rice (PI 653424) outcrossing to four, late-maturing indica cultivars averaged 0.0086% and ranged from 0.002% for ‘TeQing’ to 0.0173% for ‘4484’ (PI 615022). Rates of outcrossing to a tropical japonica cultivar standard, ‘Kaybonnet’ (0.032%), were substantially greater than for the indica cultivars. These differences in outcrossing were due largely to synchronization of flowering times between rice and red rice, with Kaybonnet and TeQing exhibiting the greatest and least synchronization, respectively. Outcrossing rates also may have been affected by rice–red rice flower density differences within the rice plots. Outcrossing from cultivated rice to the red rice (as pollen recipient), which was taller than all rice cultivars, was undetectable in these studies, and environmental conditions (e.g., temperature, humidity, solar radiation, and rainfall) were not strongly correlated with the outcrossing rates observed. Grain yields of the original BH red rice line were greatest in the Kaybonnet plots, demonstrating that the indica cultivars were superior competitors against this weed. Collectively, these results suggest that red rice biotypes that flower synchronously with rice cultivars are a potential source of pollen for outcrossing and gene flow in rice fields in the southern United States.

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Genetic diversity of weedy red rice (Oryza sativa) in Arkansas, USA

Cited by 67 publications

References 37 publications

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice

Outcrossing Potential between U.S. Blackhull Red Rice and Indica Rice Cultivars

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