Enhanced photosynthesis endows seedling growth vigour contributing to the competitive dominance of weedy rice over cultivated rice

AbstractWeedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

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Weedy Rice Diversity in Southern Brazil

Weed Science ◽

10.1017/wsc.2021.23 ◽

2021 ◽

pp. 1-37

Author(s):

Leonard Bonilla Piveta ◽

José Alberto Noldin ◽

Nilda Roma-Burgos ◽

Vívian Ebeling Viana ◽

Lariza Benedetti ◽

...

Keyword(s):

Oryza Sativa ◽

Flowering Time ◽

Weed Management ◽

Phenotypic Diversity ◽

Weedy Rice ◽

Phenotypic Traits ◽

Southern Brazil ◽

Variable Response ◽

Cultivated Rice ◽

Flowering Synchrony

Abstract Weedy rice (Oryza sativa L.) is one of the most troublesome weeds affecting rice (Oryza sativa L.) production in many countries. Weedy rice control is difficult in rice fields because the weed and crop are phenotypically and morphologically similar. Weedy rice can be a source of genetic diversity to cultivated rice. Thus, this study aimed to characterize the morphological diversity of weedy rice in Southern Brazil. Qualitative and quantitative traits of 249 accessions from eight rice growing mesoregions in Rio Grande do Sul (RS) and Santa Catarina (SC) states were analyzed. For each accession, 24 morphological descriptors (14 qualitative and 10 quantitative) were evaluated. All the 249 accessions from RS and SC are of indica lineage. Considering all the phenotypic traits evaluated, the accessions separated into 14 distinct groups. One of the largest groups consisted of plants that were predominantly tall and with green leaves, intermediate shattering, and variable in flowering time. Distinct subgroups exist within larger clusters, showing discernable phenotypic diversity within the main clusters. The variability in flowering time was high (77 to 110 d after emergence), indicating high potential for flowering synchrony with rice cultivars and, consequently, gene flow. This indicates the need to remove escapes when planting herbicide-resistant rice. Thus, weedy rice populations in Southern Brazil are highly diverse and this diversity could result in variable response to weed management.

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Explore the genetics of weedy traits using rice 3K database

Botanical Studies ◽

10.1186/s40529-020-00309-y ◽

2021 ◽

Vol 62 (1) ◽

Author(s):

Yu-Lan Lin ◽

Dong-Hong Wu ◽

Cheng-Chieh Wu ◽

Yung-Fen Huang

Keyword(s):

Seed Coat ◽

Coat Color ◽

Rice Genome ◽

Genome Project ◽

Weedy Rice ◽

Seed Coat Color ◽

Allele Mining ◽

Cultivated Rice ◽

Population Structure Analysis ◽

Public Data

Abstract Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

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Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice

Gene ◽

10.1016/j.gene.2018.10.066 ◽

2019 ◽

Vol 685 ◽

pp. 96-105 ◽

Cited By ~ 11

Author(s):

Shixin Guan ◽

Quan Xu ◽

Dianrong Ma ◽

Wenzhong Zhang ◽

Zhengjin Xu ◽

...

Keyword(s):

Cold Stress ◽

Weedy Rice ◽

Cultivated Rice

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Snorkeling Strategy: Tolerance to Flooding in Rice and Potential Application for Weed Management

Genes ◽

10.3390/genes11090975 ◽

2020 ◽

Vol 11 (9) ◽

pp. 975

Author(s):

Tiago Edu Kaspary ◽

Nilda Roma-Burgos ◽

Aldo Merotto

Keyword(s):

Weed Control ◽

Weed Management ◽

Potential Application ◽

Genetic Manipulation ◽

Weedy Rice ◽

Flood Tolerance ◽

Flooding Tolerance ◽

Cultivated Rice ◽

Tolerance Mechanisms ◽

Crop Models

Flooding is an important strategy for weed control in paddy rice fields. However, terrestrial weeds had evolved mechanisms of tolerance to flooding, resulting in new ‘snorkeling’ ecotypes. The aim of this review is to discuss the mechanisms of flooding tolerance in cultivated and weedy rice at different plant stages and the putative utility of this trait for weed management. Knowledge about flooding tolerance is derived primarily from crop models, mainly rice. The rice model informs us about the possible flooding tolerance mechanisms in weedy rice, Echinochloa species, and other weeds. During germination, the gene related to carbohydrate mobilization and energy intake (RAmy3D), and genes involved in metabolism maintenance under anoxia (ADH, PDC, and OsB12D1) are the most important for flooding tolerance. Flooding tolerance during emergence involved responses promoted by ethylene and induction of RAmy3D, ADH, PDC, and OsB12D1. Plant species tolerant to complete submersion also employ escape strategies or the ability to become quiescent during the submergence period. In weedy rice, the expression of PDC1, SUS3, and SUB1 genes is not directly related to flooding tolerance, contrary to what was learned in cultivated rice. Mitigation of flooding tolerance in weeds could be achieved with biotechnological approaches and genetic manipulation of flood tolerance genes through RNAi and transposons, providing a potential new tool for weed management.

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Effect of rice establishment methods on weedy rice (Oryza sativa L.) infestation and grain yield of cultivated rice (O. sativa L.) in Sri Lanka

Crop Protection ◽

10.1016/j.cropro.2013.09.008 ◽

2014 ◽

Vol 55 ◽

pp. 42-49 ◽

Cited By ~ 12

Author(s):

Bhagirath S. Chauhan ◽

Anuruddhika S.K. Abeysekera ◽

Manoja S. Wickramarathe ◽

Sakinda D. Kulatunga ◽

Upali B. Wickrama

Keyword(s):

Oryza Sativa ◽

Sri Lanka ◽

Grain Yield ◽

Oryza Sativa L ◽

Weedy Rice ◽

Cultivated Rice

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Phenotypic diversity of weedy rice (Oryza sativa f. spontanea) biotypes found in California and implications for management

Weed Science ◽

10.1017/wsc.2020.43 ◽

2020 ◽

Vol 68 (5) ◽

pp. 485-495

Author(s):

Elizabeth Karn ◽

Teresa De Leon ◽

Luis Espino ◽

Kassim Al-Khatib ◽

Whitney Brim-DeForest

Keyword(s):

Oryza Sativa ◽

Chlorophyll Content ◽

Plant Height ◽

Wild Rice ◽

Early Growth ◽

Weedy Rice ◽

Phenotypic Traits ◽

Growth Stages ◽

Cultivated Rice ◽

Leaf Pubescence

AbstractWeedy rice (Oryza sativa f. spontanea Rosh.) is an emerging weed of California rice (Oryza sativa L.) that has potential to cause large yield losses. Early detection of weedy rice in the field is ideal to effectively control and prevent the spread of this weed. However, it is difficult to differentiate weedy rice from cultivated rice during early growth stages due to the close genetic and phenotypic relatedness of cultivated rice and weedy rice. The objective of this study is to examine phenotypic variation in weedy rice biotypes from California and to identify traits that could be used to visually identify weedy rice infestations at early growth stages for effective management. Greenhouse experiments were conducted in 2017 and 2018 using five phenotypically distinct biotypes of weedy rice found in California, along with diverse cultivated, weedy, and wild rice types in a randomized complete block design. We measured variation for 13 phenotypic traits associated with weedy rice and conducted principal component analysis and factor analysis to identify important weedy traits. Most weedy rice individuals within a biotype clustered together by phenotypic similarity. Pericarp color, hull color, chlorophyll content, grain length, plant height, leaf pubescence, collar color, and leaf sheath color account for most of the observed variation. California weedy rice biotypes are phenotypically distinct from wild rice and from weedy rice from the southern United States in their combinations of seed phenotypes and vegetative characteristics. In comparison with the locally grown temperate japonica cultivars, California weedy rice tends to be taller, with lower chlorophyll content and a red pericarp. Weedy rice biotypes vary in seed shattering and seed dormancy. For weedy rice management, plant height and chlorophyll content are distinct traits that could be used to differentiate weedy rice from the majority of cultivated rice varieties in California during vegetative stages of rice growth.

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