Evolving insights on weedy rice

Wedger, Marshall J.; Olsen, Kenneth M.

doi:10.1016/j.egg.2018.03.005

Cited by 18 publications

(21 citation statements)

References 24 publications

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“…There is a substantial difference in the de-domestication frequencies of rice and wheat. Weedy rice has been detected worldwide (Wedger & Olsen, 2018), and evolved repeatedly and independently from different cultivated rice varieties (Wedger & Olsen, 2018). Hexaploid wheat has been historically one of the most important and widely cultivated crops worldwide.…”

Section: Comparison Of the De-domestications Of Rice And Wheatmentioning

confidence: 99%

“…Studying de-domestication may be useful for characterizing rapid convergent evolution (Xia et al, 2011;Vigueira et al, 2013Vigueira et al, , 2019, and it is also relevant for elucidating the origins of weeds, which are a considerable problem in agriculture (Ellstrand et al, 2010;Stewart, 2017). Weedy rice, which evolved mainly from cultivated rice through de-domestication (Ellstrand et al, 2010;Wedger & Olsen, 2018), has become a worldwide problem in rice fields (Wedger & Olsen, 2018). Studies on weedy rice have advanced our understanding of crop de-domestication.…”

Section: Introductionmentioning

confidence: 99%

“…Recent genetic and genomic studies (He et al, 2017;Li et al, 2017;Qiu et al, 2017;Vigueira et al, 2019) have provided in-depth genome-level insights into the evolution of weedy rice. The diverse weedy rice lines have convergently evolved phenotypes through independent genetic mechanisms (Li et al, 2017;Wedger & Olsen, 2018;Wedger et al, 2019). The key evolutionary process requires only a few genetic changes for the emergence of wild-like traits (Li et al, 2017), and generally involves novel genes rather than the mutational reversion of domestication genes Thurber et al, 2010;Xia et al, 2011;Qi et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

et al. 2019

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Summary De‐domestication is a unique evolutionary process during which crops re‐acquire wild‐like traits to survive and persist in agricultural fields without the need for human cultivation. The re‐acquisition of seed dispersal mechanisms is crucial for crop de‐domestication. Common wheat is an important cereal crop worldwide. Tibetan semi‐wild wheat is a potential de‐domesticated common wheat subspecies. However, the crucial genes responsible for its brittle rachis trait have not been identified. Genetic mapping, functional analyses and phylogenetic analyses were completed to identify the gene associated with Qbr.sau‐5A, which is a major locus for the brittle rachis trait of Tibetan semi‐wild wheat. The cloned Qbr.sau‐5A gene is a new Q allele (Qt) with a 161‐bp transposon insertion in exon 5. Although Qt is expressed normally, its encoded peptide lacks some key features of the APETALA2 family. The abnormal functions of Qt in developing wheat spikes result in brittle rachises. Phylogenetic and genotyping analyses confirmed that Qt originated from Q in common wheat and is naturally distributed only in Tibetan semi‐wild wheat populations. The identification of Qt provides new evidence regarding the origin of Tibetan semi‐wild wheat, and new insights into the re‐acquisition of wild traits during crop de‐domestication.

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Section: Comparison Of the De-domestications Of Rice And Wheatmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

et al. 2019

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“…This agricultural weed is a feral (de‐domesticated) descendant of the genomic model crop species rice ( O. sativa ). Weedy rice has evolved multiple times independently from different domesticated rice varieties around the world (Federici et al ., ; Cao et al ., ; Londo & Schaal, ; Grimm et al ., ; Wedger & Olsen, ). The process of weedy rice evolution is associated with the repeated emergence of suites of adaptations that distinguish the weed from its domesticated ancestor and allow it to aggressively outcompete rice in the field.…”

Section: Introductionmentioning

confidence: 99%

Convergent evolution of root system architecture in two independently evolved lineages of weedy rice

2019

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Summary Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associated RSA traits and the extent to which they evolve through shared or different genetic mechanisms. We characterised 98 two‐dimensional and three‐dimensional RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains. The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a ‘weedy’ RSA phenotype. Notably, comparative QTL mapping revealed little evidence for shared underlying genetic mechanisms. Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy.

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“…), also known as red rice, is a major problematic weed of rice agriculture in many regions (Wedger & Olsen, 2018; Figure 1). ), also known as red rice, is a major problematic weed of rice agriculture in many regions (Wedger & Olsen, 2018; Figure 1).…”

mentioning

confidence: 99%

Genetic variation and possible origins of weedy rice found in California

Leon

Karn²,

Al‐Khatib

et al. 2019

Ecology and Evolution

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Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.

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Evolving insights on weedy rice

Cited by 18 publications

References 24 publications

Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

Convergent evolution of root system architecture in two independently evolved lineages of weedy rice

Genetic variation and possible origins of weedy rice found in California

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