Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

Qiu, Jie; Zhu, Jinwen; Fu, Fei; Ye, Chu-Yu; Wang, Weidi; Mao, Linfeng; Lin, Zhangxiang; Chen, Li; Zhang, Haiqiang; Guo, Longbiao; Qiang, Shen; Lu, Yongliang; Fan, Longjiang

doi:10.1007/s00425-014-2159-2

Cited by 52 publications

(66 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…According to De-Wet and Harlan (1975), weedy rice originated from the selection and adaptation of wild rice to agricultural habitats. In regions where no wild rice has been grown, weedy rice may instead originate from cultivated rice through de-domestication with adaptive mutations and the accumulation of beneficial mutants (Ishikawa et al 2005;Cao et al 2006;Reagon et al 2011;Thurber et al 2010;He et al 2014;Qiu et al 2014;Lu et al 2016;Li et al 2017;Qiu et al 2017). In the case of Brazil and Italy, where no wild Oryza types are indigenous, contamination of seed stocks with wild Oryza species has been proposed as a source of weedy rice (Carney 2004;Grimm 2014).…”

Section: Origin and Evolutionmentioning

confidence: 99%

Weedy rice in sustainable rice production. A review

Nadir

Xiong

Zhu

et al. 2017

Agron. Sustain. Dev.

View full text Add to dashboard Cite

Weedy rice refers to the unwanted plants of the genus Oryza that have some undesirable agronomic traits and pose a major threat to sustainable rice production worldwide. Widespread adoption of direct seeded rice and hybridization or gene flow between cultivated rice and their wild relatives has resulted in the creation and dissemination of weedy rice. Currently, weedy rice (Oryza sativa f. spontanea) has become one of the most common weeds infesting rice fields worldwide. In this paper, we review the biology, physiology, evolution, and genetic features of weedy rice. We also discuss the major obstacles in weedy rice management, including high diversity of weedy rice, ecological impacts of gene flow on weedy rice, changing climate, and weedy rice management. We then present a framework for the sustainable management and utilization of weedy rice. Our main emphasis is to explore the reservoir of natural variations in weedy germplasm and to utilize them for crop improvement. This review outlines some of the latest biotechnological tools to dissect the genetic backgrounds of several favorable traits of weedy rice that may prove beneficial for breeding and evolutionary studies on cultivated rice. We suggest that by merging the disciplines of genomics, breeding, and weed management, we can achieve the goal of sustainable rice production.

show abstract

Section: Origin and Evolutionmentioning

confidence: 99%

Weedy rice in sustainable rice production. A review

Nadir

Xiong

Zhu

et al. 2017

Agron. Sustain. Dev.

View full text Add to dashboard Cite

show abstract

“…Although multiple origins for weedy rice have been proposed, currently de-domestication from cultivated varieties has been acknowledged as one of the main routes for the origin of weedy rice all over the world891011121314. This kind of weed is also one of the plants identified by Ellstrand et al 3.…”

mentioning

confidence: 99%

“…Several previous studies have provided helpful insights into this process910111213141921. For instance, Reagon et al 19.…”

mentioning

confidence: 99%

Genomic variation associated with local adaptation of weedy rice during de-domestication

et al. 2017

Self Cite

View full text Add to dashboard Cite

De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication.

show abstract

“…), harbors characteristics of undomesticated Oryza species, including seed dispersal mechanisms and seed dormancy. It also possesses traits of domesticated rice, such as rapid growth, and resembles domesticated rice during the seedling stage, which promotes its invasiveness in the agroecosystem2627. The origin of weedy rice has long been discussed, which has led to several hypotheses, including the ongoing selection and adaptation of wild rice2829, hybridization between cultivated rice and its progenitor type30, hybridization between indica - japonica 26, ongoing and multidirectional hybridization between weedy rice and cultivated types, and among weedy types31.…”

mentioning

confidence: 99%

“…It also possesses traits of domesticated rice, such as rapid growth, and resembles domesticated rice during the seedling stage, which promotes its invasiveness in the agroecosystem2627. The origin of weedy rice has long been discussed, which has led to several hypotheses, including the ongoing selection and adaptation of wild rice2829, hybridization between cultivated rice and its progenitor type30, hybridization between indica - japonica 26, ongoing and multidirectional hybridization between weedy rice and cultivated types, and among weedy types31. Simple sequence repeats based analyses of the genetic diversity of weedy rice populations from China suggested that weedy rice most likely originated from local indica or japonica varieties2732.…”

mentioning

confidence: 99%

Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

Tong

Park

2017

Sci Rep

View full text Add to dashboard Cite

Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.

show abstract

Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

Cited by 52 publications

References 46 publications

Weedy rice in sustainable rice production. A review

Weedy rice in sustainable rice production. A review

Genomic variation associated with local adaptation of weedy rice during de-domestication

Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

Contact Info

Product

Resources

About