A route to de novo domestication of wild allotetraploid rice

Yu, Hong; Lin, Tao; Meng, Xiangbing; Du, Huilong; Zhang, Jingkun; Liu, Guifu; Chen, Mingjiang; Jing, Yanhui; Kou, Liquan; Li, Xiuxiu; Gao, Qiang; Liang, Yan; Liu, Xiangdong; Fan, Zhilan; Liang, Yuntao; Cheng, Zhukuan; Chen, Mingsheng; Tian, Zhixi; Wang, Yonghong; Chu, Chengcai; Zuo, Jianru; Wan, Jianmin; Qian, Qian; Han, Bin; Zuccolo, Andrea; Wing, Rod A.; Gao, Caixia; Liang, Chengzhi; Li, Jiayang

doi:10.1016/j.cell.2021.01.013

Cited by 325 publications

(213 citation statements)

References 134 publications

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“…In addition, it is the most widely grown cool-season annual forage species, representing a major source of forage for livestock globally 3 . Polyploid plants often have significant advantages concerning biomass production, vigorousness, and robust adaptation to environmental changes and contribute to the emergence of important agronomic traits in food crops [4][5][6][7][8] . Therefore, crop polyploidization may play an important role in next-generation crop improvement aimed at overcoming food security challenges 8 .…”

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confidence: 99%

“…Polyploid plants often have significant advantages concerning biomass production, vigorousness, and robust adaptation to environmental changes and contribute to the emergence of important agronomic traits in food crops [4][5][6][7][8] . Therefore, crop polyploidization may play an important role in next-generation crop improvement aimed at overcoming food security challenges 8 . Many commercially important crops have been sequenced and assembled, which has improved the understanding of crop evolutionary history and the development of efficient approaches for the selection of important traits 9 .…”

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confidence: 99%

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Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Peng

Yan

Guo

et al. 2021

Preprint

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Common oat (Avena sativa) is one of the most important cereal crops serving as a valuable source of forage and human food. While reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich, polyploid genome. By using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated the first reference-quality genome assembly of hulless common oat with a contig N50 of 93 Mb. We also assembled the genomes of diploid and tetraploid Avena ancestors, which enabled us to identify oat subgenome, large-scale structural rearrangements, and preferential gene loss in the C subgenome after hexaploidization. Phylogenomic analyses of cereal crops indicated that the oat lineage descended before wheat, offering oat as a unique window into the early evolution of polyploid plants. The origin and evolution of hexaploid oat is deduced from whole-genome sequencing, plastid genome and transcriptomes assemblies of numerous Avena species. The high-quality reference genomes of Avena species with different ploidies and the studies of their polyploidization history will facilitate the full use of crop gene resources and provide a reference for the molecular mechanisms underlying the polyploidization of higher plants, helping us to overcome food security challenges.

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confidence: 99%

mentioning

confidence: 99%

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Peng

Yan

Guo

et al. 2021

Preprint

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“…Distant hybridization and polyploidization are important trends in plant evolution, as well as important directions in crop evolution. Polyploid plants often have advantages in genome buffering, vigorousness, and robust adaptation to environmental changes [140,141]. The genome of rice is small and its DNA content is low.…”

Section: Discussionmentioning

confidence: 99%

A New Way of Rice Breeding: Polyploid Rice Breeding

Chen

Feng

Zhang

et al. 2021

Plants

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Polyploid rice, first discovered by Japanese scientist Eiiti Nakamori in 1933, has a history of nearly 90 years. In the following years, polyploid rice studies have mainly focused on innovations in breeding theory, induction technology and the creation of new germplasm, the analysis of agronomic traits and nutritional components, the study of gametophyte development and reproduction characteristics, DNA methylation modification and gene expression regulation, distant hybridization and utilization among subspecies, species and genomes. In recent years, PMeS lines and neo-tetraploid rice lines with stable high seed setting rate characteristics have been successively selected, breaking through the bottleneck of low seed setting rate of polyploid rice. Following, a series of theoretical and applied studies on high seed setting rate tetraploid rice were carried out. This has pushed research on polyploid rice to a new stage, opening new prospects for polyploid rice breeding.

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“…The importance of such genes is critical in understanding how de novo domestication and their further use in plant breeding can be achieved from wild Oryza varieties. This concept was demonstrated even in polyploid O. alta (CCDD) by (Yu et al, 2021a), targeting SD1, GS3, IPA1, Ghd7, Gn1a, Wx, Bh4, TAC1, An-1 homologs, as well as African landraces of Oryza glaberrima by disrupting the HTD1 (O. sativa Os04g0550600), GS3 (O. sativa Os03g0407400), GW2 (O. sativa Os01g0197700) and GN1A (O. sativa Os02g0244100) genes (Lacchini et al, 2020). In terms of plant breeding, having access to nondomesticated, more genetically diverse rice species that better adapt to stress conditions, such as African landraces O. glaberrima, O. barthii, O. meridionalis (AA), Australian landraces O. longistaminata (AA), O. australiensis (EE), and Asian landraces O. ru pogon (AA) or Porteresia coarctata (O.coarctata) (KKLL), enables the potential of developing more sustainable rice crops (Reddy et al, 2017;Mammadov et al, 2018).…”

Section: Domestication Genesmentioning

confidence: 93%

Rice agronomic traits and variability induced by mutagenesis

Hernández-Soto¹,

Echeverría-Beirute²,

Abdelnour-Esquivel³

et al. 2021

Preprint

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Understanding agronomic traits at a genetic level enables the leveraging of this knowledge to produce crops that are more productive and resilient, have better quality and are adjusted for consumer preferences. In the last decade, rice has become a model to validate the function of specific genes, resulting in valuable but scattered information. Here, we aimed to identify particular genes in rice related to traits that can be targeted by different mutation techniques in the breeding of crops. We selected gain of function, misfunction, and specific mutations associated with phenotypes of agronomic interest. The review includes specific trait-related genes involved in domestication, stress, herbicide tolerance, pathogen resistance, grain number, quality, weight, plant structure, nitrogen use, and others. The information presented can be used for rice and crops with similar or homologous genes to breed crops that require improvement to achieve more sustainable production in challenging farming conditions.

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A route to de novo domestication of wild allotetraploid rice

Cited by 325 publications

References 134 publications

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

A New Way of Rice Breeding: Polyploid Rice Breeding

Rice agronomic traits and variability induced by mutagenesis

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