Multiple domestications of Asian rice

Jing, Chun-Yan; Zhang, Fu-min; Wang, Xiuhua; Wang, M X; Zhou, Lian; Cai, Zhe; Han, Jing-Dan; Geng, Mu-Fan; Yu, Wenhao; Jiao, Zhongyi; Huang, Lei; Rong, Liu; Zheng, Xiaoming; Meng, Qinglin; Ren, Nanjie; Zhang, Hongxiang; Du, Yu-Su; Wang, Xin; Qiang, Cheng-Gen; Zou, Xinhui; Gaut, Brandon S.; Ge, Song

doi:10.1038/s41477-023-01476-z

Cited by 21 publications

(17 citation statements)

References 88 publications

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“…Furthermore, to explore the relationship between indica and japonica rice within Asian cultivated rice, we examined the introgression relationship between the indica and japonica subspecies in the analysis of 1,300 single-copy OGs. As in previous studies 20,22 , We found a large amount of contributing genetic material between the japonica and indica subpopulations (Fig. 2a,b) suggesting that genetic introgression between these two subspecies is very frequent through model hybrid rice breeding procedures.…”

Section: Analyses Of Hybridization Support Ancient Introgression From...supporting

confidence: 85%

“…Therefore, we speculate that there exists an unknown Asian wild rice ancestral species at the most common ancestor node of the aus and indica clades, so the actual divergence time(0.25 of this node is likely similar to that of the japonica rice in our study. In addition, the trend in genome-wide syntenic gene pair Ks distribution further corroborates that the age of two major subspecies origin is close to each other 10,20,22,85 . Concurrently, analyses of genes within the nucleotide low-diversity region revealed parallel domestication times for the indica and japonica subspecies, thereby confirming the conclusion of independent domestication.…”

Section: Discussionsupporting

confidence: 62%

“…Corroboratively, another study also proposed independent domestication of indica, japonica, and aus 10 . More recent research indicates that rice domestication likely began independently from different wild strains in various regions, followed by the continuous selection and exchange of beneficial alleles among different cultivated varietal groups 22 . The origin of cultivated rice remains a topic of considerable debate.…”

Section: Introductionmentioning

confidence: 99%

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The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice

Liu,

Yin,

et al. 2024

Preprint

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Unraveling evolutionary history and genomic basis of heterosis is fundamental for advancing rice productivity. We developed a genome-scale phylogeny of Oryzeae by coalescing 39,984 gene trees. Our analysis supports parallel, independent origins and nearly synchronous evolutionary trajectories leading to the subsequent domestication of indica and japonica, evidenced by molecular dating and synonymous substitution rates for syntenic and domestication-associated genes. Our survey of 1,383 gene duplications in ancestor of O. sativa uncovers their roles in vital biological processes, highlighting the significance in environmental adaptability. Additionally, we confirm the lack of hybridization event among subspecies ancestors through gene tree topology and D-statistical analyses. We generated 71.67 GB whole-genome sequencing data for five super-hybrid rice varieties and their progenitors, revealing differential positive selection and genetic exchanges between subspecies, essential for heterosis formation. Crucially, our study underscores the role of non-additive gene expression in heterosis, particularly in genes associated with DNA repair and recombination, which may confer resistance traits. Furthermore, eQTL and de novo mutation analyses identify key developmental and stress response genes, offering targets for enhancing heterosis in rice. Overall, our research reveals crucial insights into the genetics of rice domestication and heterosis, offering a genomic resource to improve rice's agricultural productivity.

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Section: Analyses Of Hybridization Support Ancient Introgression From...supporting

confidence: 85%

Section: Discussionsupporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

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The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice

Liu,

Yin,

et al. 2024

Preprint

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“…Comprehensive understanding of the genetic diversity of germplasms is crucial for the sustainability and improvement of crop-breeding. 8,16 The emergence of multi-omics data has substantially improved phylogenetic resolution within species (or species complexes) and 19 detected some disputed minor cultivar groups that deserve further in-depth exploration.…”

Section: Tracing Domestication History Of Key Cropsmentioning

confidence: 99%

“…27 While advanced sequencing technologies are improving resolution of genetic data, key limitations to understanding crop domestication remain due to common issues of inadequate sampling, misidentified accessions, and ineffective approaches. 19,22,23 Extensive global collaborations and in-depth exploration with bioinformatics technologies can overcome the above shortcomings and increase our understanding of crop domestication.…”

Section: Tracing Domestication History Of Key Cropsmentioning

confidence: 99%

Current progress and future prospects for understanding genetic diversity of seed plants in China

Xiong,

Zhao,

et al. 2024

Biological Diversity

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Genetic diversity represents the fundamental basis of biological variation within species, and is therefore the ultimate representation of biodiversity. Despite that all forms of diversity being defined by genomic differences, genetic diversity has received relatively less attention compared with species and ecosystem diversity. Here, we review recent literature and conclude that progress in understanding genetic diversity of seed plants, is strongly associated with advances in sequencing technology. We here present case studies to illustrate the application of genetic diversity for tracing crop domestication and delimiting species boundaries. Understanding genetic diversity is particularly critical for the field of conservation biology, and there is a clear shift to population‐level genetic studies to understand rare species. We then document additional factors that potentially influence genetic diversity, including climate change, habitat fragmentation, and species invasion. Finally, we identify current research limitations and propose directions for future studies. We highlight the need to develop broad‐scale genetic diversity knowledge, combined with other aspects of diversity to improve biodiversity conservation outcomes. We conclude that populating global databases with genomic‐scale sequence data for all species is an urgent and achievable goal now.

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Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

Chen,

et al. 2024

Plants People Planet

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Societal Impact StatementCrop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice.Summary O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction. Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection. The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north. Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance.

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Multiple domestications of Asian rice

Cited by 21 publications

References 88 publications

The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice

The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice

Current progress and future prospects for understanding genetic diversity of seed plants in China

Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

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