The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis.

@article{Chen2019TheGO,
  title={The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis.},
  author={Erwang Chen and Xuehui Huang and Zhixi Tian and Rod A. Wing and Bin Han},
  journal={Annual review of plant biology},
  year={2019},
  volume={70},
  pages={
          639-665
        }
}
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of… 

Figures from this paper

Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication

Comparative analysis of domestication genes between African and Asian rice has revealed that the two species went through an independent but convergent evolution process, and the genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species.

Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice.

Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives

Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is

Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L.

As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a

Brief Insight into the Evolutionary History and Domestication of Wild Rice Relatives

In this chapter, authors attempted to understand in brief about genetic diversity in rice, as well as a description of the processes about the domestication of rice began and at which location rice was domesticated.

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice (Oryza sativa L.)

Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the aus and japonica groups, suggesting that aroma is an important specific genomic feature of BasMati varieties.

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

Rice functional genomics: decades’ efforts and roads ahead

The research progress of rice biology over past decades is summarized, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development.
...

A map of rice genome variation reveals the origin of cultivated rice

In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and was subsequently developed from crosses between japonicas rice and local wild rice as the initial cultivars spread into South East and South Asia.

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

A pan-genome dataset of the Oryza sativa–Oryza rufipogon species complex generated through deep sequencing and de novo genome assembly of 66 divergent accessions will be helpful in pinpointing new causal variants underlying complex traits and in promoting evolutionary and functional studies in rice.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, is detected, indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

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

A Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection is identified, thereby suggesting that there might be more complexity inherent to the process of de-domestication.

Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species and provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

Domestication history and geographical adaptation inferred from a SNP map of African rice

A map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces shows a population bottleneck in this species, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation.

Phylogeny of rice genomes with emphasis on origins of allotetraploid species.

  • S. GeT. SangB. LuD. Hong
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1999
It is revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome, and that the AA genome lineage, which contains cultivated rice, is a recently diverged and rapidly radiated lineage within the rice genus.

Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice

The results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wildrelative, and indica to an admixed population of diverse annual and perennial wild ancestors.

Rapid diversification of five Oryza AA genomes associated with rice adaptation

It is shown, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation.

The domestication of plant architecture in African rice

This work shows that PROG7 (PROSTRATE GROWTH 7), a zinc-finger transcription factor gene on chromosome 7, is required for the prostrate growth of African wild rice and provides new insights into the molecular basis of plant architecture in crops.
...