The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

Abstract

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

Organization, Phylogenetic Marker Exploitation, and Gene Evolution in the Plastome of Thalictrum (Ranunculaceae)

“…Before assembly of the short reads, plastome original reads were extracted by mapping all short reads to the nine plastomes as reference with BWA ( Li and Durbin, 2009 ) and SAMtools ( Danecek et al, 2021 ). Then the two plastomes were de novo assembled with SPAdes v3.15.2 ( Bankevich et al, 2012 ) as described in He et al (2021a) . Highly accurate annotation of organelle genomes was performed by using the Organellar Genome GeSeq tool ( Tillich et al, 2017 ) with subsequent manual correction.…”

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

“…It is believed that Asian cultivated rice has the evolution progress of "One domestication and multiple origins" or "One origin and multiple interspecific introgressions." The indica, japonica, aus, and basmatic were parallel in origin, but gene introgressions among each other happened (He et al, 2021). The main domesticated genes were from japonica rice.…”

“…genomic studies suggested that the aus rice was originated from annual Oryza nivara (Kim et al, 2016), with distinct lineages of both nuclear and cytoplasm inheritance (Civán et al, 2015;Choi et al, 2017;He et al, 2021) and is relatively close to indica (Garris et al, 2005;Moner et al, 2018Moner et al, , 2020He et al, 2021).…”

“…Evidence combining agricultural production, archeology, genetics, nuclear, and cytoplasm genome datum supplied a strong indication that subgroups indica , aus , and basmatic were descended from distinct lineages ( Civán et al, 2015 ; Carpentier et al, 2019 ; He et al, 2021 ; Zhang et al, 2021 ), accompanying hybridization and introgression events, and both ancient and more recent gene flow continues to dilute the once-distinctive gene pools ( Kim et al, 2016 ; Wang et al, 2017 ). Thus, the course of origin in indica , aus , and basmatic has been gradually clear ( Figure 1 ).…”

“…Some aus varieties still remain some characters of wild relatives of rice, such as spreading tillers and easy thresh ( Khush et al, 2003 ), and are under incomplete domestication selections ( Zhao et al, 2018 ). Molecular and genomic studies suggested that the aus rice was originated from annual Oryza nivara ( Kim et al, 2016 ), with distinct lineages of both nuclear and cytoplasm inheritance ( Civán et al, 2015 ; Choi et al, 2017 ; He et al, 2021 ) and is relatively close to indica ( Garris et al, 2005 ; Moner et al, 2018 , 2020 ; He et al, 2021 ).…”