Three geographically separate domestications of Asian rice

Civáň, Peter; Craig, Hayley; Cox, Cymon J.; Brown, Terence A.

doi:10.1038/nplants.2015.164

Cited by 206 publications

(252 citation statements)

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“…Japonica and O. rufipogon show a close relationship which is consistent with the long‐accepted view that O. rufipogon is the progenitor of japonica (Wei et al ., 2012) while indica rice was found in a clade with the Asian annual O. nivara . Recent SNP analysis of genomic regions under selection suggests the independent domestication of indica rice from wild rice in an area from southern Indochina to the Brahmaputra valley (Civáň et al ., 2015). …”

Section: Resultsmentioning

confidence: 99%

“…The distinctness of the indica and japonica genomes suggests separate origins for most of each genome (Wei et al ., 2012). However, the presence of many shared domestication‐related alleles has led to suggestions that some level of introgression between the two genomes has also been a feature of their domestication history (Civáň et al ., 2015; Fuller et al ., 2010; Huang et al ., 2012a,b; Molina et al ., 2011). Geographic separation may have allowed early populations to diverge resulting in distinct O. rufipogon ‐like populations in Asia and Australia.…”

Section: Discussionmentioning

confidence: 99%

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Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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“…Within the evolution of the japonica subspecies, there was another early subdivision between a temperate and a tropical branch, which evolved into different regional adaptations after domestication (Civáň et al 2015). Temperate japonica rice was particularly important in taking rice to high latitudes, where it became associated historically with important rice production in central and northeast China, Korea and Japan.…”

Section: When Did Temperate-adapted Rices Evolve?mentioning

confidence: 99%

“…Study of genetics has made it clear that the two traditional subspecies of japonica and indica are quite distant, and there is a third lineage of ricethe aus rices -that today are at their most diverse in northeastern India and Bangladesh (Schatz et al 2014;Travis et al 2015;Civáň et al 2015). Modern genetics also indicates that despite the deep divergence between indica and japonica these subspecies share several mutations that have been selected for during domestication, which in turn implies early hybridization between these two cultivated lines; it is generally inferred that many domestication traits evolved first in japonica, then were transferred to a protoindica through hybridization under cultivation Gross and Zhao 2014).…”

Section: When and How Was Rice Domesticated?mentioning

confidence: 99%

Pathways of Rice Diversification across Asia

Fuller

Weisskopf

Castillo

2016

Archaeology International

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The archaeology of rice has made important methodological advances over the past decade that have contributed new data on the domestication process, spread and ecology of cultivation. Growing evidence from spikelet bases indicates that non-shattering, domesticated forms evolved gradually in the Yangtze basin and that there were at least two distinct processes around the Middle Yangtze region pre-dating 6000 BC, and the in the Lower Yangtze region between 6000 and 4000 BC. Early rice cultivation in these areas was based on wet field ecologies, in contrast to rainfed rice that is indicated among the earliest systems in India. When rice first spread north it was not entirely suited to shorter temperate summer growth seasons, and we are able to infer from high levels of apparently green-harvested spikelets that genetic adaptations to temperate conditions evolved after 2000 BC. When rice first spread south, to mainland Southeast Asia, after 2500 BC, it was grown in rainfed, dry ecologies that were less labourdemanding and less-productive. More productive and intensive irrigated rice then redeveloped in Southeast Asia around 2000 years ago, supporting growing population densities and social complexity. IntroductionRice is one of the world's most widely eaten and most productive cereals. Over the past decade archaeobotanical research based at the UCL Institute of Archaeology and involving a wide range of collaborators in east, south, and southeast Asia has been seeking new insights into the processes by which rice evolved and rice cultivation systems evolved, and how these relate to cultural change and long-distance cultural relationships across Monsoon Asia. While this research began with critical reflections and debate surrounding the initial cultivation of rice in China (Fuller, Harvey and Qin 2007) and India (Fuller 2006),

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“…Apple has a self-incompatibility mechanism that ensures outbreeding, facilitating these domestic-wild interactions [30]. Finally, domesticated rice (Oryza sativa L.) has the strongest evidence for polyphyletic origins, with independent, spatially separate domestication in China (japonica gene pool), Indochina to Brahmaputra valley (indica gene pool), and central India to Bangladesh (aus gene pool) [31,32]. Subsequently, there was geneflow between each of these genepools, which may [32] or may not [33] be responsible for the introgression of domestication syndrome traits from the japonica to the indica pool.…”

Section: Centers Of Crop Origin and Domestication Speedmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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Three geographically separate domestications of Asian rice

Cited by 206 publications

References 24 publications

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Pathways of Rice Diversification across Asia

The Impact of Genetic Changes during Crop Domestication

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