Rice Domestication by Reducing Shattering

Li, Changbao; Zhang, Ailing; Su, Tao

doi:10.1126/science.1123604

Cited by 766 publications

(731 citation statements)

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“…Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 .…”

mentioning

confidence: 83%

“…We noticed that many loci with strong signals of selection were nearly identical in both indica and japonica where F ST between indica and japonica was extremely low, indicating that introduction of traits during domestication has in many cases involved introgression events. We noted that most well-characterized domestication genes, including Bh4 (hull colour 9 ), PROG1 (tiller angle 7,8 ), sh4 (seed shattering 5,6 ), qSW5 (grain width 35 ) and OsC1 (leaf sheath colour and apiculus colour 32 ), were among the 55 loci detected in the full population (Fig. 3).…”

Section: Screens and Annotation Of Domestication Locimentioning

confidence: 95%

“…The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated.…”

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confidence: 99%

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

Huang

Kurata

Wei

et al. 2012

Nature

1,341

107

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Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. 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 that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.Cultivated rice (Oryza sativa L.), which is grown worldwide and is one of the most important cereals for human nutrition, is considered to have been domesticated from wild rice (Oryza rufipogon) thousands of years ago 1-4 . The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 1...

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mentioning

confidence: 83%

Section: Screens and Annotation Of Domestication Locimentioning

confidence: 95%

See 1 more Smart Citation

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

Huang

Kurata

Wei

et al. 2012

Nature

1,341

107

1,449

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“…In this case three different domestication trait mutants, waxy (wx), shattering (qsh1) and seed width (qsw5) appear to come from three different geographic regions, giving rise to a mosaic very much like that predicted in Fig 3b. The rice studies also indicate that there are multiple shattering mutants, sh4 (Li et al, 2006) and qsh1 (Konishi et al, 2006). In this case sh4 is present in all tested domesticated rice varieties (Lin et al, 2007), while qsh1 is restricted to the Japanese area where it presumably arose, and occurred after the wx and qsw5 mutants had arisen in different areas and been combined, possibly in the Thailand area (Shomura et al, 2008).…”

Section: The Chronology Of Trait Fixationmentioning

confidence: 99%

Integrating the processes in the evolutionary system of domestication

Allaby

2010

Journal of Experimental Botany

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Genetics has long been used as a source of evidence to understand domestication origins.A recent shift in the emphasis of archaeological evidence from a rapid transition paradigm of hunter-gatherers to agriculturalists to a protracted transition paradigm has highlighted how the scientific framework of interpretation of genetic data was quite dependent on archaeological evidence, resulting in a period of discord in which the two evidence types appeared to support different paradigms. Further examination showed that the discriminatory power of the approaches employed in genetics was low, and framed within the rapid paradigm rather than testing it. In order to interpret genetic data under the new protracted paradigm it must be taken into account how that paradigm changes our expectations of genetic diversity. Preliminary examination suggests that a number of features that constituted key evidences in the rapid paradigm are likely to be interpreted very differently in the protracted paradigm. Specifically, in the protracted transition the mode and mechanisms involved in the evolution of the domestication syndrome have become much more influential in the shape of genetic diversity. The result is that numerous factors interacting over several levels of organization in a domestication system need to be taken into account in order to understand the evolution of the process. This presents a complex problem of integration of different data types which is difficult to describe formally. One possible way forward is to use Bayesian Approximation approaches that allow complex systems to be measured in a way that does not require such formality.

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“…Recent functional genomic studies have helped to excavate a number of domestication genes [26][27][28][29]. For example, sh4 and qSH1 are essential for effective field harvest because of their ability to reduce grain shattering [29,30]. In addition, grain or fruit size was important in the evolution of wild species because of the continuous selection for large ones during early domestication.…”

Section: Introductionmentioning

confidence: 99%