Deletion in a gene associated with grain size increased yields during rice domestication

Shomura, Ayahiko; Izawa, Takeshi; Ebana, Kaworu; Ebitani, Takeshi; Kitano, Hiromi; Konishi, Saeko; Yano, Masahiro

doi:10.1038/ng.169

Cited by 812 publications

(667 citation statements)

References 22 publications

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“…Evidence for the corollary of the expectation of the fate of parallelisms outlined above, a mosaic genome of trait mutants, has also been seen with rice in the study of Shomura et al (2008). 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).…”

Section: The Chronology Of Trait Fixationmentioning

confidence: 69%

“…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%

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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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Section: The Chronology Of Trait Fixationmentioning

confidence: 69%

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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“…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%

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

Huang

Kurata

Wei

et al. 2012

Nature

1,379

109

1,518

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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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“…The genetics of sink size (e.g., grain size and grain number) has been well analyzed in rice plants, and several QTLs controlling grain number per panicle and grain size have been identified (Ashikari et al 2005;Fan et al 2006;Song et al 2007;Shomura et al 2008;Huang et al 2009). On the other hand, genetic analyses of factors affecting source capacity, such as photosynthetic rate, have been limited, probably because of the need for time- C1006 G2009 C479 C383 G1068 C145 R646 R1440 R2394 R2677 R1245 C847 R1789 G379 C596 C924 C213 8 R1943 G278 C277 C1121 C1107 G104 C347 R1394A G1073 S10622 G187 R2382 R202 S14074 G1149 R2662 R1963 9 C711 G36 R1164 R1751 G385 R2272 S1057 C609 C1263 C570 C506 G1445 10 C701 S2083 R2174 C148 R1629 C1166 R2447 R3285 C1286 R1877 R844 G2155 R716 C16 C809 C405 11 G24A R77 R3202 C794A S1057 C410 C477 G320B G320A C535 G44 C3 R728 G257 C1172 S723 C50 G1465 C82 C950 G181 12 G24B R1957 C1336 R2672A R367 R3375 R...…”

Section: Discussionmentioning

confidence: 99%

A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice

Takai

Kondo

Yano

et al. 2010

Rice

Self Cite

116

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Leaf photosynthesis, an important determinant of yield potential in rice, can be estimated from measurements of chlorophyll content. We searched for quantitative trait loci (QTLs) for Soil and Plant Analyzer Development (SPAD) value, an index of leaf chlorophyll content, and assessed their association with leaf photosynthesis. QTL analysis derived from a cross between japonica cultivar Sasanishiki and high-yielding indica cultivar Habataki detected a QTL for SPAD value on chromosome 4. This QTL explained 31% of the total phenotypic variance, and the Habataki allele increased the SPAD value. Chromosomal segment substitution line (CSSL) with the corresponding segment from Habataki had a higher leaf photosynthetic rate and SPAD value than Sasanishiki, suggesting an association between SPAD value and leaf photosynthesis. The CSSL also had a lower specific leaf area (SLA) than Sasanishiki, reflecting its thicker leaves. Substitution mapping under Sasanishiki genetic background demonstrated that QTLs for SPAD value and SLA were co-localized in the 1,798-kb interval. The results suggest that the phenotypes for SPAD value and SLA are controlled by a single locus or two tightly linked loci, and may play an important role in increasing leaf photosynthesis by increasing chlorophyll content or leaf thickness, or both.

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Deletion in a gene associated with grain size increased yields during rice domestication

Cited by 812 publications

References 22 publications

Integrating the processes in the evolutionary system of domestication

Integrating the processes in the evolutionary system of domestication

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

A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice

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