Transitions in Productivity: Rice Intensification from Domestication to Urbanisation

Fuller, Dorian Q.

doi:10.14324/111.444.ai.2020.08

Cited by 20 publications

(28 citation statements)

References 49 publications

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“…Rice cultivation was brought to Taiwan and was established by 4,600 BP, possibly via Jiangxi and overland cultural expansion from the mixed rice-millet farmers of Jiangxi and interior Fujian ( Gao et al 2020 ; Deng, Yan, et al 2020 ). Based on site locations, some arable weed flora assemblages and the co-occurrence with millets, this early rice is inferred to be ancestral japonica and grown under upland conditions ( Qin and Fuller 2019 ; Deng, Yan, et al 2020 ; Fuller 2020 ). From this region of southern China upland rice and millets also dispersed through mainland SE Asia from northern Vietnam to central Thailand between 4,300 and 3,700 years ago ( Castillo 2017 ; Higham 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

Alam

Gutaker

et al. 2021

Molecular Biology and Evolution

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The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast Asia. The history of dispersal across islands of Southeast Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice through Taiwan and the northern Philippines using whole-genome re-sequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3500 BP. In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland Southeast Asia respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2600 BP, while gene flow from the northern Philippines occurred before ∼1300 years BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.

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Section: Discussionmentioning

confidence: 99%

Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

Alam

Gutaker

et al. 2021

Molecular Biology and Evolution

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“…In this study, we identified key functional genes that contributed to rice domestication by increasing harvest yields. We identified the causal SNP at qSH3 involved in reduced seed shattering, whereas the previously proposed sh4 mutation alone could not trigger the nonshattering morphology in rice (6,17). We also explained how the early selection of a closed panicle and the resulting mechanics of spikelet retention would have increased yields and facilitated the selection for non-shattering.…”

Section: Discussionmentioning

confidence: 79%

“…When plants were sown from harvests, closed panicles would have been selected for, and unintentionally would have selected also for reduced shattering, because of the enhanced gathering rate that would occur in the presence of the domesticated alleles. As these alleles increased in frequency and became fixed this would have increased yields, which would have encouraged further investment in rice cultivation (16). The selection for closed panicle instigates self-pollination behaviour owing to the long awns, which disturb the free exposure of anthers and stigmas (stigmas and closed panicle) (17).…”

Section: Resultsmentioning

confidence: 99%

“…As these alleles increased in frequency and became fixed this would have increased yields, which would have encouraged further investment in rice cultivation (16). The selection for closed panicle instigates self-pollination behaviour owing to the long awns, which disturb the free exposure of anthers and stigmas (stigmas and closed panicle) (17). Thus, a closed panicle may also be advantageous in mitigating natural variations in seed-shattering loci by reducing outcrossing.…”

Section: Resultsmentioning

confidence: 99%

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A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Ishikawa

Castillo

Htun

et al. 2021

Preprint

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Rice (Oryza sativa L.) is consumed by more than half of the world’s population, but despite its global importance the mechanisms of domestication remain unclear. During domestication, wild rice (O. rufipogon Griff.) was transformed by acquiring non-seed-shattering behaviour, an important genetic change that allowed humans to increase grain yield. However, we show previously identified loci, sh4 and qSH3, are individually insufficient to explain loss of seed shattering nor increases in harvest yield in wild rice. We identify the complementary interaction of key mutations for abscission layer interruption and panicle architecture that were causal in the early domestication of Asian rice. An interruption of abscission layer formation requires both sh4 and qSH3, which presents an apparent barrier to selection of shattering loss. We identified the causal single nucleotide polymorphism at qSH3 within a seed-shattering gene OsSh1 conserved in indica and japonica subspecies, but absent in the circum-aus group of rice. We demonstrate through harvest experiments that seed-shattering alone does not significantly impact yield. Instead, we observed yield increases under a SRR3-controlled closed panicle formation, which is augmented by the integration of sh4 and qSH3 alleles causing a slight inhibition of abscission layer. Complementary manipulation of seed shattering and panicle shape result in a panicle structure that is mechanically stable. We propose a stepwise route in the earliest phase of rice domestication in which selection for visible SRR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 and leading to loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 is insufficient on its own to cause abscission layer disruption and other genes, such as qSH3 are required, making mechanisms for the initial selection of non-shattering unclear. We show that shattering loss in wild rice genetic backgrounds does not increase yields. We identify an interaction in which a second trait, closed panicle formation controlled by SPR3, both increases yield and facilitates recruitment of sh4 and qSH3 which synergistically augment yield, leading to a stepwise route for rice domestication.

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“…Two main sources of information are provided by archeological records and molecular analysis (Fuller, 2007; Gross and Zhao, 2014; Ishikawa et al, 2020). Concerning archeological records, it is now widely agreed that Asian rice was domesticated in the lower Yangtze basin around 6700 BP (Fuller, 2020). Such domestication was the issue of a protracted process spanning from 1 to 2 millennia or more.…”

Section: Introductionmentioning

confidence: 99%

How gathering wild rice under human-mediated drought stress could have inadvertently paved the way to Asian rice incipient domestication and cultivation

Svizzero¹

2021

The Holocene

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In eastern China, on the southern end of the Yangtze Valley, early Holocene hunter-gatherers were foraging various plants, including wild rice – Oryza rufipogon Griff. – an aquatic and perennial plant which is the wild progenitor of domesticated rice. According to optimal foraging theory, these foragers should have tried to enhance the efficiency of harvesting wild rice seeds by draining water around the plants before seeds ripened and shattered. This proto-cultivation practice led to unintended consequences given that wild rice responds to drought stress owing to its phenotypic plasticity. Plant and panicle architectures were modified with transitions to more compact and erect tillers and to a closed panicle shape. They provide incentives to early foragers for intensifying their proto-cultivation practices and so could have also triggered initial cultivation of rice. They also triggered incipient domestication of rice, starting by the transition to selfing. According to this narrative, it is even possible that rice incipient domestication preceded cultivation.

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Transitions in Productivity: Rice Intensification from Domestication to Urbanisation

Cited by 20 publications

References 49 publications

Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

How gathering wild rice under human-mediated drought stress could have inadvertently paved the way to Asian rice incipient domestication and cultivation

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