Genomic history and ecology of the geographic spread of rice

Gutaker, Rafał M.; Groen, Simon C.; Bellis, Emily S.; Choi, Jae Young; Pires, Inês S.; Bocinsky, R. Kyle; Slayton, Emma; Wilkins, Olivia; Castillo, Cristina; Negrão, Sónia; Oliveira, M. Margarida; Fuller, Dorian Q.; Guedes, Jade A. d’Alpoim; Lasky, Jesse R.; Purugganan, Michael D.

doi:10.1038/s41477-020-0659-6

Cited by 181 publications

(159 citation statements)

References 94 publications

(115 reference statements)

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“…2). Tropical japonica, diverged from temperate japonica, is thought to have originated in the upper Thai-Malay Peninsula and might have moved from the Malay Archipelago northward through Indonesia, the Philippines, Taiwan, Ryukyus, and Japan (Chang 1976;Gutaker et al 2020). Thus, Taiwan was on the dispersal route of tropical japonica and 2/3 of carbonized rice grains unearthed from remains of Niaosung Culture (1400-1000 B.P.)…”

Section: Unveiling Taiwanese Rice Germplasmmentioning

confidence: 99%

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Hour

Hsieh

Chang

et al. 2020

Rice

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Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

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Section: Unveiling Taiwanese Rice Germplasmmentioning

confidence: 99%

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Hour

Hsieh

Chang

et al. 2020

Rice

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“…The technical, technological and digital divide affecting researchers in some countries has increasingly important implications in terms of access to and use of genetic resources in breeding for climate relevant objectives. For example the opportunities to link historical climate change data with genomic analysis of germplasm stored in long-established collections, could provide an additional tool for breeders to select wild varieties with potential adaptive traits, particularly in centres of crop diversity [52]. Eco-geographical modelling tools could aid the identification of sites where to conduct multi-environment trials allowing the evaluation of germplasm across a range of climate-relevant target environments [100,101].…”

Section: Discussionmentioning

confidence: 99%

“…In developing new cultivars, breeders can start from a range of different germplasm types and germplasm sources. Among the former, landraces and crop wild relatives remain perhaps the largest reservoir of genetic diversity, including traits of tolerance or resistance to environmental stressors, even those associated with climate change [30,36,[41][42][43][44][45][46][47][48][49][50][51][52][53][54]. On the other hand, advanced breeding or elite lines which have undergone pre-breeding efforts, may harbour less genetic diversity but be more "ready to use" materials for breeders, thanks to the useful information accumulated on their structure and properties [49,[55][56][57][58][59].…”

Section: Introductionmentioning

confidence: 99%

The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries

Galluzzi

Seyoum

Halewood

et al. 2020

Plants

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The role of plant breeding in adapting crops to climate changes that affect food production in developing countries is recognized as extremely important and urgent, alongside other agronomic, socio-economic and policy adaptation pathways. To enhance plant breeders’ capacity to respond to climate challenges, it is acknowledged that they need to be able to access and use as much genetic diversity as they can get. Through an analysis of data from a global survey, we explore if and how public breeders in selected developing countries are responding to climate challenges through a renewed or innovative use of plant genetic resources, particularly in terms of types of material incorporated into their breeding work as well as sources of such germplasm. It also looks at the possible limitations breeders encounter in their efforts towards exploring diversity for adaptation. Breeders are clearly considering climate challenges. In general, their efforts are aimed at intensifying their breeding work on traits that they were already working on before climate change was so widely discussed. Similarly, the kinds of germplasm they use, and the sources from which they obtain it, do not appear to have changed significantly over the course of recent years. The main challenges breeders faced in accessing germplasm were linked to administrative/legal factors, particularly related to obtaining genetic resources across national borders. They also underscore technical challenges such as a lack of appropriate technologies to exploit germplasm sets such as crop wild relatives and landraces. Addressing these limitations will be crucial to fully enhance the role of public sector breeders in helping to adapt vulnerable agricultural systems to the challenges of climate change.

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“…Asian rice has a well-recognized genetic subdivision into indica-type rice, japonicatype, and aus-type rice [55]. Archaeological and genetic evidence suggested that japonica rice cultivation began in the Yangtze valley, China c.9000BP with the pre-domestication cultivation of wild O. rufipogon [56,57]. This led to domestication with several key genes becoming fixed in the population [57], but this was not the only domestication process [56,58], and rather hybridization between japonica and South Asian rice was necessary for the domestication of O. sativa.…”

Section: Domestication and Proto-indicamentioning

confidence: 99%

Is Domestication Speciation? The Implications of a Messy Domestication Model in the Holocene

Bates

2021

Agronomy

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Domestication is one of the fundamental process that has shaped our world in the last 12,000 years. Changes in the morphology, genetics, and behavior of plants and animals have redefined our interactions with our environments and ourselves. However, while great strides have been made towards understanding the mechanics, timing, and localities of domestication, a fundamental question remains at the heart of archaeological and scientific modelling of this process—how does domestication fit into a framework of evolution and natural selection? At the core of this is the ontological problem of what is a species? In this paper, the complicated concepts and constructs underlying ‘species’ and how this can be applied to the process of domestication are explored. The case studies of soybean and proto-indica rice are used to illustrate that our choice of ‘species’ definitions carries with it ramifications for our interpretations, and that care needs to be made when handling this challenging classificatory system.

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Genomic history and ecology of the geographic spread of rice

Cited by 181 publications

References 94 publications

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

The Role of Genetic Resources in Breeding for Climate Change: The Case of Public Breeding Programmes in Eighteen Developing Countries

Is Domestication Speciation? The Implications of a Messy Domestication Model in the Holocene

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