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:10.1101/748178

Cited by 48 publications

(93 citation statements)

References 47 publications

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“…Recent evidence from ancient DNA sequencing of human genomes also points to population changes in MSEA ≈ 4 ka ago 18 , which the authors propose may be related to societal movements in East Asia, including some emigration into MSEA. The population movements may have been instigated in part by mid-Holocene climate changes and those movements in turn may have introduced cereal agriculture into MSEA 31 . The establishment and initial proliferation of this nucleated village agrarian lifeway in MSEA is remarkable in that it occurred during a period of extreme climate variability across the broader East Asian region.…”

Section: Resultsmentioning

confidence: 99%

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia

et al. 2020

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Between 5 and 4 thousand years ago, crippling megadroughts led to the disruption of ancient civilizations across parts of Africa and Asia, yet the extent of these climate extremes in mainland Southeast Asia (MSEA) has never been defined. This is despite archeological evidence showing a shift in human settlement patterns across the region during this period. We report evidence from stalagmite climate records indicating a major decrease of monsoon rainfall in MSEA during the mid- to late Holocene, coincident with African monsoon failure during the end of the Green Sahara. Through a set of modeling experiments, we show that reduced vegetation and increased dust loads during the Green Sahara termination shifted the Walker circulation eastward and cooled the Indian Ocean, causing a reduction in monsoon rainfall in MSEA. Our results indicate that vegetation-dust climate feedbacks from Sahara drying may have been the catalyst for societal shifts in MSEA via ocean-atmospheric teleconnections.

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Section: Resultsmentioning

confidence: 99%

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia

et al. 2020

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“…In order to get more insight on the dynamics of the different types of TEs we analyzed the TIP frequency distribution for each type of TEs in a subset of 382 varieties that correspond to traditional varieties and are a good representation of the variability of the species (Gutaker et al, 2020). As 6 shown in Figure 3A, the frequency distribution is different for different orders of TEs.…”

Section: Te Dynamics In Rice Varietiesmentioning

confidence: 99%

The replicative amplification of MITEs and their impact on rice trait variability

Castanera

Vendrell‐Mir

Bardil

et al. 2020

Preprint

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Transposable elements (TEs) are a rich source of genetic variability. Among TEs, Miniature Inverted-repeat Transposable Elements (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latters through a typical cut-and-paste mechanism. However, this mechanism cannot account for the high copy number MITEs attain in plant genomes. We present here an analysis of the distribution of Transposon Insertion Polymorphisms (TIPs) in 1,059 O. sativa genomes representing the main rice population groups. We performed MITE TIP-GWAS to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than SNPs on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidences of the replicative amplification of MITEs, suggesting a mechanism of amplification uncoupled from the typical cut-and-paste mechanism of class II transposons.

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“…The analysis of population genomic data and pangenomic analysis is critically important for demographic, evolutionary, and breeding studies (Gutaker et al 2020, Brohammer et al 2018, Saisho and Purugganan 2007. In contrast to the extensive information from population genomic studies of rice and maize (van Heerwaarden et al 2011, Wang et al 2018, Gutaker et al 2020, little is known about wheat, although it is one of the three species most widely grown and consumed. The first draft genome assembly of bread wheat released by the IWGSC was highly fragmented, with ≈10 kb of N50 statistics (IWGSC 2014).…”

Section: Introductionmentioning

confidence: 99%

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time andFusarium-Resistant Genes in East Asian Genotypes

Shimizu

Copetti

Okada

et al. 2020

Plant and Cell Physiology

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Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 23 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related-13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog, and the association of its A homeologous alleles with the spring/winter growth habit. Further, the Norin 61 genome carries typical East Asian functional variants from CS ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality, and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

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Genomic history and ecology of the geographic spread of rice

Abstract: 28Rice (Oryza sativa) is one of the world's most important food crops. We reconstruct 29

Cited by 48 publications

References 47 publications

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia

The replicative amplification of MITEs and their impact on rice trait variability

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time andFusarium-Resistant Genes in East Asian Genotypes

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