Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Gan, Xiangchao; Stegle, Oliver; Behr, Jonas; Steffen, Joshua G.; Drewe, Philipp; Hildebrand, Katie L.; Lyngsoe, Rune; Schultheiß, Sebastian J.; Osborne, Edward J.; Sreedharan, Vipin T.; Kahles, André; Bohnert, Regina; Jean, Géraldine; Derwent, Paul S.; Kersey, Paul J.; Belfield, Eric J.; Harberd, Nicholas P.; Kemen, Eric; Toomajian, Christopher; Kover, Paula X.; Clark, Richard M.; Rätsch, Gunnar; Mott, Richard

doi:10.1038/nature10414

Cited by 617 publications

(727 citation statements)

References 37 publications

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“…Over 1300 lines have been genotyped using a 250k SNP chip (Horton et al, 2012), and a thousand more will be sequenced by the end of this year (Cao et al, 2011;Gan et al, 2011;www.1001genomes.org). It is our hope that these lines will be routinely phenotyped to reveal functionally important polymorphisms via GWAS.…”

Section: Discussionmentioning

confidence: 99%

“…It can be extended in several ways, and we are actively working on this. Most obviously, we will continuously increase the SNP data set by including overlapping SNP data from newly sequenced accessions (Cao et al, 2011;Gan et al, 2011). We will of course make it possible to use full sequence data from the 1001 genomes project, but this will require optimizations in order to run in real time.…”

Section: Discussionmentioning

confidence: 99%

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GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

et al. 2012

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Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

et al. 2012

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“…A r t i c l e s we identified 4,312 disrupted genes, which are defined as those genes that contain frame shift or premature stop codons compared to their orthologous genes 29 . Consistent with asymmetric gene loss, there were significantly more disrupted genes in the A subgenome (2,425) than in the D subgenome (1,887) (P < 0.01, Fisher's exact test, Fig.…”

Section: Npgmentioning

confidence: 99%

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

et al. 2015

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“…Characterization of domestication-associated genes and their genetic variation relies on high-quality genome sequences of both the cultivated species and its immediate progenitor 44,45 . Hence, we further sequenced the O. rufipogon accession W1943 with 100-fold genome coverage and carried out de novo genome assembly.…”

Section: Identification Of Domestication-associated Variantsmentioning

confidence: 99%

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

Huang

Kurata

Wei

et al. 2012

Nature

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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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Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Cited by 617 publications

References 37 publications

GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

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

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