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

Nature, Journal Year: 2012, Volume and Issue: 490(7421), P. 497 - 501

Published: Oct. 2, 2012

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one the most important developments in history. However, its origins and processes controversial long been debated. Here we generate genome sequences from 446 geographically diverse accessions wild species Oryza rufipogon, immediate ancestral progenitor rice, 1,083 indica japonica varieties to construct a comprehensive map variation. In search for signatures selection, identify 55 selective sweeps occurred during domestication. In-depth analyses genome-wide patterns reveal was first domesticated specific population O. rufipogon around middle area Pearl River southern China, subsequently developed crosses between local initial cultivars spread into South East Asia. domestication-associated traits analysed through high-resolution genetic mapping. This study provides an resource breeding effective genomics approach crop research. Whole-genome used produce variation, show probably China. Cultivated sativa) is thought rufipogon) thousands years ago. Chinese/Japanese collaboration reports whole-genome isolates across Asia Oceana, more than 1,000 subspecies rice. resulting variation will be crop-domestication

Language: Английский

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Improved maize reference genome with single-molecule technologies

Nature, Journal Year: 2017, Volume and Issue: 546(7659), P. 524 - 527

Published: June 1, 2017

Language: Английский

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Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

Proceedings of the National Academy of Sciences, Journal Year: 2013, Volume and Issue: 110(20), P. 8057 - 8062

Published: April 29, 2013

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject during improvement, we developed a high-throughput array interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in worldwide sample 2,994 accessions hexaploid including landraces and modern cultivars. Using SNP-based diversity map characterized impact crop improvement on genomic geographic patterns genetic diversity. We found evidence small population bottleneck extensive use ancestral variation often traceable founders cultivars from diverse regions. Analyzing differentiation among populations extent haplotype sharing, identified allelic variants subjected improvement. Selective sweeps were around genes involved regulation flowering time phenology. An introgression wild relative-derived gene conferring resistance fungal pathogen was detected by haplotype-based analysis. Comparing selective different populations, show that likely acts distinct targets or multiple functionally equivalent alleles portions range wheat. The majority selected present low frequency suggesting either weak pressure temporal directional breeding probably associated with changing agricultural practices environmental SNP chip provide resource for advancing supporting future genome-wide association studies

Language: Английский

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Building coral reef resilience through assisted evolution

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(8), P. 2307 - 2313

Published: Feb. 2, 2015

The genetic enhancement of wild animals and plants for characteristics that benefit human populations has been practiced thousands years, resulting in impressive improvements commercially valuable species. Despite these benefits, manipulations are rarely considered noncommercial purposes, such as conservation restoration initiatives. Over the last century, humans have driven global climate change through industrialization release increasing amounts CO 2 , shifts ocean temperature, chemistry, sea level, well frequency storms, all which can profoundly impact marine ecosystems. Coral reefs highly diverse ecosystems suffered massive declines health abundance a result other direct anthropogenic disturbances. There is great concern high rates, magnitudes, complexity environmental overwhelming intrinsic capacity corals to adapt survive. Although it important address root causes changing climate, also prudent explore potential augment reef organisms tolerate stress facilitate recovery after Here, we review risks benefits improvement natural commercial stocks noncoral systems advocate series experiments determine feasibility developing coral with enhanced tolerance acceleration naturally occurring processes, an approach known (human)-assisted evolution, while at same time initiating public dialogue on this approach.

Language: Английский

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Genotyping‐by‐Sequencing for Plant Breeding and Genetics

The Plant Genome, Journal Year: 2012, Volume and Issue: 5(3)

Published: Nov. 1, 2012

Rapid advances in “next‐generation” DNA sequencing technology have brought the US$1000 human ( Homo sapiens ) genome within reach while providing raw output for researchers to revolutionize way populations are genotyped. To capitalize on these advancements, genotyping‐by‐sequencing (GBS) has been developed as a rapid and robust approach reduced‐representation of multiplexed samples that combines genome‐wide molecular marker discovery genotyping. The flexibility low cost GBS makes this an excellent tool many applications research questions plant genetics breeding. Here we address some new opportunities becoming more feasible with GBS. Furthermore, highlight areas which will become powerful continued increase output, development reference genomes, improvement bioinformatics. ultimate goal biology scientists is connect phenotype genotype. In breeding, genotype can then be used predict phenotypes select improved cultivars. Furthering our understanding connection between heritable genetic factors resulting enable genomics‐assisted breeding exist scale needed global food supplies face decreasing arable land climate change.

Language: Английский

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Opportunities for improving phosphorus‐use efficiency in crop plants

New Phytologist, Journal Year: 2012, Volume and Issue: 195(2), P. 306 - 320

Published: June 12, 2012

Summary Limitation of grain crop productivity by phosphorus (P) is widespread and will probably increase in the future. Enhanced P efficiency can be achieved improved uptake phosphate from soil (P‐acquisition efficiency) per unit taken up (P‐use efficiency). This review focuses on P‐use efficiency, which plants that have overall lower concentrations, optimal distribution redistribution plant allowing maximum growth biomass allocation to harvestable parts. Significant decreases pools may possible, for example, through reductions superfluous ribosomal RNA replacement phospholipids sulfolipids galactolipids. Improvements within possible increased remobilization tissues no longer need it (e.g. senescing leaves) reduced partitioning developing grains. Such changes would prolong enhance productive use photosynthesis nutritional environmental benefits. Research considering physiological, metabolic, molecular biological, genetic phylogenetic aspects urgently needed allow significant progress made our understanding this complex trait. Contents 306 I. The efficiently 307 II. dynamics a growing III. IV. Phosphorus rates 310 V. Are crops different other their concentration? VI. 311 VII. Crop development canopy 312 VIII. Internal vegetative 313 IX. Allocation reproductive structures 314 X. Constraints remobilisation 315 XI. Do physiological or trade‐offs constrain traits could improve PUE? 316 XII. Identifying loci associated with PUE XIII. Conclusions 317 Acknowledgements References

Language: Английский

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Potential for evolutionary responses to climate change – evidence from tree populations

Global Change Biology, Journal Year: 2013, Volume and Issue: 19(6), P. 1645 - 1661

Published: Feb. 22, 2013

Evolutionary responses are required for tree populations to be able track climate change. Results of 250 years common garden experiments show that most forest trees have evolved local adaptation, as evidenced by the adaptive differentiation in quantitative traits, reflecting environmental conditions population origins. On basis patterns variation 19 adaptation-related traits studied 59 species (mostly temperate and boreal from Northern hemisphere), we found genetic between clinal along gradients were very (respectively, 90% 78% cases). Thus, responding change will likely require again match their environments. We examine what kind information is needed evaluating potential respond, already available. review models related selection responses, known currently about traits. address special problems at range margins, highlight need more modeling understand specific issues southern northern margins. new less species. For extensively species, outside current ranges. Improving genomic allow better prediction responses. Competitive other interactions within deserve consideration. Despite long generation times, strong background genetics growing resources make useful research. The greatest response expected when large, high variability, strong, there ecological opportunity establishment adapted genotypes.

Language: Английский

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Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Proceedings of the National Academy of Sciences, Journal Year: 2012, Volume and Issue: 110(2), P. 453 - 458

Published: Dec. 24, 2012

Accelerating crop improvement in sorghum, a staple food for people semiarid regions across the developing world, is key to ensuring global security context of climate change. To facilitate gene discovery and molecular breeding we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) 971 worldwide accessions that adapted diverse agroclimatic conditions. Using this genome-wide SNP map, population structure with respect geographic origin morphological type identified patterns ancient diffusion Africa Asia. better understand genomic diversification quantified variation diversity, linkage disequilibrium, recombination rates genome. Analyzing diversity landraces, find evidence selective sweeps around starch metabolism genes, whereas landrace-derived introgression lines, introgressions known height maturity loci. identify additional loci underlying major traits, performed association studies (GWAS) on plant components inflorescence architecture. GWAS maps several classical height, candidate genes Finally, trace independent spread multiple haplotypes carrying alleles short stature or long branches. This map sorghum provides basis through marker-assisted selection.

Language: Английский

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Nature Biotechnology, Journal Year: 2014, Volume and Issue: 32(7), P. 656 - 662

Published: June 8, 2014

Genome sequences of nine species citrus, including oranges, pummelos and mandarins, reveal pathways domestication provide resources for breeding. Cultivated citrus are selections from, or hybrids of, wild progenitor whose identities contributions to remain controversial. Here we sequence compare genomes—a high-quality reference haploid clementine genome mandarin, pummelo, sweet-orange sour-orange genomes—and show that cultivated types derive from two species. Although represent one species, Citrus maxima, mandarins introgressions C. maxima into the ancestral mandarin reticulata. The most widely sweet orange, is offspring previously admixed individuals, but sour orange an F1 hybrid pure reticulata parents, thus implying were part early breeding germplasm. A Chinese 'mandarin' diverges substantially reticulata, suggesting possibility other unrecognized Understanding phylogeny through analysis clarifies taxonomic relationships facilitates sequence-directed genetic improvement.

Language: Английский

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Comprehensive genotyping of the USA national maize inbred seed bank

Genome biology, Journal Year: 2013, Volume and Issue: 14(6)

Published: June 11, 2013

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in USA. The collection includes lines from breeding programs all over world.The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across entire genome, with ability detect rare alleles high confidence levels. More than half of SNPs are rare. Although most have been incorporated into public temperate programs, only modest amount available diversity is present commercial germplasm. Analysis genetic distances shows population stratification, including small number large clusters centered on key lines. Nevertheless, an average fixation index 0.06 indicates moderate differentiation between three major subpopulations. Linkage disequilibrium (LD) decays very rapidly, but extent LD highly dependent particular group germplasm and region genome. utility these data for performing genome-wide association studies tested two simply inherited traits one complex trait. We identified trait associations close known candidate genes kernel color, sweet corn, flowering time; however, results suggest that more needed better explore architecture traits.The genotypic information described here allows this publicly panel be exploited researchers facing challenges sustainable agriculture through knowledge nature diversity.

Language: Английский

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