Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

Nature Plants, Journal Year: 2020, Volume and Issue: 6(1), P. 34 - 45

Published: Jan. 13, 2020

Abstract Rapeseed ( Brassica napus ) is the second most important oilseed crop in world but genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report sequencing, de novo assembly and annotation of eight B. accessions. Using pan-genome comparative analysis, millions small 77.2–149.6 megabase presence absence (PAVs) were identified. More than 9.4% genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal for silique length, seed weight flowering time a nested mapping population with ZS11 (reference line) as donor, which not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS identifying associations traits. Further analysis showed PAVs three FLOWERING LOCUS C closely related ecotype differentiation. This provides resources support better understanding genome architecture acceleration improvement .

Language: Английский

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Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved

Biological Conservation, Journal Year: 2020, Volume and Issue: 248, P. 108654 - 108654

Published: July 2, 2020

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree a post-2020 global framework for conserving three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development benefit sharing. As most significant conservation policy mechanism, new CBD has far-reaching consequences- it guide actions reporting each member country until 2050. In previous strategies, as well other major mechanisms, targets indicators genetic diversity (variation at DNA level within which facilitates species adaptation function) were undeveloped focused agricultural relevance. We assert that, meet goals, all not just domesticated their wild relatives, must be conserved monitored using appropriate metrics. Building suggestions in recent Letter Science (Laikre et al., 2020) we expand argumentation new, pragmatic modifications two current maintaining adaptive capacity provide guidance practical use. are: 1) number populations with effective population size above versus below 500, 2) proportion maintained 3) is DNA-based methods. also present discuss Goals Action Targets are connected these underlying data. These goals have utility beyond CBD; they should monitoring via national decades come.

Language: Английский

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De Novo Domestication: An Alternative Route toward New Crops for the Future

Molecular Plant, Journal Year: 2019, Volume and Issue: 12(5), P. 615 - 631

Published: April 15, 2019

Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land climate change associated environmental deterioration. Moreover, increase in human population size dietary changes are putting an ever greater burden on agriculture. The majority of this met by cultivation a very small number species, largely locations that differ their origin domestication. Recent technological advances have raised possibility de novo domestication wild plants as viable solution designing ideal crops while maintaining food security more sustainable low-input Here we discuss how discovery multiple key genes alongside development technologies accurate manipulation several target simultaneously renders route toward future.

Language: Английский

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Biomass from microalgae: the potential of domestication towards sustainable biofactories

Microbial Cell Factories, Journal Year: 2018, Volume and Issue: 17(1)

Published: Nov. 10, 2018

Interest in bulk biomass from microalgae, for the extraction of high-value nutraceuticals, bio-products, animal feed and as a source renewable fuels, is high. Advantages microalgal vs. plant production include higher yield, use non-arable land, recovery nutrients wastewater, efficient carbon capture faster development new domesticated strains. Moreover, adaptation to wide range environmental conditions evolved great genetic diversity within this polyphyletic group, making microalgae rich interesting useful metabolites. Microalgae have potential satisfy many global demands; however, realization requires decrease current costs. Average productivity most common industrial strains far lower than maximal theoretical estimations, suggesting that identification factors limiting yield removing bottlenecks are pivotal domestication strategies aimed make algal-derived bio-products profitable on scale. In particular, light-to-biomass conversion efficiency represents major constraint finally fill gap between productivity. respect, recent results suggest significant enhancement feasible. Full further advances cultivation techniques, together with manipulation both algal physiology metabolic networks, maximize which solar energy converted into bio-products. review, we draft molecular events photosynthesis regulate light biomass, discuss how these can be targeted enhance through mutagenesis, strain selection or engineering. We outline successes reached, promising achieving contributions future microalgae-based biotechnology.

Language: Английский

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Evolutionary Insights into the Nature of Plant Domestication

Current Biology, Journal Year: 2019, Volume and Issue: 29(14), P. R705 - R714

Published: July 1, 2019

Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations critical for human survival. Darwin used domesticated as early models evolution, highlighting their variation and the key role selection in differentiation. Over last two decades, growing synthesis plant genetics, genomics, archaeobotany has led challenges old orthodoxies advent fresh perspectives on how crop domestication diversification proceed. I discuss four insights — general protracted process, unconscious (natural) plays prominent role, interspecific hybridization may be an important mechanism range expansion, similar genes across multiple underlies parallel/convergent phenotypic evolution between taxa. Insights evolutionary can help us developing varieties (and possibly even species) deal with current future environmental sustainable manner.

Language: Английский

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The population genetics of structural variants in grapevine domestication

Nature Plants, Journal Year: 2019, Volume and Issue: 5(9), P. 965 - 979

Published: Sept. 9, 2019

Language: Английский

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The evolutionary genomics of species’ responses to climate change

Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(10), P. 1350 - 1360

Published: Aug. 9, 2021

Language: Английский

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Population genomics unravels the Holocene history of bread wheat and its relatives

Nature Plants, Journal Year: 2023, Volume and Issue: 9(3), P. 403 - 419

Published: March 16, 2023

Language: Английский

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Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Cell, Journal Year: 2023, Volume and Issue: 186(11), P. 2313 - 2328.e15

Published: May 1, 2023

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to seed-reproducing diploid. Historical accumulation of deleterious mutations in genomes has hindered development elite inbred lines and hybrids. Utilizing whole-genome phylogeny 92 Solanaceae its sister clade species, we employ an evolutionary strategy identify mutations. The deep reveals genome-wide landscape highly constrained sites, comprising ∼2.4% genome. Based on diploid diversity panel, infer 367,499 variants, which 50% occur at non-coding 15% synonymous sites. Counterintuitively, with relatively high homozygous burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion inferred increases genomic-prediction accuracy yield by 24.7%. Our study generates insights into incidence properties their far-reaching consequences breeding.

Language: Английский

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Multiple domestications of Asian rice

Nature Plants, Journal Year: 2023, Volume and Issue: 9(8), P. 1221 - 1235

Published: Aug. 7, 2023

Language: Английский

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