Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: Feb. 21, 2019

Human selection has a long history of transforming crop genomes. Peach (Prunus persica) undergone more than 5000 years domestication that led to remarkable changes in series agronomically important traits, but genetic bases underlying these and the effects artificial on genomic diversity are not well understood.Here, we report comprehensive analysis peach evolution based genome sequences 480 wild cultivated accessions. By focusing set quantitative trait loci (QTLs), provide evidence supporting distinct phases improvement have an increase fruit size taste extended its geographic distribution. Fruit was predominantly selected during domestication, for large fruits loss several weight QTLs. In contrast, taste-related QTLs were successively by improvement, with improvement. Genome-wide association studies 11 agronomic traits suggest candidate genes controlling potential markers molecular breeding. Candidate contributed adaption low-chill regions identified. Furthermore, divergent texture local breeding different flavors between Asian European/North American cultivars also determined.Our results elucidate basis new resources future genomics-guided

Language: Английский

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Dual domestications and origin of traits in grapevine evolution

Science, Journal Year: 2023, Volume and Issue: 379(6635), P. 892 - 901

Published: March 2, 2023

We elucidate grapevine evolution and domestication histories with 3525 cultivated wild accessions worldwide. In the Pleistocene, harsh climate drove separation of grape ecotypes caused by continuous habitat fragmentation. Then, occurred concurrently about 11,000 years ago in Western Asia Caucasus to yield table wine grapevines. The domesticates dispersed into Europe early farmers, introgressed ancient western ecotypes, subsequently diversified along human migration trails muscat unique ancestries late Neolithic. Analyses traits also reveal new insights selection for berry palatability, hermaphroditism, flavor, skin color. These data demonstrate role grapevines inception agriculture across Eurasia.

Language: Английский

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The genetic basis of sex determination in grapes

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: June 9, 2020

Abstract It remains a major challenge to identify the genes and mutations that lead plant sexual differentiation. Here, we study structure evolution of sex-determining region (SDR) in Vitis species. We report an improved, chromosome-scale Cabernet Sauvignon genome sequence phased assembly nine wild cultivated grape genomes. By resolving twenty SDR haplotypes, compare male, female, hermaphrodite haplotype structures sex-linked regions. Coupled with gene expression data, candidate male-sterility mutation VviINP1 potential female-sterility function associated transcription factor VviYABBY3 . Our data suggest dioecy has been lost during domestication through rare recombination event between male female haplotypes. This work significantly advances understanding genetic basis sex determination provides information necessary rapidly types breeding programs.

Language: Английский

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The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(5)

Published: April 4, 2023

Grapevine is one of the most economically important crops worldwide. However, previous versions grapevine reference genome tipically consist thousands fragments with missing centromeres and telomeres, limiting accessibility repetitive sequences, centromeric telomeric regions, study inheritance agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free for cultivar PN40024 using PacBio HiFi long reads. The T2T (PN_T2T) 69 Mb longer 9018 more genes identified than 12X.v0 version. We annotated 67% 19 36 incorporated gene annotations into PN_T2T assembly. detected total 377 clusters, which showed associations complex traits, such as aroma disease resistance. Even though derives from nine generations selfing, still found genomic hotspots heterozygous sites associated biological processes, oxidation-reduction process protein phosphorylation. fully complete therefore constitutes an resource genetic studies breeding programs.

Language: Английский

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The integrated genomics of crop domestication and breeding

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2828 - 2839

Published: May 27, 2022

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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Adaptive and maladaptive introgression in grapevine domestication

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(24)

Published: June 5, 2023

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild cultivated grapes in Europe, but the time, mode, pattern, and biological effects these events not been investigated. Here, we studied resequencing data 345 samples spanning distributional range (Vitis vinifera ssp. sylvestris) (V. vinifera) grapes. Based on machine learning-based population genetic analyses, detected evidence for a single domestication grapevine, followed by continuous gene flow between European (EU) over past ~2,000 y, especially EU wine We also inferred that soft-selective sweeps were dominant artificial selection. Gene pathways associated with synthesis aromatic compounds enriched regions both selected introgressed, suggesting an important resource improving flavor Despite potential benefits grape improvement, introgressed fragments introduced higher deleterious burden, most SNPs structural variants hidden heterozygous state. Cultivated benefited adaptive grapes, has increased load. In general, our study beneficial harmful is critical breeding grapevine take advantage resources.

Language: Английский

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Population comparative genomics discovers gene gain and loss during grapevine domestication

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(2), P. 1401 - 1413

Published: Jan. 29, 2024

Abstract Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors artificially selected for desired agronomic traits along with dramatic genomic variation in course of moderate to severe bottlenecks. However, previous investigations mainly focused on small-effect variants, while changes gene contents rarely investigated due lack population-level assemblies both and its relatives. Here, we applied comparative analyses discover gain loss grapevine using long-read representative population samples domesticated grapevines (V. vinifera ssp. vinifera) their sylvestris). Only ∼7% families were shared 16 Vitis genomes ∼8% specific each accession, suggesting variations genomes. Compared progenitors, accessions exhibited an increased presence genes associated asexual reproduction, showcased a higher abundance related pollination, revealing transition from sexual reproduction clonal propagation processes. Moreover, harbored fewer disease-resistance than progenitors. The SVs occurred frequently aroma between indicating rapid diversification these domestication. Our study provides insights resources biological studies breeding programs grapevine.

Language: Английский

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Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(5), P. 1227 - 1241

Published: Jan. 18, 2024

Domestication can be considered a specialized mutualism in which domesticator exerts control over the reproduction or propagation (fitness) of domesticated species to gain resources services. The evolution crops by human-associated selection provides powerful set models study recent evolutionary adaptations and their genetic bases. Moreover, domestication dispersal such as rice, maize, wheat during Holocene transformed human social political organization serving key mechanism societies fed themselves. Here we review major themes identify emerging questions three fundamental areas crop research: phenotypes syndromes, architecture underlying evolution, ecology domestication. Current insights on syndrome largely come from research cereal rice work indicates distinct arise different histories. While early studies genetics often identified single large-effect loci traits, evidence supports polygenic bases for many canonical traits shattering plant architecture. Adaptation human-constructed environments also influenced ecological domesticates resource acquisition rates interactions with other organisms root mycorrhizal fungi pollinators. Understanding context will developing resource-efficient implementing more sustainable land management cultivation practices.

Language: Английский

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Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs

PLoS ONE, Journal Year: 2018, Volume and Issue: 13(2), P. e0192540 - e0192540

Published: Feb. 8, 2018

Grapevine is a very important crop species that mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases performance traits through association mapping studies requires precise knowledge available diversity how this structured varies across whole genome. An 18k SNP genotyping array was evaluated on panel Vitis vinifera cultivars we obtained data set with no missing values total 10207 SNPs 783 different genotypes. The average inter-SNP spacing ~47 kbp, mean minor allele frequency (MAF) 0.23 in sample high (He = 0.32). Fourteen SNPs, chosen from those highest MAF values, were sufficient to identify each genotype sample. Parentage analysis revealed 118 full parentages 490 parent-offspring duos, thus confirming close pedigree relationships within grapevine. Structure analyses also confirmed main divisions due an eastern-western gradient human usage (table vs. wine). Using multivariate approach, refined structure identified eight clusters. Both (He, 0.26–0.32) linkage disequilibrium (LD, 28.8–58.2 kbp) varied between Despite short span LD, some non-recombining haplotype blocks may complicate mapping. Finally, performed genome-wide study previous works new regions such as acidity. Taken together, all results contribute better genetics

Language: Английский

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