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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Leveraging a phased pangenome for haplotype design of hybrid potato

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Language: Английский

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A super-pangenome of the North American wild grape species

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: Dec. 19, 2023

Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because species are valuable sources agronomic traits that essential to enhance sustainability and adaptability domesticated cultivars. Genetic across a genus can be captured in super-pangenomes, which provide framework interpreting genomic variations. Results Here we report sequencing, assembly, annotation nine North American grape genomes, phased scaffolded at chromosome scale. We generate reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing extent among from sequence gene level. The pangenome graph captures variation between haplotypes within different species, it accurately assesses similarity hybrids their parents. selected build great representation genus, as illustrated by capturing known allelic variants sex-determining region Pierce’s disease resistance loci. Using pangenome-wide association analysis, demonstrate utility effectively mapping short reads genus-wide samples identifying loci associated with salt tolerance natural populations grapes. Conclusions This study highlights how reveal basis adaptive accelerate crop breeding research.

Language: Английский

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Grapevine pangenome facilitates trait genetics and genomic breeding

Nature Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 4, 2024

Grapevine breeding is hindered by a limited understanding of the genetic basis complex agronomic traits. This study constructs graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build variation map with 9,105,787 short variations 236,449 structural (SVs) resequencing data 466 grapevine cultivars. Integrating SVs into genome-wide association study, 148 quantitative trait loci for 29 traits (50.7% identified), 12 significantly contributed SVs. The estimated heritability improves 22.78% on average when including We discovered locus regions under divergent artificial selection in metabolism berry development between wine table grapes, respectively. Moreover, significant correlations were detected among Under polygenic model, conducted genomic predictions each trait. In general, our facilitates superior cultivars via multiple By constructing incorporating phenotypic maps, investigates traits, empowering breeding.

Language: Английский

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Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1408 - 1426

Published: April 5, 2024

ABSTRACT Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on phenotypic traits and local adaptation to abiotic biotic stress. In this study, we employed woolly grape ( Vitis retordii ), species native the tropical subtropical regions East Asia with both coastal inland habitats, as valuable model for examining SVs adaptation. We assembled haplotype‐resolved chromosomal reference genome grape, conducted population genetic analyses based whole‐genome sequencing (WGS) data from populations. The demographic revealed recent bottlenecks in all populations asymmetric gene flow population. total, 1,035 genes associated adaptive regulation salt stress, radiation, environmental were detected underlying selection by SNPs population, which 37.29% 65.26% SNPs, respectively. Candidate such FSD2 , RGA1 AAP8 tolerance found be highly differentiated selected during process habitats SV regions. Our study highlights importance adaptation; candidate related stress climatic environments important genomic resources future breeding programs grapevine its rootstocks.

Language: Английский

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Integrative genomics reveals the polygenic basis of seedlessness in grapevine

Current Biology, Journal Year: 2024, Volume and Issue: 34(16), P. 3763 - 3777.e5

Published: Aug. 1, 2024

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and polygenic basis seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative integrative genomics to unravel evolution seedlessness grapes. We generated haplotype-resolved genomes for two seedless cultivars, "Thompson Seedless" (TS, syn. "Sultania") "Black Monukka" (BM). Comparative identified ∼4.25 Mb hemizygous inversion on Chr10 specific with seedless-associated genes VvTT16 VvSUS2 located at breakpoints. Population genomic analyses 548 grapevine accessions revealed distinct clusters identity-by-descent (IBD) results indicated that origin could be traced back "Sultania." Introgression, rather than convergent selection, shaped evolutionary history improvement. Genome-wide association study (GWAS) analysis 110 loci (QTLs) associated 634 candidate genes, including previously unidentified such as three 11S GLOBULIN SEED STORAGE PROTEIN CYTOCHROME P450 well-known like VviAGL11. Integrative resulted 339 core categorized into 13 functional categories related development. Machine learning-based selection achieved remarkable prediction accuracy 97% grapevines. Our findings highlight nature provide molecular genetics an effective

Language: Английский

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Phased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 195(4), P. 2799 - 2814

Published: May 14, 2024

Abstract The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies breeding programs. In this study, we assembled haplotype-resolved telomere-to-telomere (T2T) genome for diploid cultivar Golden Delicious. Subsequently, constructed pangenome based on 12 assemblies from wild species to investigate dynamic changes functional genes. Our results revealed gene gain loss events during domestication. Compared with species, more families significantly enriched oxidative phosphorylation, pentose metabolic process, responses salt, abscisic acid biosynthesis process. analyses also demonstrated higher prevalence different types resistance analogs (RGAs) cultivars than their relatives, partially attributed segmental tandem duplication certain RGAs classes. Structural variations, mainly deletions insertions, have affected presence absence TIR-NB-ARC-LRR, NB-ARC-LRR, CC-NB-ARC-LRR Additionally, hybridization/introgression has contributed expansion genes domesticated apples. T2T provide important resources apples, emphasizing need study evolutionary mechanisms breeding.

Language: Английский

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Impacts of reproductive systems on grapevine genome and breeding

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 3, 2025

Diversified reproductive systems can be observed in the plant kingdom and applied crop breeding; however, their impacts on genomic variation breeding remain unclear. Grapevine (Vitis vinifera L.), a widely planted fruit tree, underwent shift from dioecism to monoecism during domestication involves crossing, self-pollination, clonal propagation for its cultivation. In this study, we discover that types, namely, selfing, cloning, dramatically impact landscapes grapevine based comparative population genetics of wild complex pedigree Pinot Noir. The are divergent, which show interesting patterns purging Hill-Robertson interference. Selfing reduces heterozygosity, while cloning increases it, resulting "double U-shaped" site frequency spectrum (SFS). Crossing conceal selfing purges most deleterious structural burdens. Moreover, close leakage large-effect variations repulsion phases maintains heterozygous regions 4.3% genome after successive nine generations. Our study provides new insights into genetic basis crops by variants integrating beneficial through various systems. Effects Here, authors report types analyses

Language: Английский

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The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Horticulture Research, Journal Year: 2023, Volume and Issue: 10(11)

Published: Oct. 13, 2023

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin, flesh, and vegetative tissues, endowing them with high utility value red wine blending nutrient-enriched foods developing. However, due to lack genome information, mechanism involved regulating teinturier coloring has not yet been elucidated their genetic utilization research is still insufficient. Here, cultivar 'Yan73' was used for assembling telomere-to-telomere (T2T) combining High Fidelity (HiFi)， Hi-C ultralong Oxford Nanopore Technologies (ONT) reads. Two haplotype genomes were assembled, at sizes 501.68 Mb 493.38 Mb, respectively. In 1 genome, transposable elements (TEs) contained 32.77% long terminal repeats (LTRs), while 2 31.53% LTRs detected TEs. Furthermore, obvious inversions identified chromosome 18 between two haplotypes. Transcriptome profiling suggested that gene expression patterns 'Cabernet Sauvignon' diverse depending on developmental stages, varieties. The transcription program genes biosynthesis pathway cultivars exhibited similarity different tissues whereas levels numerous showed significant differences. Compared other genes, VvMYBA1 VvUFGT4 all samples, VvCHS2 except young shoots VvPAL9 E-L23 stage higher than those Sauvignon'. Further sequence alignments revealed potential variant loci structure variations related a 816 bp insertion found promoter genome. T2T assembly comparative analysis provided valuable foundations further revealing improvement traits.

Language: Английский

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Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(6), P. 867 - 883

Published: April 27, 2024

Given the escalating impact of climate change on agriculture and food security, gaining insights into evolutionary dynamics climatic adaptation uncovering climate-adapted variation can empower breeding climate-resilient crops to face future change. Alfalfa (Medicago sativa subsp. sativa), queen forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses In this study, we performed population genomic analyses using genome resequencing data from 702 accessions 24 Medicago unravel alfalfa's genetic susceptibility We found that interspecific exchange has contributed gene pool alfalfa, particularly enriching defense stress-response genes. Intersubspecific introgression between M. falcata (subsp. falcata) alfalfa not only aids but also introduces burden. A total 1671 genes were associated with adaptation, 5.7% them introgressions falcata. By integrating climate-associated variants data, identified populations are vulnerable change, in higher latitudes Northern Hemisphere. These findings serve as a clarion call targeted conservation initiatives efforts. pre-adaptive demonstrate heightened resilience fluctuations, illuminating pathway strategies. Collectively, study enhances our understanding about local mechanisms facilitates cultivars, contributing effective agricultural strategies facing

Language: Английский

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