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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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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Comparative gametogenesis and genomic signatures associated with pollen sterility in the seedless mutant of grapevine

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 3, 2025

Seedless grapes are in high demand for fresh and dry fruit consumption. Seedlessness (Vitis vinifera L.) is triggered by two different mechanisms: stenospermocarpy parthenocarpy. However, the key regulators of seed development their targets not well characterized. The present study used seeded grape hybrid ARI 516 its seedless mutant to understand molecular mechanisms controlling phenotype grapes. Gametogenesis studies demonstrated that exhibits pollen sterility due abnormal morphology, significantly low viability, a complete lack germination ability. macrogametophyte was smaller than 516. Transcriptomic comparisons were performed during three developmental stages, including pre-flowering stage E-L 15, anthesis 23, berry formation 31, altered processes Genes downregulated enriched male gametophyte development-related pathways, which may cause sterility. RNAseq results validated qRT-PCR. Genome sequence data also identify induced mutations mutant, revealed homozygous 25 heterozygous InDels genes related development. genome sequencing collectively indicate parthenocarpic aberrant physiological involved formation, maturation showed downregulation transcription factors target cell division, gibberellin biosynthesis signalling, wall development, organization, germination. This represents comprehensive attempt putative candidate associated with using genomic approaches.

Language: Английский

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PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Transposable element (TE) annotation is crucial for understanding genetics, genomics and evolution, yet current methods struggle to identify TEs in graph-based pangenomes. We developed a framework PanTE construct accurate representative TE libraries both single genomes graph the first of its kind capable being directly applied pangenomes build population-level libraries. By partially reimplementing RepeatModeler2 integrating key innovations, including pangenome disassembly, alignment-free LTR structure detection, machine learning-based classifier efficiency-boosting strategies, outperformed by efficiently handling large genomes, detecting high-abundance LTR-retrotransposons, providing robust classification with superior computational efficiency. Compared EDTA, it annotated ~ 26% more grapevine genome achieved up 13 times faster runtimes wheat genome. represents significant advancement population-wide discovery, making particularly valuable pangenomic studies.

Language: Английский

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The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(6)

Published: Feb. 7, 2025

Hemizygous genes, which are present on only one of the two homologous chromosomes diploid organisms, have been mainly studied in context sex and sex-linked genes. However, these genes can also occur autosomes plants due to structural variants (SVs), such as a deletion/insertion allele, this phenomenon largely unexplored plants. Here, we investigated genomic epigenomic landscapes hemizygous across 22 genomes with varying propagation histories: eleven clonal lineages, seven outcrossed samples, four inbred putatively homozygous genomes. We identified SVs leading genic hemizygosity. As expected, very few (0.01 1.2%) were genomes, representing negative controls. Hemizygosity was appreciable among averaging 8.7% but consistently elevated for samples at 13.8% likely reflecting heterozygous SV accumulation during propagation. Compared more often situated centromeric than telomeric regions experienced weaker purifying selection. They had reduced levels expression, ~20% expression violating evolutionary model dosage compensation. detected higher DNA methylation transposable elements, may contribute their expression. Finally, profiles showed that specifically expressed contexts related fruit development, organ differentiation, stress responses. Overall, accumulate clonally propagated lineages display distinct genetic epigenetic features compared shedding unique insights into studies breeding programs crops.

Language: Английский

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Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine

Horticultural Plant Journal, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

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Telomere‐to‐telomere reference genome reveals subgenome divergence and large structural variants in Capsella bursa‐pastoris (Brassicaceae)

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

Published: March 29, 2025

Abstract Capsella is a model genus for studying polyploid speciation and mating system transitions. Here, we report subgenome‐resolved telomere‐to‐telomere reference genome of bursa‐pastoris , the only species in genus, generated by incorporating PacBio HiFi reads, Nanopore ultra‐long Hi‐C data. The assembled genome, named Cbp_T2T, consisted 16 chromosomes, with 8 each two subgenomes. size final assembly was 330.91 Mb. Multiple evaluation methods confirmed contiguity (contig N50: 20.28 Mb), completeness (Benchmarking Universal Single ‐ Copy Orthologue: 98.70%), accuracy (QV: 35.76) genome. Repetitive sequences accounted 37.04% size. In total, 27,626 28,096 protein‐coding genes were annotated subgenomes, respectively. Large structural variants observed between Additionally, large inversions on chromosomes 6 7, spanning approximately 1.93 2.33 Mb, respectively, detected comparing Cbp_T2T to previously published chromosome‐scale C. assembly. This high‐quality will facilitate evolutionary biological functional genomic studies species.

Language: Английский

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Somatic variations in the meiosis‐specific gene CrMER3 confer seedlessness in a citrus bud sport

Journal of Integrative Plant Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Seedlessness is a most valuable trait in fruit crops for fresh consumption and processing. The mutations essential meiosis genes are known to confer sterility seed abortion plants. However, defects have rarely been reported crops. Here, we found caused seedless citrus bud sport cultivar, with massive unpaired univalents during diakinesis, indicating disruption crossover formation. A non-functional CrMER3A-103 bp allele 103-bp deletion the gene body, together other CrMER3a T exon, were identified cultivar. CrMER3 protein was undetectable at meiotic prophase I knock out of resulted precocious Mini-citrus. Therefore, natural variation responsible seedlessness this originated from primitive wild mandarin passed cultivated mandarins. Kompetitive Allele-Specific PCR (KASP) marker developed identify germplasm screen potential sterile hybrids cross breeding. Uncovering enhances our understanding mechanisms controlling facilitates breeding varieties.

Language: Английский

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Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in Xingjiang

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 14, 2024

Abstracts Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is recognized its exceptional fruit traits. There are two main types Munage: white (WM) and red (RM). However, the lack a high-quality genomic resources impeded effective breeding restricted potential expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies WM RM, alongside integrated whole resequencing (WGS) data transcriptome illuminate specific mutations associated genes Munake with color Selective analysis between Munage clones Eurasian grapes suggested adaptive selection exists grapes, enriched processes including cell maturation, plant epidermal differentiation, root differentiation. The study examined within found PMAT2 on chromosome 12 MYB123 13 likely responsible variation RM. These findings provide crucial genetic investigating genetics Chinese variety, will facilitate improvement grapevine.

Language: Английский

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A simple method to efficiently generate structural variation in plants

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 21, 2024

Abstract Phenotypic variation is essential for the selection of new traits interest. Structural variants, consisting deletions, duplications, inversions, and translocations, have greater potential phenotypic consequences than single nucleotide variants. Pan-genome studies highlighted importance structural in evolution novel traits. Here, we describe a simple method to induce plants. We demonstrate that short period growth on topoisomerase II inhibitor etoposide induces heritable altered phenotypes Arabidopsis thaliana at high frequency. Using long-read sequencing genetic analyses, identified deletions inversions underlying semi-dominant recessive phenotypes. This requires minimal resources, potentially applicable any plant species, can replace irradiation as source induced large-effect variation.

Language: Английский

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