Population sequencing of cherry accessions unravels the evolution of Cerasus species and the selection of genetic characteristics in edible cherries

Molecular Horticulture, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 8, 2025

Abstract Cerasus is a subgenus of Prunus in the family Rosaceae that popular owing to its ornamental, edible, and medicinal properties. Understanding evolution identifying selective trait loci edible cherries are crucial for improvement cherry cultivars meet producer consumer demands. In this study, we performed de novo assembly chromosome-scale genome sweet ( avium L . ) cultivar ‘Burlat’, covering 297.55 Mb consisting eight chromosomes with 33,756 protein-coding genes. The resequencing population structural analysis 384 representative accessions revealed they could be divided into four groups (Group 1, Group 2, 3, 4). We inferred 1 was oldest Groups 4 were clades derived from it. addition, found sweeps fruit flavor improved stress resistance different varieties P. , cerasus pseudocerasus Transcriptome significant differential expression genes associated key pathways, such as sucrose starch metabolism, fructose mannose pentose phosphate pathway, between leaves fruits This study enhances understanding evolutionary processes provides resources functional genomics research cherries.

Язык: Английский

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Identifying Candidate Genes for Grape (Vitis vinifera L.) Fruit Firmness through Genome-Wide Association Studies

Journal of Agricultural and Food Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Март 26, 2025

The firmness of grape berries is a critical factor influencing their commercial feasibility and highly valued by both breeders consumers. However, berry complex quantitative trait governed multiple genes, our understanding its genetic regulatory network remains incomplete. To elucidate the mechanisms underlying firmness, this study employed genome-wide association studies (GWAS) to identify potential candidate genes associated with fruit cellulose content explore gene that controls variation. comprehensive GWAS results identified CesA as potentially regulating through involvement in biosynthesis. validate these findings, whole-genome family identification analysis was conducted. Furthermore, key VvCslD5 selected for functional validation, which included overexpression subcellular localization. This provides valuable insights into regulation biosynthesis transcriptional signaling pathways govern structure cell walls well variations firmness. These findings establish solid foundation future analyses traits will enhance breeding practices aimed at improving quality.

Язык: Английский

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Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits

Horticulture Research, Год журнала: 2023, Номер 10(10)

Опубликована: Сен. 15, 2023

In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need discover the genetic architecture of these in order enhance efficiency breeding strategies consumer and producer demands. With this objective, germplasm collection consisting 116 accessions was evaluated 23 agronomic quality over 2-6 years, characterized using genotyping-by-sequencing approach. The SNP coverage collected used conduct genome-wide association study two multilocus models three reference genomes. We identified numerous SNP-trait associations global size (weight, width, thickness), cracking, firmness, stone size, we pinpointed several candidate genes involved phytohormone, calcium, cell wall metabolisms. Finally, conducted precise literature review focusing on compare our results with potential colocalizations marker-trait associations. This brings new knowledge control important quality, development marker-assisted selection targeted towards facilitation efforts.

Язык: Английский

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A 5.2‐kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase‐like enhances fruit firmness in Prunus avium

Plant Biotechnology Journal, Год журнала: 2024, Номер 22(6), С. 1622 - 1635

Опубликована: Фев. 28, 2024

Summary Fruit firmness is an important trait in sweet cherry breeding because it directly positively influences fruit transportability, storage and shelf life. However, the underlying genes responsible molecular mechanisms that control remain unknown. In this study, we identified a candidate gene, PavSCPL , encoding serine carboxypeptidase‐like protein with natural allelic variation, controls using map‐based cloning functionally characterized during softening. Genetic analysis revealed ‘Rainier’ × ‘Summit’ F 1 population was controlled by single dominant gene. Bulked segregant combined fine mapping narrowed gene to 473‐kb region (7418778–7 891 914 bp) on chromosome 6 which included 72 genes. The null allele harbouring 5244‐bp insertion second exon completely inactivated expression resulted extra‐hard‐flesh phenotype, were RNA‐sequencing cloning. Quantitative RT‐PCR level increased Virus‐induced silencing of enhanced suppressed activities certain pectin‐degrading enzymes fruit. addition, developed functional markers for Pavscpl 5.2‐k co‐segregated trait. Overall, research crucial firmness. results provide insights into genetic mechanism present useful molecular‐assisted cherry.

Язык: Английский

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Cracking susceptibility of full-sibs of a cross of a cracking tolerant and cracking susceptible sweet cherry: Relation to cuticle characteristics, microcracking and calcium

PLoS ONE, Год журнала: 2025, Номер 20(1), С. e0316637 - e0316637

Опубликована: Янв. 3, 2025

Rain cracking compromises quality and quantity of sweet cherries worldwide. Cracking susceptibility differs among genotypes. The objective was to (1) phenotype the progeny a cross between tolerant susceptible cherry cultivar for cuticle mass per unit area, strain release on isolation, cuticular microcracking calcium/dry ratio (2) relate these characteristics susceptibilities evaluated in laboratory immersion assays published multiyear field observations. Mass dewaxed area upon isolation were significantly related lab or field. Cuticular stylar end region as indexed by infiltration with acridine orange more severe than genotypes correlated Ca/dry lower (-8%) Fruit that cracked early had less Ca those later. Only Based stepwise regression analyses accounted most (partial r 2 = 0.331 0.338 vs. 0.326 0.453 lab). variability increased 0.571 (lab) when adding cuticle, up 0.421 (field) 0.478 entering into model. A protocol phenotyping is suggested allows larger progenies be phenotyped microcracking, DCM release.

Язык: Английский

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Overview of fruit cracking in sweet cherry (Prunus avium L.): causes, testing methods, mitigation strategies, and research perspectives

Frontiers in Sustainable Food Systems, Год журнала: 2025, Номер 9

Опубликована: Апрель 30, 2025

Sweet cherry ( Prunus avium L.) is one of the fruits that are widely acclaimed around world. However, its prone to cracking from onset color full maturity, especially in cherry-producing regions where rain events common near harvest. Cracked cherries have an unpleasant appearance, as well susceptible invasion by fungal pathogens, therefore dramatically depreciated, incurring considerable economic losses growers, quite dampening their planting enthusiasm, subsequently restricting advancement sweet industry. The incidence and severity fruit affected genotypic, environmental, agronomic factors. This review provides overview causes, testing methods, mitigation strategies related cherry. Based on recent research advances, this proposes perspectives developing crack resistant varieties a promising strategy mitigate

Язык: Английский

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Genomes and integrative genomic insights into the genetic architecture of main agronomic traits in the edible cherries

Horticulture Research, Год журнала: 2024, Номер 12(1)

Опубликована: Сен. 20, 2024

Язык: Английский

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A major QTL identification and candidate gene analysis of watermelon fruit cracking using QTL-seq and RNA-seq

Frontiers in Plant Science, Год журнала: 2023, Номер 14

Опубликована: Май 15, 2023

Fruit cracking decreases the total production and commercial value of watermelon. The molecular mechanisms fruit are unknown. In this study, 164 recombinant inbred lines (RILs) watermelon, derived from crossing WQ1 (cracking-sensitive) WQ2 (cracking-tolerant) lines, were sequenced using specific length amplified fragment sequencing (SLAF-seq). A high-density genetic linkage map was constructed with 3,335 markers spanning 1,322.74 cM, at an average 0.40 cM across whole-genome flanking markers. tolerance capacity (CTC), depth (DFC), rind thickness (RT), hardness (RH) measured for quantitative trait locus (QTL) analysis. Of four traits analyzed, one major QTL high phenotypic variation (41.04%–61.37%) detected 76.613–76.919 on chromosome 2, which contained 104 annotated genes. Differential gene expression analysis RNA (RNA-seq) data between two parents identified 4,508 differentially expressed genes (DEGs). Comparison region DEGs obtained eight coexisting Quantitative real-time PCR (qRT-PCR) revealed that these significant parents. These results provide new insights into identification QTLs or marker-assisted breeding in

Язык: Английский

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Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry

PLoS ONE, Год журнала: 2023, Номер 18(2), С. e0272888 - e0272888

Опубликована: Фев. 7, 2023

Breeders, collection curators, and other germplasm users require genetic information, both genome-wide locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform provide profiles for elite could also locus-specific genotypic information. However, information loci of interest such as those within PCR-based DNA fingerprinting panels trait-predictive tests is not readily extracted from array data, thus creating a disconnect between historic new data sets. This study aimed establish method deducing genotypes at associated haplotypes, demonstrated two fruit crops three locus types: quantitative trait Ma Ma3 acidity in apple, apple microsatellite marker GD12, Mendelian R f sweet cherry color. Using phased an 8K 6K array, unique haplotypes spanning each target were with alleles important breeding parents. These compared via identity-by-descent (IBD) or identity-by-state (IBS) present U.S. programs deduce this germplasm. While IBD segments confidently tracked through pedigrees, confidence allele identity among IBS used shared length threshold. At least one per was deduced 64–93% 181 individuals. Successful validation GD12 reported newly obtained genotypes. Our approach can efficiently merge expand sets, missing identifying errors, appropriate any crop especially where linkage disequilibrium high. Locus-specific expected enhance management resources.

Язык: Английский

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Genome-Wide Exploration of the Ethylene-Responsive Element-Binding Factor Gene Family in Sweet Cherry (Prunus avium L.): Preliminarily Unveiling Insights into Normal Development and Fruit Cracking

Horticulturae, Год журнала: 2024, Номер 10(3), С. 247 - 247

Опубликована: Март 3, 2024

The ERF subfamily, a significant part of the APETALA2/ethylene-responsive element-binding factor (AP2/ERF) transcription family, plays crucial role in plant growth, development, and stress responses. Despite its importance, research on this gene family sweet cherry (Prunus avium L.) is limited. This study identified analyzed subfamily terms classification, physicochemical properties, structural characteristics, chromosome distribution, replication collinearity, Cis-acting elements, potential protein interactions. Preliminary investigations during fruit cracking normal development were also conducted. Fifty ERFs (PatiERF1~50) identified, distributed unevenly across eight chromosomes classified into ten groups with nineteen conserved motifs. Collinearity analysis other species revealed homology, highest number orthologous genes found apple (Malus domestica L.). particularly abscisic acid response factor, abundant PatiERF promoters. Weighted co-expression network (WGCNA) quantitative real-time PCR (RT-qPCR) indicated involvement PatiERFs cracking, nine four candidates related to these processes speculated, respectively. Furthermore, classes factors (TFs), namely MYB, GRAS, BHLH, BZIP, as well 23 structure genes, predicted have interaction relationships development. suggests their synergistic regulation process. Our represents first comprehensive genome-wide cherry, laying foundation for deeper understanding molecular mechanisms correlated mediated by genes.

Язык: Английский

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