Biology subjects

Vrebalov, J.

Publications and source records attributed to Vrebalov, J..

4 recordsLinked to original sources

bioRxiv2026

Allele-specific expression reveals complex cis- and trans-regulatory divergence underlying fruit phenotypic differences between cultivated and wild tomato species

Tomato (Solanum lycopersicum) is one of the most important agricultural crops and serves as a model system for fleshy fruit biology. However, domestication bottlenecks have led to limited genetic diversity for further crop improvement. Wild relatives represent a rich reservoir of phenotypic diversity, yet the molecular basis underlying such phenotypic diversity remains largely unknown. As gene expression variation is a major driver of phenotypic diversity, we performed genome-wide allele-specific expression analyses in F1 hybrids between cultivated tomato and three wild relatives spanning a range of evolutionary distances, across three fruit tissues and multiple developmental stages. Our analysis generated a multi-species map of cis - and trans-regulatory variation, revealing a predominant role of cis-regulatory effects in expression divergence across species, tissues, and stages. The majority of cis effects were tissue- and/or stage-specific, underscoring the importance of tissue context in regulatory variation. Regulatory mechanisms and inheritance patterns shifted with evolutionary distance, with more distantly related species showing increased cis-regulatory contributions. Finally, we identified extensive regulatory divergence in biosynthetic pathways related to fruit nutritional value and flavor quality, including carotenoids, flavonoids, alkaloids, sugars, and volatiles. This study presents a high-resolution map of regulatory variation underlying tomato fruit development and provides evolutionary insights into the regulation of fruit nutrition and flavor traits.

genomics↗

bioRxiv2021

Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controlling the onset and progression of ripening could prove essential to maintain high-quality grapes and wines. Through a deep inspection of previously published transcriptomic data we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation whose induction precedes the expression of well-known ripening associated genes. We explored VviCARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient VviCARPO overexpressing grapevine plants to define a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that VviCARPO induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated through a VviCARPO-VviNAC03 regulatory complex. Despite showing a closer phylogenetic relationship to senescent-related AtNAP homologues, VviCARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our data supports CARPO as a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience. SIGNIFICANT STATEMENTCARPO is a grape NAC transcription factor central to fruit ripening and tissue senescence. This regulator influences multiple biological pathways common to both processes including cell wall metabolism, chlorophyll degradation, pigment production and hormone synthesis/signaling through regulation of their key genes. As various external stresses and changing climatic conditions influence vegetative growth and berry ripening, CARPO could prove a useful genetic and breeding target towards maintaining necessary crop performance and fruit-quality characteristics.

plant biology↗

bioRxiv2020

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern breeding of tomato. Here we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 high-confidence structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions unravels alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous novel SVs underlying genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and novel SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

genomics↗

bioRxiv2019

Allelic diversity of NAC18.1 is a major determinant of fruit firmness and harvest date in apple (Malus domestica)

Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of ripening and associated textural changes are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from [~]800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after three months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein with high similarity to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). To test whether these genes are functionally orthologous, we introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.

plant biology↗