Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of the Ve Locus

Udriște, Anca-Amalia; IORDĂCHESCU, Mihaela; Ciceoi, R.; Bădulescu, L.

doi:10.3390/ijms23179750

Cited by 8 publications

(6 citation statements)

References 37 publications

(51 reference statements)

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“…Higher SNP and InDel densities have been observed in other plant species such as Sorghum spp. [75,76], Solanum lycopersicum L. [77,78], and Capsicum spp. [79].…”

Section: Discussionmentioning

confidence: 99%

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Genomic Analysis of Romanian Lycium Genotypes: Exploring BODYGUARD Genes for Stress Resistance Breeding

Ciceoi,

Asanica,

Luchian

et al. 2024

IJMS

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Goji berries, long valued in Traditional Chinese Medicine and Asian cuisine for their wide range of medicinal benefits, are now considered a ‘superfruit’ and functional food worldwide. Because of growing demand, Europe and North America are increasing their goji berry production, using goji berry varieties that are not originally from these regions. European breeding programs are focusing on producing Lycium varieties adapted to local conditions and market demands. By 2023, seven varieties of goji berries were successfully registered in Romania, developed using germplasm that originated from sources outside the country. A broader project focused on goji berry breeding was initiated in 2014 at USAMV Bucharest. In the present research, five cultivated and three wild L. barbarum genotypes were compared to analyse genetic variation at the whole genome level. In addition, a case study presents the differences in the genomic coding sequences of BODYGUARD (BDG) 3 and 4 genes from chromosomes 4, 8, and 9, which are involved in cuticle-related resistance. All three BDG genes show distinctive differences between the cultivated and wild-type genotypes at the SNP level. In the BDG 4 gene located on chromosome 8, 69% of SNPs differentiate the wild from the cultivated genotypes, while in BDG 3 on chromosome 4, 64% of SNPs could tell the difference between the wild and cultivated goji berry. The research also uncovered significant SNP and InDel differences between cultivated and wild genotypes, in the entire genome, providing crucial insights for goji berry breeders to support the development of goji berry cultivation in Romania.

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“…Higher SNP and InDel densities have been observed in other plant species such as Sorghum spp. [75,76], Solanum lycopersicum L. [77,78], and Capsicum spp. [79].…”

Section: Discussionmentioning

confidence: 99%

“…Following this external lysis step, the automatic DNA extraction continued in the InnuPure C16 automated system, as per the manufacturer's guidelines. DNA quantification was performed using a NanoDrop™ 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) [78].…”

Section: Dna Extractionmentioning

confidence: 99%

Genomic Analysis of Romanian Lycium Genotypes: Exploring BODYGUARD Genes for Stress Resistance Breeding

Ciceoi,

Asanica,

Luchian

et al. 2024

IJMS

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“…When looking at the SNP data, predictably, the highest number of SNP types were transitions (C:G>T:A and T:A>C:G), a phenomenon observed before [46], due to mutations resulting from the deamination of methylated cytosine residues [47]. Although the effective number of SNPs and InDels originate from just ~19-28% of the genome, it still indicates high numbers of mutations in regions of interest such as exonic regions.…”

Section: Discussionmentioning

confidence: 99%

Looking in the Scaffold 22 Hotspot for Differentially Regulated Genes Genomic Sequence Variation in Romanian Blueberry Cultivars

Mihai,

Bădulescu,

Asănică

et al. 2024

Horticulturae

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Since its domestication about a century ago in North America, highbush blueberry (Vaccinium corymbosum L.) has gained appreciation by consumers worldwide, and the demand for new blueberry varieties is increasing. Whole-genome resequencing can help plant breeders to decrease the time needed to create novel varieties by identifying novel genes linked to fruit-quality traits. The present study analyzed the genetic variability of eight V. corymbosum genotypes, seven Romanian varieties (‘Prod’, ‘Vital’, ‘Azur’, ‘Simultan’, ‘Delicia’, ‘Compact’, and ‘Safir’), and the American variety, ‘Bluecrop’. The analysis of the first ~10 Mb from scaffold 22, a hotspot of genomic variation, in the above-mentioned varieties revealed multiple differences in 11 upregulated and 50 downregulated genes involved in fruit growth and development. Of these differentially regulated genes, two upregulated and five downregulated genes were fully covered by at least 1× coverage depth by sequencing. The genes’ sequence analysis confirmed the high genetic variability of the region, with most of the genes presenting numerous SNPs and some InDels, and indicated that an attempted 10× medium-coverage depth of sequencing for V. corymbosum varieties yields useful preliminary data for use in breeding programs.

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“…To date, the genomic sequence for several crop plants such as rice, wheat, maize, sorghum, soybean and tomato has been published. Apart from these crop plants, the sequence of model plants such as Arabidopsis thaliana and Brachypodium distachyon has also been published [ 74 ]. Genome sequencing provides detailed data on the features of genomes (coding as well as non-coding genes), GC content, repetitive elements as well as regulatory sequences [ 75 ].…”

Section: Genomicsmentioning

confidence: 99%

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses

Roychowdhury

Das²,

Gupta

et al. 2023

Genes

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The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the ‘omics’ toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant’s genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence ‘multi-omics’) integrated-omics approaches can decipher the plant’s abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop’s variable abiotic stress tolerance to ensure food security under changing environmental circumstances.

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Next-Generation Sequencing of Local Romanian Tomato Varieties and Bioinformatics Analysis of the Ve Locus

Cited by 8 publications

References 37 publications

Genomic Analysis of Romanian Lycium Genotypes: Exploring BODYGUARD Genes for Stress Resistance Breeding

Genomic Analysis of Romanian Lycium Genotypes: Exploring BODYGUARD Genes for Stress Resistance Breeding

Looking in the Scaffold 22 Hotspot for Differentially Regulated Genes Genomic Sequence Variation in Romanian Blueberry Cultivars

Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses

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