Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber

N, Pradeepkumara; Sharma, Parva Kumar; Munshi, A. D.; Behera, Tusar Kanti; Bhatia, Reeta; Kumari, Khushboo; Singh, Jogendra; Jaiswal, Sarika; Iquebal, Mir Asif; Arora, Ajay; Rai, Anil; Kumar, Dinesh; Bhattacharya, Ramcharan; Dey, S. S.

doi:10.1016/j.ygeno.2022.110273

Cited by 7 publications

(11 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Two contrasting genotypes, DC-48 (better keeping quality) and DC-83 (poor keeping quality) were grown in the research field of the Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi (28.6377° N, 77.1571° E) under protected condition using insect proof net during the spring summer season of 2019. The genotype, DC-48 and DC-83, were slicing type cucumbers and belong to the same species, C. sativus L. Description of the genotypes and their detailed characterization for keeping quality is discussed in our earlier report ( Pradeepkumara et al, 2022 ). Suitable cultural practices were followed for raising a healthy crop.…”

Section: Methodsmentioning

confidence: 99%

“…Samples were collected at 5DAP and 10DAP using the normally developed fruits for RNA-seq. Sampling of the fruits and isolation of RNA was done in triplicate as per the procedure discussed by Pradeepkumara et al (2022) . Uniformly peeled surface tissues of the fruit epicarp (2 mm) were used for RNA extraction and high throughput sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Roles of lncRNA and circRNA associated with this extremely important trait in the genotype, DC-48 will provide insight into the complex mechanisms associated with the extended shelf-life. Another contrasting genotype, DC-83 with very poor shelf life and become unfit for marketing within 2–3 days after harvesting ( Pradeepkumara et al, 2022 ) was taken along with DC-48 for the present study to understand the role of lncRNA and circRNA in regulating shelf-life of cucumber. In most vegetable crops, it is widely known that pre-harvest metabolic processes driven by the genetic makeup of the mother plant play important role in determining the post-harvest behavior of the fruits ( Weston and Barth, 1997 ; Arah et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

et al. 2022

Self Cite

View full text Add to dashboard Cite

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2–3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10–15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…To maintain the shelf life with natural colour and flavour, an antisense gene was introduced in tomatoes by a Californian company Calgene in the 1980s and developed improved shelf-life tomatoes, i.e., popularly known as FlavrSavr tomatoes ( Bruening and Lyons, 2000 ). In addition to that natural variant of cucumber fruit (DC-48:high shelf life) was also explored through qRT-PCR for fresh green colour and shelf life and found that Expansin (EXP), Polygalacturunase (PG), and xyloglucan endotransglucosylase linked with cell wall degradation process and regulates to maintain the fruit firmness ( Pradeepkumara et al, 2022 ). Several such efforts are underway in several vegetable and fruit crops.…”

Section: Strategies To Overcome Limitations Of Microgreen Productionmentioning

confidence: 99%

Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security

Gupta

Sharma

Singh³

et al. 2023

Front. Genet.

View full text Add to dashboard Cite

Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered “living superfood/functional food” due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens’stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.

show abstract

“…Cucumber ( Cucumis sativus L.) is grown commercially in tropical and subtropical climates around the world ( Pradeepkumara et al., 2022 ). In the Indian sub-continent, cucumber is grown from the highlands to the plains under open fields and protected conditions, including riverbeds.…”

Section: Introductionmentioning

confidence: 99%

Identification of a major QTL, Parth6.1 associated with parthenocarpic fruit development in slicing cucumber genotype, Pusa Parthenocarpic Cucumber-6

et al. 2022

Self Cite

View full text Add to dashboard Cite

Parthenocarpy is an extremely important trait that revolutionized the worldwide cultivation of cucumber under protected conditions. Pusa Parthenocarpic Cucumber-6 (PPC-6) is one of the important commercially cultivated varieties under protected conditions in India. Understanding the genetics of parthenocarpy, molecular mapping and the development of molecular markers closely associated with the trait will facilitate the introgression of parthenocarpic traits into non-conventional germplasm and elite varieties. The F1, F2 and back-crosses progenies with a non-parthenocarpic genotype, Pusa Uday indicated a single incomplete dominant gene controlling parthenocarpy in PPC-6. QTL-seq comprising of the early parthenocarpy and non-parthenocarpic bulks along with the parental lines identified two major genomic regions, one each in chromosome 3 and chromosome 6 spanning over a region of 2.7 Mb and 7.8 Mb, respectively. Conventional mapping using F2:3 population also identified two QTLs, Parth6.1 and Parth6.2 in chromosome 6 which indicated the presence of a major effect QTL in chromosome 6 determining parthenocarpy in PPC-6. The flanking markers, SSR01148 and SSR 01012 for Parth6.1 locus and SSR10476 and SSR 19174 for Parth6.2 locus were identified and can be used for introgression of parthenocarpy through the marker-assisted back-crossing programme. Functional annotation of the QTL-region identified two major genes, Csa_6G396640 and Csa_6G405890 designated as probable indole-3-pyruvate monooxygenase YUCCA11 and Auxin response factor 16, respectively associated with auxin biosynthesis as potential candidate genes. Csa_6G396640 showed only one insertion at position 2179 in the non-parthenocarpic parent. In the case of Csa_6G405890, more variations were observed between the two parents in the form of SNPs and InDels. The study provides insight about genomic regions, closely associated markers and possible candidate genes associated with parthenocarpy in PPC-6 which will be instrumental for functional genomics study and better understanding of parthenocarpy in cucumber.

show abstract

Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber

Cited by 7 publications

References 87 publications

Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.)

Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security

Identification of a major QTL, Parth6.1 associated with parthenocarpic fruit development in slicing cucumber genotype, Pusa Parthenocarpic Cucumber-6

Contact Info

Product

Resources

About