Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.)
Abstract Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertil...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-29660-3 |
| _version_ | 1811165969070948352 |
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| author | Harleen Kaur Pooja Manchanda Pankaj Kumar Rajinder Kumar Dhall Parveen Chhuneja Yiqun Weng |
| author_facet | Harleen Kaur Pooja Manchanda Pankaj Kumar Rajinder Kumar Dhall Parveen Chhuneja Yiqun Weng |
| author_sort | Harleen Kaur |
| collection | DOAJ |
| description | Abstract Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon–intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents. |
| first_indexed | 2024-04-10T15:45:52Z |
| format | Article |
| id | doaj.art-f0d8b1f4a96643cc8acd9e7ca69445a4 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T15:45:52Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-f0d8b1f4a96643cc8acd9e7ca69445a42023-02-12T12:10:43ZengNature PortfolioScientific Reports2045-23222023-02-0113112110.1038/s41598-023-29660-3Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.)Harleen Kaur0Pooja Manchanda1Pankaj Kumar2Rajinder Kumar Dhall3Parveen Chhuneja4Yiqun Weng5School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural UniversityDepartment of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural UniversityUSDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of WisconsinAbstract Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon–intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.https://doi.org/10.1038/s41598-023-29660-3 |
| spellingShingle | Harleen Kaur Pooja Manchanda Pankaj Kumar Rajinder Kumar Dhall Parveen Chhuneja Yiqun Weng Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) Scientific Reports |
| title | Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) |
| title_full | Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) |
| title_fullStr | Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) |
| title_full_unstemmed | Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) |
| title_short | Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.) |
| title_sort | genome wide identification and characterization of parthenocarpic fruit set related gene homologs in cucumber cucumis sativus l |
| url | https://doi.org/10.1038/s41598-023-29660-3 |
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