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Xiong Y, He J, Li M, Du K, Lang H, Gao P, Xie Y. Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Yellow-Fleshed Kiwifruit. Int J Mol Sci 2023; 24:ijms24021573. [PMID: 36675098 PMCID: PMC9867141 DOI: 10.3390/ijms24021573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
During the development of yellow-fleshed kiwifruit (Actinidia chinensis), the flesh appeared light pink at the initial stage, the pink faded at the fastest growth stage, and gradually changed into green. At the maturity stage, it showed bright yellow. In order to analyze the mechanism of flesh color change at the metabolic and gene transcription level, the relationship between color and changes of metabolites and key enzyme genes was studied. In this study, five time points (20 d, 58 d, 97 d, 136 d, and 175 d) of yellow-fleshed kiwifruit were used for flavonoid metabolites detection and transcriptome, and four time points (20 d, 97 d, 136 d, and 175 d) were used for targeted detection of carotenoids. Through the analysis of the content changes of flavonoid metabolites, it was found that the accumulation of pelargonidin and cyanidin and their respective anthocyanin derivatives was related to the pink flesh of young fruit, but not to delphinidin and its derivative anthocyanins. A total of 140 flavonoid compounds were detected in the flesh, among which anthocyanin and 76% of the flavonoid compounds had the highest content at 20 d, and began to decrease significantly at 58 d until 175 d, resulting in the pale-pink fading of the flesh. At the mature stage of fruit development (175 d), the degradation of chlorophyll and the increase of carotenoids jointly led to the change of flesh color from green to yellow, in addition to chlorophyll degradation. In kiwifruit flesh, 10 carotenoids were detected, with none of them being linear carotenoids. During the whole development process of kiwifruit, the content of β-carotene was always higher than that of α-carotene. In addition, β-cryptoxanthin was the most-accumulated pigment in the kiwifruit at 175 d. Through transcriptome analysis of kiwifruit flesh, seven key transcription factors for flavonoid biosynthesis and ten key transcription factors for carotenoid synthesis were screened. This study was the first to analyze the effect of flavonoid accumulation on the pink color of yellow-fleshed kiwifruit. The high proportion of β-cryptoxanthin in yellow-fleshed kiwifruit was preliminarily found. This provides information on metabolite accumulation for further revealing the pink color of yellow-fleshed kiwifruit, and also provides a new direction for the study of carotenoid biosynthesis and regulation in yellow-fleshed kiwifruit.
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Affiliation(s)
- Yun Xiong
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Junya He
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Mingzhang Li
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
| | - Kui Du
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
| | - Hangyu Lang
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ping Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yue Xie
- Key Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610065, China
- Correspondence:
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Kaur B, Garcha KS, Bhatia D, Khosa JS, Sharma M, Mittal A, Verma N, Dhatt AS. Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin. FRONTIERS IN PLANT SCIENCE 2022; 13:948106. [PMID: 36035714 PMCID: PMC9406289 DOI: 10.3389/fpls.2022.948106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/12/2022] [Indexed: 06/01/2023]
Abstract
The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., "NAC" (Cp4.1LG12g04350) and "MYB" (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.
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Affiliation(s)
- Barinder Kaur
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karmvir Singh Garcha
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jiffinvir Singh Khosa
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Madhu Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Neha Verma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ajmer Singh Dhatt
- Directorate of Research, Punjab Agricultural University, Ludhiana, Punjab, India
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Amoroso CG, Andolfo G, Capuozzo C, Di Donato A, Martinez C, Tomassoli L, Ercolano MR. Transcriptomic and genomic analysis provides new insights in molecular and genetic processes involved in zucchini ZYMV tolerance. BMC Genomics 2022; 23:371. [PMID: 35578183 PMCID: PMC9109310 DOI: 10.1186/s12864-022-08596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cucurbita pepo is highly susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species cannot be considered as complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post-inoculation (DPI) at transcriptomic and genomic levels. RESULTS The comparative RNA-sequencing (RNA-Seq) of TF (susceptible to ZYMV) and 381e (tolerant to ZYMV) allowed the evaluation of about 33,000 expressed transcripts and the identification of 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible cultivar TF triggered oxidative processes related to response to biotic stimulus and activated key regulators of plant virus intercellular movement. In addition, the discovery of variants located in transcripts allowed the identification of two chromosome regions rich in Single Nucleotide Polymorphisms (SNPs), putatively introgressed from C. moschata, containing genes exclusively expressed in 381e. CONCLUSION 381e transcriptome analysis confirmed a global improvement of plant fitness by reducing the virus titer and movement. Furthermore, genes implicated in ZYMV tolerance in C. moschata introgressed regions were detected. Our work provides new insight into the plant virus recovery process and a better understanding of the molecular basis of 381e tolerance.
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Affiliation(s)
- C G Amoroso
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - G Andolfo
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - C Capuozzo
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - A Di Donato
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy
| | - C Martinez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, 04120, Almería, Spain
| | - L Tomassoli
- Consiglio Per La Ricerca in Agricoltura e l'Analisi Dell'Economia Agraria, Research Centre of Plant Control and Certification, Rome, Italy
| | - M R Ercolano
- Department of Agricultural Science, University of Naples "Federico II", Portici, NA, Naples, Italy.
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Influence of the Electrical Conductivity of the Nutrient Solution in Different Phenological Stages on the Growth and Yield of Cherry Tomato. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Soilless cultivation is an important alternative to traditional agriculture and facilitates harvest by allowing for the precise control of plant nutrients to maximize the vegetable production of uniform fruits. Nutrient solution concentration is a critical factor affecting nutrient supply in soilless cultivation. Although some nutrient solution concentrations throughout the growth cycle for tomatoes have been developed, there are limited studies on nutrient solution concentrations at different phenological stages. Hence, we studied the effects of nutrient solution concentrations in different growth stages on the physiology, yield and fruit quality of cherry tomatoes with a previously developed nutrient solution formulation. The whole growth cycle of the tomato was divided into three stages which were irrigated with a nutrient solution with different electrical conductivities (ECs). A total of five treatments were set: CK (EC was 3.0 ms·cm−1 for the 1st–3rd stage), T1 (EC was 1.5 ms·cm−1 for the 1st stage, 3.0 ms·cm−1 for the 2nd–3rd stage), T2 (EC was 1.5 ms·cm−1 for the 1st stage, 3.0 ms·cm−1 for the 2nd stage, 4.5 ms·cm−1 for the 3rd stage ), T3 (EC was 1.5 ms·cm−1 for the 1st–2nd stage, 3.0 ms·cm−1 for the 3rd stage), and T4 (EC was 1.5 ms·cm−1 for the 1st stage, 4.5 ms·cm−1 for the 2nd–3rd stage). The results showed that the tomato plants treated with T2 and T4 had the strongest growth (with the highest plant height and leaf formation) as well as the best leaf photosynthetic performance (the chlorophyll content and the net photosynthetic rate were significantly increased). Additionally, the use of T2 and T4 significantly improved cherry tomato fruit quality as reflected by the significant promotion of total soluble solids by 9.1% and 9.8%, respectively, as well as by the improvement of maturity by 12.9% and 13.7%, respectively. Additionally, the yields for treatments T2 and T4 were increased by 7.3% and 13.4%, respectively, which was mainly due to the increase in single fruit weight. More importantly, nutrient solution EC management improved fertilizer use efficiency: the partial fertilizer productivity of T1, T2, and T4 was increased by 2%, 7% and 14%, respectively, while that of T3 was reduced by 7%. A comprehensive comparison showed that the ranking of the effect on production was T4 > T2 > T1 > CK > T3. Our results suggest that the regulation of EC in different growth stages affects the growth and yield characteristics of cherry tomatoes. This study may provide some references for further research to adjust the concentration of nutrient solutions to improve the utilization rate of fertilizer and fruit quality.
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Wang X, Wang A, Li Y, Xu Y, Wei Q, Wang J, Lin F, Gong D, Liu F, Wang Y, Peng L, Li J. A Novel Banana Mutant " RF 1" ( Musa spp. ABB, Pisang Awak Subgroup) for Improved Agronomic Traits and Enhanced Cold Tolerance and Disease Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:730718. [PMID: 34630479 PMCID: PMC8496975 DOI: 10.3389/fpls.2021.730718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Banana is a major fruit crop grown in tropical and subtropical regions worldwide. Among cultivars, "FenJiao, FJ" (Musa spp. ABB, Pisang Awak subgroup) is a popular variety of bananas, due to its better sugar-acid blend and relatively small fruit shape. However, because the traditional FJ variety grows relatively high in height, it is vulnerable to lodging and unsuitable for harvesting. In this study, we sought desirable banana mutants by carrying out ethyl methanesulfonate (EMS) mutagenesis with the FJ cultivar. After the FJ shoot tips had been treated with 0.8% (v/v) EMS for 4 h, we obtained a stably inherited mutant, here called "ReFen 1" (RF1), and also observed a semi-dwarfing phenotype. Compared with the wild type (FJ), this RF1 mutant featured consistently improved agronomic traits during 5-year field experiments conducted in three distinct locations in China. Notably, the RF1 plants showed significantly enhanced cold tolerance and Sigatoka disease resistance, mainly due to a substantially increased soluble content of sugar and greater starch accumulation along with reduced cellulose deposition. Therefore, this study not only demonstrated how a powerful genetic strategy can be used in fruit crop breeding but also provided insight into the identification of novel genes for agronomic trait improvement in bananas and beyond.
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Affiliation(s)
- Xiaoyi Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Anbang Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yujia Li
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Xu
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qing Wei
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashui Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Fei Lin
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Deyong Gong
- The Fruit Tree Research Center, Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xinyi, China
| | - Fei Liu
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingyang Li
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Xu X, Lu X, Tang Z, Zhang X, Lei F, Hou L, Li M. Combined analysis of carotenoid metabolites and the transcriptome to reveal the molecular mechanism underlying fruit colouration in zucchini ( Cucurbita pepo L.). FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 2:100021. [PMID: 35415627 PMCID: PMC8991947 DOI: 10.1016/j.fochms.2021.100021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
14 Carotenoids were detected and quantified in three Zucchini fruits by LC-MS/MS. Plenty Lutein and less Chlorophyll were identified in yellow and orange fruits. A total of 664 DEGs were identified by transcriptome analysis. Hub DEGs related to Chlorophyll and Carotenoids were associated by WGCNA. A model of gene regulatory network was proposed for Zucchini peel coloration.
To reveal the molecular mechanism underlying peel colouration, carotenoid metabolites and the transcriptome were jointly analysed in zucchini peels with three different colours: light green (Lg), yellow (Y), and orange (O). Our results showed that the carotenoid levels in O (157.075 μg/g) and Y (22.734 μg/g) were both significantly higher than in Lg (7.435 μg/g), while the chlorophyll content was highest in Lg (32.326 μg/g), followed by O (7.294 μg/g) and Y (4.617 μg/g). A total of 14 carotenoids were detected in zucchini peels, primarily lutein (103.167 μg/g in Lg, 509.667 μg/g in Y, and 1543.333 μg/g in O). In particular, significant accumulation of antheraxanthin, zeaxanthin, neoxanthin, and β-cryptoxanthin was first reported in orange zucchini in this study. Furthermore, two modules with hub genes related to carotenoid or chlorophyll content were identified through weighted gene coexpression network analysis. Additionally, the transcription level of some hub genes (PIF4, APRR2, bHLH128, ERF4, PSY1, LCYE2, and RCCR3) was highly correlated with pigment content in the peel, which may be responsible for carotenoid accumulation and chlorophyll degradation in the Y and O varieties. Taken together, the results obtained in this study help to provide a novel mechanism underlying peel colouration in zucchini.
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Affiliation(s)
- Xiaoyong Xu
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
| | - Xiaonan Lu
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
| | - Zhongli Tang
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
| | - Xiaoning Zhang
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
| | - Fengjin Lei
- Institute of Cotton, Shanxi Agricultural University, Yuncheng, Shanxi 044000, China
| | - Leiping Hou
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
| | - Meilan Li
- College of Horticulture, Shanxi Agricultural University, Collaborative Innovation Centre for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi Province, Taigu, Shanxi 030801, China
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Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7060143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.
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Xanthopoulou A, Montero-Pau J, Picó B, Boumpas P, Tsaliki E, Paris HS, Tsaftaris A, Kalivas A, Mellidou I, Ganopoulos I. A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms. BMC Genomics 2021; 22:341. [PMID: 33980145 PMCID: PMC8114506 DOI: 10.1186/s12864-021-07683-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. RESULTS In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. CONCLUSIONS These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.
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Affiliation(s)
- Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
| | - Javier Montero-Pau
- Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE), Universitat de València, 46022 Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Panagiotis Boumpas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
| | - Eleni Tsaliki
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
| | - Harry S. Paris
- Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya‘ar Research Center, 3009500 Ramat Yishay, Israel
| | | | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001 Thermi, Macedonia Greece
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Abbas HMK, Huang HX, Wang AJ, Wu TQ, Xue SD, Ahmad A, Xie DS, Li JX, Zhong YJ. Metabolic and transcriptomic analysis of two Cucurbita moschata germplasms throughout fruit development. BMC Genomics 2020; 21:365. [PMID: 32414328 PMCID: PMC7227267 DOI: 10.1186/s12864-020-6774-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/06/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quality. RESULTS Two pumpkin germplasms, CMO-X and CMO-E, were analyzed regarding the essential quality traits such as dry weight, soluble solids, organic acids, carotenoids and sugar contents. For the comparison of fruit development in these two germplasms, fruit transcriptome was analyzed at 5 different developmental stages from 0 d to 40 d in a time course manner. Putative pathways for carotenoids biosynthesis and sucrose metabolism were developed in C. moschata fruit and homologs were identified for each key gene involved in the pathways. Gene expression data was found consistent with the accumulation of metabolites across developmental stages and also between two germplasms. PSY, PDS, ZEP, CRTISO and SUS, SPS, HK, FK were found highly correlated with the accumulation of carotenoids and sucrose metabolites, respectively, at different growth stages of C. moschata as shown by whole transcriptomic analysis. The results of qRT-PCR analysis further confirmed the association of these genes. CONCLUSION Developmental regulation of the genes associated with the metabolite accumulation can be considered as an important factor for the determination of C. moschata fruit quality. This research will facilitate the investigation of metabolic profiles in other cultivars.
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Affiliation(s)
- Hafiz Muhammad Khalid Abbas
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - He-Xun Huang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - An-Jun Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ting-Quan Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shu-Dan Xue
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aqeel Ahmad
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Da-Sen Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun-Xing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yu-Juan Zhong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Wang Y, Yan C, Zou B, Wang C, Xu W, Cui C, Qu S. Morphological, Transcriptomic and Hormonal Characterization of Trimonoecious and Subandroecious Pumpkin ( Cucurbita maxima) Suggests Important Roles of Ethylene in Sex Expression. Int J Mol Sci 2019; 20:ijms20133185. [PMID: 31261811 PMCID: PMC6651883 DOI: 10.3390/ijms20133185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Sex expression is a complex process, and in-depth knowledge of its mechanism in pumpkin is important. In this study, young shoot apices at the one-true-leaf stage and 10-leaf stage in Cucurbita maxima trimonoecious line ‘2013–12’ and subandroecious line ‘9–6’ were collected as materials, and transcriptome sequencing was performed using an Illumina HiSeqTM 2000 System. 496 up-regulated genes and 375 down-regulated genes were identified between shoot apices containing mostly male flower buds and only female flower buds. Based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the differentially expressed genes were mainly enriched in the ethylene and auxin synthesis and signal transduction pathways. In addition, shoot apices at the 4-leaf stage were treated with the ethylene-releasing agent 2-chloroethylphosphonic acid (Ethrel), aminoethoxyvinyl glycine (AVG), AgNO3 and indoleacetic acid (IAA). The number of female flowers up to node 20 on the main stem of ‘2013–12’ increased significantly after Ethrel and IAA treatment and decreased significantly after AVG and AgNO3 treatment. The female flowers in ‘9–6’ showed slight changes after treatment with the exogenous chemicals. The expression of key genes in ethylene synthesis and signal transduction (CmaACS7, CmaACO1, CmaETR1 and CmaEIN3) was determined using quantitative RT-PCR, and the expression of these four genes was positively correlated with the number of female flowers in ‘2013–12’. The variations in gene expression, especially that of CmaACS7, after chemical treatment were small in ‘9–6’. From stage 1 (S1) to stage 7 (S7) of flower development, the expression of CmaACS7 in the stamen was much lower than that in the ovary, stigma and style. These transcriptome data and chemical treatment results indicated that IAA might affect pumpkin sex expression by inducing CmaACS7 expression and indirectly affecting ethylene production, and the ethylene synthesis and signal transduction pathways play crucial roles in pumpkin flower sex expression. A possible reason for the differences in sex expression between pumpkin lines ‘2013–12’ and ‘9–6’ was proposed based on the key gene expression. Overall, these transcriptome data and chemical treatment results suggest important roles for ethylene in pumpkin sex expression.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Chundong Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Bingxue Zou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Chongshi Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Harbin 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China.
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11
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Pomares-Viciana T, Del Río-Celestino M, Román B, Die J, Pico B, Gómez P. First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). BMC PLANT BIOLOGY 2019; 19:61. [PMID: 30727959 PMCID: PMC6366093 DOI: 10.1186/s12870-019-1632-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 01/04/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy. RESULTS RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set. CONCLUSION This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.
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Affiliation(s)
- Teresa Pomares-Viciana
- Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain
| | - Mercedes Del Río-Celestino
- Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain
| | - Belén Román
- Genomics and Biotechnology Department, IFAPA Research Centre Alameda del Obispo, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Jose Die
- Genetics Department, University of Cordoba, Av. de Medina Azahara, 5, 14071 Córdoba, Spain
| | - Belén Pico
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Pedro Gómez
- Genomics and Biotechnology Department, IFAPA Research Centre La Mojonera, Camino de San Nicolás, 1, 04745 La Mojonera, Almería, Spain
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Xanthopoulou A, Montero-Pau J, Mellidou I, Kissoudis C, Blanca J, Picó B, Tsaballa A, Tsaliki E, Dalakouras A, Paris HS, Ganopoulou M, Moysiadis T, Osathanunkul M, Tsaftaris A, Madesis P, Kalivas A, Ganopoulos I. Whole-genome resequencing of Cucurbita pepo morphotypes to discover genomic variants associated with morphology and horticulturally valuable traits. HORTICULTURE RESEARCH 2019; 6:94. [PMID: 31645952 PMCID: PMC6804688 DOI: 10.1038/s41438-019-0176-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 05/20/2023]
Abstract
Cucurbita pepo contains two cultivated subspecies, each of which encompasses four fruit-shape morphotypes (cultivar groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchini genome was published, providing insights into its evolution. To expand our knowledge of evolutionary processes within C. pepo and to identify variants associated with particular morphotypes, we performed whole-genome resequencing of seven of these eight C. pepo morphotypes. We report for the first time whole-genome resequencing of the four subsp. pepo (Pumpkin, Vegetable Marrow, Cocozelle, green Zucchini, and yellow Zucchini) morphotypes and three of the subsp. ovifera (Acorn, Crookneck, and Scallop) morphotypes. A high-depth resequencing approach was followed, using the BGISEQ-500 platform that enables the identification of rare variants, with an average of 33.5X. Approximately 94.5% of the clean reads were mapped against the reference Zucchini genome. In total, 3,823,977 high confidence single-nucleotide polymorphisms (SNPs) were identified. Within each accession, SNPs varied from 636,918 in green Zucchini to 2,656,513 in Crookneck, and were distributed homogeneously along the chromosomes. Clear differences between subspecies pepo and ovifera in genetic variation and linkage disequilibrium are highlighted. In fact, comparison between subspecies pepo and ovifera indicated 5710 genes (22.5%) with Fst > 0.80 and 1059 genes (4.1%) with Fst = 1.00 as potential candidate genes that were fixed during the independent evolution and domestication of the two subspecies. Linkage disequilibrium was greater in subsp. ovifera than in subsp. pepo, perhaps reflective of the earlier differentiation of morphotypes within subsp. ovifera. Some morphotype-specific genes have been localized. Our results offer new clues that may provide an improved understanding of the underlying genomic regions involved in the independent evolution and domestication of the two subspecies. Comparisons among SNPs unique to particular subspecies or morphotypes may provide candidate genes responsible for traits of high economic importance.
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Affiliation(s)
- Aliki Xanthopoulou
- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki, 54124 Greece
| | - Javier Montero-Pau
- Department of Biochemistry and Molecular Biology, Universitat de València, 46022 Valencia, Spain
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | | | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Aphrodite Tsaballa
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Eleni Tsaliki
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Athanasios Dalakouras
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Harry S. Paris
- Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishay, Israel
| | - Maria Ganopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and MedicineChiang Mai University, Chiang Mai, Thailand
| | | | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, 57001 Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DEMETER (ex NAGREF), Thermi, Macedonia 57001 Greece
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Abstract
Zucchini (Cucurbita pepo L.), extensively cultivated in temperate areas, belongs to the Cucurbitaceae family and it is a species with great economic value. One major threat related to zucchini cultivation is the damage imposed by the cotton/melon aphid Aphis gossypii Glover (Homoptera: Aphididae). We performed RNA-sequencing on cultivar “San Pasquale” leaves, uninfested and infested by A. gossypii, that were collected at three time points (24, 48, and 96 h post infestation). Then, we combined all high-quality reads for de novo assembly of the transcriptome. This resource was primarily established to be used as a reference for gene expression studies in order to investigate the transcriptome reprogramming of zucchini plants following aphid infestation. In addition, raw reads will be valuable for new experiments based on the latest bioinformatic tools and analytical approaches. The assembled transcripts will serve as an important reference for sequence-based studies and for primer design. Both datasets can be used to support/improve the prediction of protein-coding genes in the zucchini genome, which has been recently released into the public domain.
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14
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The Potential Use of Hot Water Rinsing and Brushing Technology to Extend Storability and Shelf Life of Sweet Acorn Squash (Cucurbita pepo L.). HORTICULTURAE 2018. [DOI: 10.3390/horticulturae4030019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Acorn squash fruits (Cucurbita pepo L.) are very sweet and are an excellent source of nutrients and vitamins. Very little information is available about their optimal storage temperature or how to extend their shelf life. The present goal was to elucidate the best storage temperature of this fruit, and to evaluate hot water rinsing and brushing (HWRB) technology to maintain fruit quality for several months. The optimal storage temperature was found to be 15 °C. However, treating the fruits with HWRB at 54 °C for 15 s and then storing them at 15 °C significantly maintained fruit quality for 3.5 months, as indicated by higher fruit firmness, lower decay incidence, and improved retention of green skin color.
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15
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Montero-Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí-Gómez C, Ferriol M, Gómez P, Jamilena M, Mueller L, Picó B, Cañizares J. De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. PLANT BIOTECHNOLOGY JOURNAL 2018. [PMID: 29112324 DOI: 10.1101/147702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.
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Affiliation(s)
- Javier Montero-Pau
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Peio Ziarsolo
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - Carlos Martí-Gómez
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - María Ferriol
- Instituto Agroforestal Mediterráneo (IAM), Universitat Politècnica de València, Valencia, Spain
| | - Pedro Gómez
- IFAPA Centro La Mojonera, La Mojonera, Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almeria, Almería, Spain
| | - Lukas Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
| | - Joaquín Cañizares
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia, Spain
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16
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Montero‐Pau J, Blanca J, Bombarely A, Ziarsolo P, Esteras C, Martí‐Gómez C, Ferriol M, Gómez P, Jamilena M, Mueller L, Picó B, Cañizares J. De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1161-1171. [PMID: 29112324 PMCID: PMC5978595 DOI: 10.1111/pbi.12860] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/17/2017] [Accepted: 10/31/2017] [Indexed: 05/17/2023]
Abstract
The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the topology of the gene family phylogenies, the karyotype organization and the distribution of 4DTv distances. Additionally, 40 transcriptomes of 12 species of the genus were assembled and analysed together with all the other published genomes of the Cucurbitaceae family. The duplication was detected in all the Cucurbita species analysed, including C. maxima and C. moschata, but not in the more distant cucurbits belonging to the Cucumis and Citrullus genera, and it is likely to have occurred 30 ± 4 Mya in the ancestral species that gave rise to the genus.
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Affiliation(s)
- Javier Montero‐Pau
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - José Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Aureliano Bombarely
- Department of HorticultureVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Peio Ziarsolo
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Cristina Esteras
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Carlos Martí‐Gómez
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - María Ferriol
- Instituto Agroforestal Mediterráneo (IAM)Universitat Politècnica de ValènciaValenciaSpain
| | - Pedro Gómez
- IFAPA Centro La MojoneraLa MojoneraAlmeríaSpain
| | - Manuel Jamilena
- Department of Biology and GeologyResearch Centers CIAIMBITAL and CeiA3University of AlmeriaAlmeríaSpain
| | - Lukas Mueller
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Joaquín Cañizares
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
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Šlosár M, Mezeyová I, Hegedűsová A, Hegedűs O. Quantitative and qualitative parameters in Acorn squash cultivar in the conditions of the Slovak Republic. POTRAVINARSTVO 2018. [DOI: 10.5219/851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Cucurbita pepo includes several types of squashes; in Slovak Republic, well-known and oftenly grown squash types are patisson, zucchini, spaghetti squash, oil pumpkin etc. Several interesting squash types of Cucurbita pepo are grown abroad, including Acorn squash which is well-known mainly in USA. The aim of this study was to evaluate the important quantitative (yield per hectare, average fruit weight) and qualitative (total carotenoids, ascorbic acid, antioxidant activity, total soluble solids) yield parameters of Acorn squash fruits in comparison with patisson which is typical squash type of Cucurbita pepo in Slovak Republic. The field trial was realised in Košice-Šaca in 2016. Within experiment, four cultivars of Acorn type pumpkin were tested (Thelma Sanders; Jet Set; Table Gold; Cream of The Crop). The patisson 'Orfeus' was used as a comparative cultivar for evaluation of individual parameters of Acorn type pumpkin cultivars. Matured pumpkin fruits were harvested on the 7th September 2016. From aspect of yield quantity, Acorn cultivars are appeared as very interesting squash type with good yield potential for growing. The highest yield of squash fruits was found in the cultivar 'Cream of The Crop' (17.8 t.ha-1). In mentioned Acorn cultivar, the yield was higher about 87.4% compared to the tested patisson cultivar 'Orfeus' (9.5 t.ha-1). On the contrary, the average weight of squash fruits was reached in patisson cultivar 'Orfeus' (780.7 g). The qualitative parameters of fruits were expressively influenced by squash cultivar. The content of total carotenoids, ascorbic acid and total soluble solids was markedly higher in all Acorn cultivars, compared to the patisson cultivar 'Orfeus'. The highest content of total carotenoids (26.74 mg.kg-1 fresh weight) and ascorbic acid (238.79 mg.kg-1 f. w.) was found in the squash cultivar 'Table Gold'. The highest content of total soluble solids was determined in the cultivar 'Jet Set' (3.8 °Brix). On the contrary, the highest antioxidant activity (DPPH) was found in the patisson cultivar 'Orfeus' (10.80 %). On the basis of obtained results, it is possible to state that Acorn cultivars are very interesting squash type with promising yield potential for possible growing in conditions of Slovak Republic. In addition, Acorn squashes were expressed by higher content of several nutritional parameters compared to the typical squash type - patisson. Thus, these squashes could be an interesting vegetable for human nutrition.
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18
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Guo WL, Chen BH, Chen XJ, Guo YY, Yang HL, Li XZ, Wang GY. Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew. PLoS One 2018; 13:e0190175. [PMID: 29320569 PMCID: PMC5761878 DOI: 10.1371/journal.pone.0190175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 12/08/2017] [Indexed: 01/08/2023] Open
Abstract
Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line “112–2” using RNA sequencing (RNA-Seq). The inbred line “112–2” has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line “112–2” at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant “112–2” were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar “Jiujiangjiaoding”). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.
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Affiliation(s)
- Wei-Li Guo
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Bi-Hua Chen
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Xue-Jin Chen
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Yan-Yan Guo
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - He-Lian Yang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Xin-Zheng Li
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
- * E-mail:
| | - Guang-Yin Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
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Andolfo G, Di Donato A, Darrudi R, Errico A, Aiese Cigliano R, Ercolano MR. Draft of Zucchini ( Cucurbita pepo L.) Proteome: A Resource for Genetic and Genomic Studies. Front Genet 2017; 8:181. [PMID: 29209358 PMCID: PMC5702489 DOI: 10.3389/fgene.2017.00181] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/06/2017] [Indexed: 11/20/2022] Open
Affiliation(s)
- Giuseppe Andolfo
- Department of Agriculture Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antimo Di Donato
- Department of Agriculture Sciences, University of Naples 'Federico II', Naples, Italy
| | - Reza Darrudi
- Department of Agriculture Sciences, University of Naples 'Federico II', Naples, Italy.,Department of Horticulture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Angela Errico
- Department of Agriculture Sciences, University of Naples 'Federico II', Naples, Italy
| | | | - Maria R Ercolano
- Department of Agriculture Sciences, University of Naples 'Federico II', Naples, Italy
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Xanthopoulou A, Ganopoulos I, Psomopoulos F, Manioudaki M, Moysiadis T, Kapazoglou A, Osathanunkul M, Michailidou S, Kalivas A, Tsaftaris A, Nianiou-Obeidat I, Madesis P. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers. Gene 2017; 622:50-66. [PMID: 28435133 DOI: 10.1016/j.gene.2017.04.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/03/2023]
Abstract
The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits.
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Affiliation(s)
- Aliki Xanthopoulou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Fotis Psomopoulos
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
| | - Maria Manioudaki
- Centre for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Aliki Kapazoglou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sofia Michailidou
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece
| | - Apostolos Kalivas
- Institute of Plant Breeding and Genetic Resources ELGO-DEMETER (ex NAGREF), Thermi, Macedonia GR-57001, Greece
| | - Athanasios Tsaftaris
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece; Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece
| | - Irini Nianiou-Obeidat
- Lab of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 261, Thessaloniki GR-54124, Greece.
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thermi, Thessaloniki 570 01, Greece.
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Wyatt LE, Strickler SR, Mueller LA, Mazourek M. Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. HORTICULTURE RESEARCH 2016; 3:16045. [PMID: 27688889 PMCID: PMC5030761 DOI: 10.1038/hortres.2016.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 05/23/2023]
Abstract
Both the fruit mesocarp and the seeds of winter squash can be used for consumption, although the focus of breeding efforts varies by cultivar. Cultivars bred for fruit consumption are selected for fruit mesocarp quality traits such as carotenoid content, percent dry matter, and percent soluble solids, while these traits are essentially ignored in oilseed pumpkins. To compare fruit development in these two types of squash, we sequenced the fruit transcriptome of two cultivars bred for different purposes: an acorn squash, 'Sweet REBA', and an oilseed pumpkin, 'Lady Godiva'. Putative metabolic pathways were developed for carotenoid, starch, and sucrose synthesis in winter squash fruit and squash homologs were identified for each of the structural genes in the pathways. Gene expression, especially of known rate-limiting and branch point genes, corresponded with metabolite accumulation both across development and between the two cultivars. Thus, developmental regulation of metabolite genes is an important factor in winter squash fruit quality.
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Affiliation(s)
- Lindsay E Wyatt
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Michael Mazourek
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
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