De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers

Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

doi:10.1016/j.gene.2017.04.035

Cited by 32 publications

(18 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This study describes the identification of QTLs for important fruit traits of C. maxima, which is the most diverse species of Cucurbita, characterized by fruit morphological complexity [7,11]. Certain cultivars of C. maxima produce one of the biggest fruits among all plants, which makes this cucurbit an interesting model plant to investigate genetic mechanisms underlying fruit size and its evolution [6,23]. In this study, advanced F 6 RILs were used to investigate nine agronomically important fruit-associated traits (Figure 1, Table 1).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Kaźmińska

Hallmann

Korzeniewska

et al. 2020

Genes

View full text Add to dashboard Cite

Cucurbita maxima Duchesne squash and pumpkins are cultivated world-wide. Cucurbita maxima fruits are produced for fresh market and are valuable for food processing. Therefore, fruit characteristics and yield are the traits of high economic importance for breeders. To date, the genetic basis of fruit-associated traits in C. maxima have been poorly understood. In the present study, we evaluated fruit-associated traits and conducted quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from a cross of two inbred lines with different fruit morphotypes. Phenotypic data for nine fruit traits (earliness, weight, number per plant, yield per plant, length and diameter, shape index, flesh thickness, sucrose content and dry matter content) were collected for RILs in two open-field experiments. Pairwise analysis of the phenotypic data revealed correlations among the fruit and yield-associated traits. Using a previously developed genetic map, we identified 26 QTLs for eight traits. The QTLs were found in 10 locations on eight chromosomes of C. maxima. The QTLs were detected across experiments and explained up to 41.4% of the observed phenotypic variations. Major-effect QTLs for multiple fruit-associated traits were clustered on chromosome 4, suggesting that this genomic region has been under selection during diversification and/or domestication of C. maxima.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Rimu was sequenced and annotated [2]. Several transcriptomic studies performed on C. maxima focused on agrobotanical traits, which revealed gene expression patterns of sex expression, fruit development and ripening in this allotetraploid species [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Kaźmińska

Hallmann

Korzeniewska

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

“…The evidence of wheat morphology, metabolism and physiology changes can be found from transcriptome [19][20][21]. In the photosynthesis pathway ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Transcription strategies related to photosynthesis and nitrogen metabolism of wheat in response to nitrogen deficiency

Liu

Yin

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: It is a great challenge to reduce nitrogen application without yield reduction in agricultural production. Screening response gene related to important pathways will be helpful to understand the physiology, metabolism, and morphology response of wheat (Triticum aestivum) under nitrogen deficiency condition. Results: We conducted a hydroponic experiment with two nitrogen levels, which were complete nutrient solution (N1) and nutrient solution without nitrogen (N0). The results showed that the wheat phenotype were greatly changed under nitrogen deficiency, e.g., the decreased crop height, leaf area, root volume, photosynthetic rate, crop weight, and the increased root length, root surface area and root/shoot ratio. After a comprehensive analysis of the phenotype, transcriptome, GO pathways and KEGG pathways of wheat under nitrogen deficiency, we found that, the up-regulated Exp (24 genes) and Nrt (9 genes) families members were the positive response related to the increase of nitrogen absorption; the down-regulated Pet (3 genes), Psb (8 genes), Nar (3 genes) and Nir (1 genes) were related to the limitation of photosynthesis and nitrogen metabolism. Conclusions: This study provides 48 reference genes for improving photosynthesis and nitrogen metabolism of wheat under nitrogen deficiency, which can provide molecular markers for gene editing breeding.

show abstract

“…"Big Moose" and "Munchkin"), were de novo assembled from Illumina reads in order to provide further genomic resources within the Cucurbita genus [6,7]. Comparative analysis performed on "Big Moose" and "Munchkin" transcriptomes allowed genes with potential roles in fruit size and morphology to be identified, as well as microsatellite markers derived from expressed sequence tags (EST-SSR) to be generated [8]. Also, the transcriptome of zucchini cultivar "True French", used as parent in crossing scheme of pathogen-resistant commercial varieties, has been sequenced and assembled as a valuable resource for genetic and genomic studies [9].…”

Section: Discussionmentioning

confidence: 99%

De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii

Vitiello

Rao

Corrado

et al. 2018

Data

View full text Add to dashboard Cite

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.

show abstract

De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers

Cited by 32 publications

References 79 publications

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Identification of Fruit-Associated QTLs in Winter Squash (Cucurbita maxima Duchesne) Using Recombinant Inbred Lines

Transcription strategies related to photosynthesis and nitrogen metabolism of wheat in response to nitrogen deficiency

De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii

Contact Info

Product

Resources

About