Validation of reference genes for quantitative real-time PCR in Périgord black truffle ( Tuber melanosporum ) developmental stages

Zarivi, Osvaldo; Cesare, Patrizia; Ragnelli, Anna Maria; Aimola, Pierpaolo; Leonardi, Marco; Bonfigli, Antonella; Colafarina, Sabrina; Poma, Anna; Miranda, Marta; Pacioni, Giovanni

doi:10.1016/j.phytochem.2015.02.024

Cited by 42 publications

(27 citation statements)

References 37 publications

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“…ACT as traditional reference genes is not always stable in different experimental conditions, which was somewhat in accordance with several studies demonstrating ACT as an unsuitable internal control for RT-PCR in other cell types or species (Lord et al 2010). Recent studies have shown that ACT expression can change in response to a variety of conditions (Ruan & Lai 2007;Zarivi et al 2015;Wrzesińska et al 2016). Thus, these traditionally used reference genes are not persistently and stably expressed in many species or different experimental treatments (Chandna 2012;Cheng et al 2013;Ma et al 2016), which emphasised the need to evaluate reference genes in A. fatua.…”

Section: Discussionsupporting

confidence: 84%

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Liu¹,

Li²,

Lu³

et al. 2019

Plant Prot. Sci.

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Citation: Liu J., Li P., Lu L., Xie L., Chen X., Zhang B. (2019): Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua. Plant Protect. Sci., 55: 61-71.Abstract: Eight commonly used candidate reference genes, 18S ribosomal RNA (rRNA) (18S), 28S rRNA (28S), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1α), ribosomal protein L7 (RPL7), Alpha-tubulin (α-TUB), and TATA box binding protein-associated factor (TBP), were evaluated under various experimental conditions to assess their suitability in different developmental stages, tissues and herbicide treatments in Avena fatua. The results indicated the most suitable reference genes for the different experimental conditions. For developmental stages, 28S and EF1α were the optimal reference genes, both EF1α and 28S were suitable for experiments of different tissues, whereas for herbicide treatments, GAPDH and ACT were suitable for normalizations of expression data. In addition, GAPDH and EF1α were the suitable reference genes.

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Section: Discussionsupporting

confidence: 84%

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Liu¹,

Li²,

Lu³

et al. 2019

Plant Prot. Sci.

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“…Spore maturity showed a clear within-season temporal trend, with no apparent influence of the remaining predictors. According to Zarivi et al (2015) 24 , spore melanisation only happens after the FB swelling is completed. Our results show a fast increase in spore maturity from early November to early December that agrees with that view, but in our case maturity continues to increase -much more modestly-throughout the fruiting season.…”

Section: Discussionmentioning

confidence: 99%

“…However, considering that in 2017-2018 no differences among soils were found, this effect appears to be strongly dependent www.nature.com/scientificreports www.nature.com/scientificreports/ on annual environmental conditions, either through their influence on soil microclimate or on host physiology. We hypothesise that interannual differences could be related to soil conditions or tree status during the July-October period, the FB growth stage, during which the more intense development and growth take place 11,23,24 . However, interannual differences in July-October temperature and rainfall in our study site were minor and restricted to the beginning of September (Supplementary Tables S9 and S10, Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

Edaphic and temporal patterns of Tuber melanosporum fruitbody traits and effect of localised peat-based amendment

García-Barreda

Marco

Martín-Santafé

et al. 2020

Sci Rep

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Tuber melanosporum cultivation, fruitbody traits are gaining relevance due to their increasing prominence on prices. We investigated the edaphic and temporal patterns of fruitbody traits and characterised the effect of truffle nests (localised peat-based amendment supplemented with T. melanosporum spores) on traits. We monitored fruitbody traits throughout two fruiting seasons in three blocks along a soil gradient. Each trait followed specific edaphic and temporal patterns. The number of fruitbodies per dig and spore maturity followed characteristic within-season trends, whereas fruitbody weight and infestation by truffle beetles were subject to complex interactions among edaphic and temporal variables, suggesting a relevant influence of annual environmental conditions. The application of truffle nests increased fruitbody depth, improved its shape and decreased infestation by truffle beetles. Nests increased the number of fruitbodies per dig, but only in two of the soils, suggesting a relevant role of the bulk soil/substrate interface in fruiting initiation. These results outline a complex scenario, with each trait being differently affected by environmental factors. In this scenario, nests proved to effectively modify several traits, although not always in the desired direction. The European black truffle (Tuber melanosporum) is an ectomycorrhizal fungus highly appreciated in "haute cuisine" due to its organoleptic properties. It grows wild in open oak forests of southern Europe, although nowadays most T. melanosporum production is harvested in orchards planted with seedlings previously inoculated in controlled conditions. Truffle cultivation has advanced greatly in recent decades and has expanded worldwide 1. This is leading to an increased and more stable supply of truffles to markets in recent years, thus encouraging price differentiation by quality 2. Commercial quality standards are defined by both pre-harvest fruitbody (FB) traits and post-harvest practices 3. The most important among the former are FB ripeness, gleba colour (associated to spore maturity), abiotic and biotic damages, fresh weight and shape 4. Despite recent advances, truffle cultivation is not completely domesticated yet, as the uncertainties around the mating process and the FB formation process remain 5,6. The environmental mechanisms triggering fruiting and influencing FB development and maturation are still poorly understood 6,7. Edaphic and climatic factors have a key role in ectomycorrhizal FB yields, phenology and morphology 8-10. This is particularly likely to apply to truffles, which grow below ground and require several months to develop and ripen 11,12. Information on the influence of environmental factors on FB traits could help to clarify the ecology of T. melanosporum and could be useful for improving productivity and sustainability in truffle cultivation. Unraveling the linkages between FB traits and edaphoclimatic conditions is difficult because: (1) the long period of formation of truffle FBs hinders the identification of ...

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“…Comparative transcriptome analysis between the early‐ and late‐heading stages was performed based on HiSeq 4000 platform. The qRT‐PCR analysis is often used to confirm the accuracy of sequencing data in plants (Zarivi et al ). Sixteen DEGs were chosen randomly and the relative expression levels were consistent with those in RNA‐Seq results, indicating the reliability of the sequencing data in this study (Fig.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome profiling of yellow leafy head development during the heading stage in Chinese cabbage (Brassica rapa subsp. pekinensis)

Fan

Jiao

et al. 2018

Physiologia Plantarum

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The yellow leafy head of Brassica rapa is known to be tasty and nutritional. Therefore, the heading stage of leaf development is critical to realize high yield and economic benefits. A widely planted commercial cultivar of B. rapa ('Qiubao', deep yellow leafy head) was used to conduct transcriptome analysis. The results showed that the yellowing of the inner leaf was likely induced by the predominant β-carotene biosynthesis pathway due to the upregulated gene geranylgeranyl diphosphate and phytoene synthase, and the downregulated gene CrtL-e, NCED4 and DWARF-27. Some genes related to chlorophyll synthesis were also found to be downregulated, such as nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase and protochlorophyllide reductase A. Transcript profiling also revealed strong changes in expression levels of hormonal genes related to auxin, cytokinin, ethylene, abscisic acid, gibberellin and brassinosteroids, suggesting the crucial role that hormones play in heading stage. Examination of carbohydrate and sucrose metabolism pathways revealed that sucrose biosynthesis is probably regulated by 6-phosphofructokinase and sucrose synthase 1 (SUS1/SuSy1) branch, instead of the sucrose-phosphate synthase branch. Several cold-response genes were induced in the late-heading stage, but the results suggest that the common C-repeat binding factor responsive pathway may not be involved in cold adaption. We also identified a series of upregulated transcription factors-AP2/ERF, MYB, bHLH, NAC and WRKY were found to be predominant. The transcripts analysis provides a preliminary genetic resource to unravel key genes and molecular mechanisms responsible for leafy head development in B. rapa, therefore, improving leafy head quality and yield through genetic means in future.

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Validation of reference genes for quantitative real-time PCR in Périgord black truffle ( Tuber melanosporum ) developmental stages

Cited by 42 publications

References 37 publications

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

Edaphic and temporal patterns of Tuber melanosporum fruitbody traits and effect of localised peat-based amendment

Transcriptome profiling of yellow leafy head development during the heading stage in Chinese cabbage (Brassica rapa subsp. pekinensis)

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