Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.)

Zheng, Yanan; Wang, Kai; Aziz, Usman; Zhang, Meng

doi:10.1186/s13007-020-00679-1

Cited by 22 publications

(24 citation statements)

References 57 publications

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“…Ideally, the stability of the reference gene should not be influenced by the experimental conditions. Nevertheless, several studies point out that the mRNA transcript levels could be affected by tissue type [ 19 , 20 ], developmental stage [ 26 ], treatment type [ 27 , 28 ], and genotype [ 26 ] as well. Furthermore, the expression stability of the same reference gene may also depend on the investigated species [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

“…Jarošová and Kundu [ 17 ] examined the stability of different reference gene candidates in virus-infected wheat, barley and oat. Furthermore, stable reference genes under herbicide stress were identified in wild relatives of cultivated oat [ 18 , 19 ], while the effects of different tissues and developmental stages were also examined [ 19 , 20 ]. Reference gene stability under salt stress was investigated by Duan et al [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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Validation of Reference Genes for Studying Different Abiotic Stresses in Oat (Avena sativa L.) by RT-qPCR

Tajti

Pál

Janda

2021

Plants

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Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value and it is grown mainly in temperate regions. The number of studies dealing with gene expression changes in oat continues to increase, and to obtain reliable RT-qPCR results it is essential to establish and use reference genes with the least possible influence caused by experimental conditions. However, no detailed study has been conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. In our work, nine candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by four statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to five abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis, which further confirmed their reliability. These results can contribute to reliable gene expression studies for future research in cultivated oat.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Validation of Reference Genes for Studying Different Abiotic Stresses in Oat (Avena sativa L.) by RT-qPCR

Tajti

Pál

Janda

2021

Plants

View full text Add to dashboard Cite

show abstract

“…Ideally, the stability of the reference gene should not be in uenced by the experimental conditions. Nevertheless, several studies point out, that the mRNA transcript levels could be affected by tissue type [11,12], developmental stage [18] treatment type [19,20] and genotype [18] as well. Furthermore, the expression stability of the same reference gene may also depend on the investigated species [21].…”

Section: Discussionmentioning

confidence: 99%

“…Jarošová and Kundu (2010) examined the stability of different reference gene candidates in virus-infected wheat, barley and oat. Furthermore, stable reference genes under herbicide stress were identi ed in wild relatives of cultivated oat [10,11] while the effects of different tissues and developmental stages were also examined [11,12].…”

Section: Introductionmentioning

confidence: 99%

Validation of Reference Genes for Studying Different Abiotic Stresses by RT-qPCR in Oat (Avena Sativa L.)

Tajti

Pál

Janda

2021

Preprint

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Background: Oat (Avena sativa L.) is a widely cultivated cereal with high nutritional value growing mainly in temperate regions. The number of studies dealing with gene expression changes in oat increases and to obtain reliable RT-qPCR results it is essential to use references genes that are least influenced by experimental conditions. However, no detailed study was conducted on reference genes in different tissues of oat under diverse abiotic stress conditions. Results: In our work 9 candidate reference genes (ACT, TUB, CYP, GAPD, UBC, EF1, TBP, ADPR, PGD) were chosen and analysed by 4 statistical methods (GeNorm, Normfinder, BestKeeper, RefFinder). Samples were taken from two tissues (leaves and roots) of 13-day-old oat plants exposed to 5 abiotic stresses (drought, salt, heavy metal, low and high temperatures). ADPR was the top-rated reference gene for all samples, while different genes proved to be the most stable depending on tissue type and treatment combinations. TUB and EF1 were most affected by the treatments in general. Validation of reference genes was carried out by PAL expression analysis which further confirmed their reliability. Conclusions: Our main goal was to identify reference genes with stable expression in oat under different abiotic stress conditions in different tissues. These results can contribute to reliable gene expression studies for future researches in cultivated oat.

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“…Additionally, RT-PCR also confirmed the presence of RBSDV in only YP library. The HNR was used as an internal control [39]. Amplified PCR products were visualized by 1.2% agarose gel electrophoresis.…”

Section: Validation Of the Identified Viruses Using Rt-pcrmentioning

confidence: 99%

Identification of Viruses Infecting Oats in Korea by Metatranscriptomics

Kim

Lee

Kim

et al. 2022

Plants

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Controlling infectious plant viruses presents a constant challenge in agriculture. As a source of valuable nutrients for human health, the cultivation of oats (Avena sativa L.) has recently been increased in Korea. To date, however, few studies have been undertaken to identify the viruses infecting oats in this country. In this study, we carried out RNA-sequencing followed by bioinformatics analyses to understand the virosphere in six different geographical locations in Korea where oats are cultivated. We identified three different virus species, namely, barley yellow dwarf virus (BYDV) (BYDV-PAV and BYDV-PAS), cereal yellow dwarf virus (CYDV) (CYDV-RPS and CYDV-RPV), and rice black-streaked dwarf virus (RBSDV). Based on the number of virus-associated reads and contigs, BYDV-PAV was a dominant virus infecting winter oats in Korea. Interestingly, RBSDV was identified in only a single region, and this is the first report of this virus infecting oats in Korea. Single nucleotide polymorphisms analyses indicated that most BYDV, CYDV, and RBSDV isolates show considerable genetic variations. Phylogenetic analyses indicated that BYDVs and CYDVs were largely grouped in isolates from Asia and USA, whereas RBSDV was genetically similar to isolates from China. Overall, the findings of this study provide a preliminary characterization of the types of plant viruses infecting oats in six geographical regions of Korea.

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Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat (Avena sativa L.)

Cited by 22 publications

References 57 publications

Validation of Reference Genes for Studying Different Abiotic Stresses in Oat (Avena sativa L.) by RT-qPCR

Validation of Reference Genes for Studying Different Abiotic Stresses in Oat (Avena sativa L.) by RT-qPCR

Validation of Reference Genes for Studying Different Abiotic Stresses by RT-qPCR in Oat (Avena Sativa L.)

Identification of Viruses Infecting Oats in Korea by Metatranscriptomics

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