At3g08030 transcript: a molecular marker of seed ageing

Garza-Caligaris, Luz Elena; Avendaño-Vázquez, Aida Odette; Alvarado-López, Sandra; Zúñiga-Sánchez, Esther; Orozco‐Segovia, Alma; Pérez-Ruíz, Rigoberto V.; Gamboa‐deBuen, Alicia

doi:10.1093/aob/mcs200

Cited by 27 publications

(24 citation statements)

References 28 publications

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“…Much less research has been done regarding stored mRNAs and seed aging. The transcripts of an Arabidopsis gene, At3g08030, and its homologs in two other plant species were found to be present in freshly collected seeds, but reduced or not detected in aged seeds (Garza-Caligaris et al, 2012). The authors suggested that the At3g08030 transcript could be a potential biomarker for seed aging.…”

Section: Degradation Of Stored Mrnas Is Highly Correlated With Aging mentioning

confidence: 99%

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

Zhao

Wang

et al. 2020

Front. Plant Sci.

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How plant seeds age remains poorly understood and effective tools for monitoring seed aging are lacking. Dry seeds contain various stored mRNAs which are believed to be required for protein synthesis during early stages of seed germination. We reasoned that seed stored mRNAs would undergo degradation during seed aging, based on the propensity of mRNAs to degrade. We performed RT-PCR and qPCR analyses to study the changes in stored mRNA levels of Arabidopsis seeds during aging. All stored mRNAs analyzed were gradually degraded in both naturally and artificially aged seeds. The difference in Ct values between aged and control seeds (DCt value) was highly correlated with the mRNA fragment size and seed aging time. We derived mathematical equations for estimating the relative amount of undamaged stored mRNAs and frequency of the breakdown at one nucleotide level for individual mRNAs. Stored mRNAs were found to break down randomly. The frequency of breaks per nucleotide per day, which we named b value, remained fairly constant under the same aging conditions over aging time. This parameter should allow the effects of different conditions on the degradation of stored mRNAs to be quantitatively compared. Also, we showed that the change in stored mRNA levels could serve as a more precise biomarker for seed aging assessment than three existing methods. These methods and findings will advance the studies of stored mRNAs and seed ageing in plants, and likely slow RNA degradation in non-plant systems.

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Section: Degradation Of Stored Mrnas Is Highly Correlated With Aging mentioning

confidence: 99%

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

Zhao

Wang

et al. 2020

Front. Plant Sci.

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“…There are also a number of proteins that are connected by a domain of unknown function (DUF) deeply involved in cell wall metabolism (lower left in Fig. 6) (e.g., Garza-Caligaris et al, 2012;Vazquez-Lobo et al, 2012).…”

Section: Functional Category Comparisons Among the Differentially Rmentioning

confidence: 99%

Spaceflight Induces Specific Alterations in the Proteomes of Arabidopsis

Ferl

Koh²,

Denison³

et al. 2015

Astrobiology

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Life in spaceflight demonstrates remarkable acclimation processes within the specialized habitats of vehicles subjected to the myriad of unique environmental issues associated with orbital trajectories. To examine the response processes that occur in plants in space, leaves and roots from Arabidopsis (Arabidopsis thaliana) seedlings from three GFP reporter lines that were grown from seed for 12 days on the International Space Station and preserved on orbit in RNAlater were returned to Earth and analyzed by using iTRAQ broad-scale proteomics procedures. Using stringent criteria, we identified over 1500 proteins, which included 1167 leaf proteins and 1150 root proteins we were able to accurately quantify. Quantification revealed 256 leaf proteins and 358 root proteins that showed statistically significant differential abundance in the spaceflight samples compared to ground controls, with few proteins differentially regulated in common between leaves and roots. This indicates that there are measurable proteomics responses to spaceflight and that the responses are organspecific. These proteomics data were compared with transcriptome data from similar spaceflight samples, showing that there is a positive but limited relationship between transcriptome and proteome regulation of the overall spaceflight responses of plants. These results are discussed in terms of emergence understanding of plant responses to spaceflight particularly with regard to cell wall remodeling, as well as in the context of deriving multiple omics data sets from a single on-orbit preservation and operations approach.

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“…Pre-storage conditions and genotypic effects also play crucial roles in influencing longevity characteristics. Markers of quantitative trait loci (QTL) detected after artificial ageing have been associated with abiotic and biotic stress response genes (Nagel et al 2009) and a range of loci linked to stress response and longevity were identified (Miura et al 2002;Clerkx et al 2004;Garza-Caligaris et al 2012;Nguyen et al 2012). Hence, seed ageing is genotype dependent, but it is poorly understood which factors affect seed response in relation to maternal environment, ageing treatment and genetic background.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association mapping and biochemical markers reveal that seed ageing and longevity are intricately affected by genetic background and developmental and environmental conditions in barley

Nagel

Kranner

Neumann

et al. 2014

Plant Cell & Environment

109

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Globally, over 7.4 million accessions of crop seeds are stored in gene banks, and conservation of genotypic variation is pivotal for breeding. We combined genetic and biochemical approaches to obtain a broad overview of factors that influence seed storability and ageing in barley (Hordeum vulgare). Seeds from a germplasm collection of 175 genotypes from four continents grown in field plots with different nutrient supply were subjected to two artificial ageing regimes. Genome-wide association mapping revealed 107 marker trait associations, and hence, genotypic effects on seed ageing. Abiotic and biotic stresses were found to affect seed longevity. To address aspects of abiotic, including oxidative, stress, two major antioxidant groups were analysed. No correlation was found between seed deterioration and the lipid-soluble tocochromanols, nor with oil, starch and protein contents. Conversely, the water-soluble glutathione and related thiols were converted to disulphides, indicating a strong shift towards more oxidizing intracellular conditions, in seeds subjected to long-term dry storage at two temperatures or to two artificial ageing treatments. The data suggest that intracellular pH and (bio)chemical processes leading to seed deterioration were influenced by the type of ageing or storage. Moreover, seed response to ageing or storage treatment appears to be significantly influenced by both maternal environment and genetic background.

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At3g08030 transcript: a molecular marker of seed ageing

Abstract: At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species.

Cited by 27 publications

References 28 publications

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

Arabidopsis Seed Stored mRNAs are Degraded Constantly over Aging Time, as Revealed by New Quantification Methods

Spaceflight Induces Specific Alterations in the Proteomes of Arabidopsis

Genome‐wide association mapping and biochemical markers reveal that seed ageing and longevity are intricately affected by genetic background and developmental and environmental conditions in barley

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