Identification of three genetic loci controlling leaf senescence in <i>Arabidopsis thaliana</i>

Miklashevichs, Edvins; Czaja, Inge; Cordeiro, A. R.; Prinsen, Els; Schell, Jeff; Walden, Richard

doi:10.1046/j.1365-313x.1997.00489.x

Cited by 24 publications

(7 citation statements)

References 9 publications

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“…Ethylene is a positive regulator of leaf senescence (102), and xrn4 alleles display ethylene insensitivity (16,53). However, unlike other ethylene-insensitive mutants that have been reported to exhibit increased tolerance to dark-accelerated starvation/senescence ( ein2 or ein3 ; (103,104)), xrn4 mutants show the opposite. They are more sensitive than WT, or the complemented mutant line, to prolonged darkness as intact seedlings or detached leaves (a typical dark-accelerated senescence assay) (Figure 6A, B and C).…”

Section: Discussionmentioning

confidence: 76%

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

Nagarajan

Kukulich

Hagel

et al. 2019

Nucleic Acids Research

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XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5′ end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5′ ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3′ fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.

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Section: Discussionmentioning

confidence: 76%

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

Nagarajan

Kukulich

Hagel

et al. 2019

Nucleic Acids Research

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“…Both of these linked SNPs, as well as the other SNPs in high LD, were intergenic with the nearest gene, NAC6 (At5g39610; Table 4), which is located 1.9 kb away. NAC6 is a transcription factor regulating leaf senescence [50] and is highly expressed in senescing leaves and in maturing seeds [47]. We phenotyped the available At5g39610 insertion mutant and found a significant decrease in mean root length (p = 5.82 × 10 -10 ; Figure 4), strongly implicating NAC6 in the regulation of root length.…”

Section: Resultsmentioning

confidence: 98%

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

Lachowiec

Shen

Queitsch

et al. 2014

Preprint

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1Efforts to identify loci underlying complex traits generally assume that most genetic variance is 2 additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the 3 narrow-sense heritability for this trait was statistically zero. This low additive genetic variance 4 likely explains why no associations to root length could be found using standard additive-model-5 based genome-wide association (GWA) approaches. However, the broad-sense heritability for 6 root length was significantly larger, and we therefore also performed an epistatic GWA analysis 7 to map loci contributing to the epistatic genetic variance. This analysis revealed four interacting 8 pairs involving seven chromosomal loci that passed a standard multiple-testing corrected 9 significance threshold. Explorations of the genotype-phenotype maps for these pairs revealed 10 that the detected epistasis cancelled out the additive genetic variance, explaining why these loci 11 were not detected in the additive GWA analysis. Small population sizes, such as in our 12 experiment, increase the risk of identifying false epistatic interactions due to testing for 13 associations with very large numbers of multi-marker genotypes in few phenotyped individuals. 14 Therefore, we estimated the false-positive risk using a new statistical approach that suggested 15 half of the associated pairs to be true positive associations. Our experimental evaluation of 16 candidate genes within the seven associated loci suggests that this estimate is conservative; we 17 identified functional candidate genes that affected root development in four loci that were part of 18 three of the pairs. In summary, statistical epistatic analyses were found to be indispensable for 19 confirming known, and identifying several new, functional candidate genes for root length using 20 a population of wild-collected A. thaliana accessions. We also illustrated how epistatic 21

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“…Both of these linked SNPs, as well as the other SNPs in high LD, were intergenic with the nearest gene, NAC6 (At5g39610; Table 5 ), which is located 1.9 kb away. NAC6 is a transcription factor regulating leaf senescence [ 46 ] and is highly expressed in senescing leaves and in maturing seeds [ 44 ]. We phenotyped the available At5g39610 insertion mutant for NAC6 and found a significant decrease in mean root length (p = 5.82 × 10 −10 ; Tukey’s post-hoc test; Fig 4 ), strongly implicating NAC6 in the regulation of root length.…”

Section: Resultsmentioning

confidence: 99%

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

et al. 2015

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Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the genomic narrow-sense heritability for this trait in the examined population was statistically zero. The low amount of additive genetic variance that could be captured by the genome-wide genotypes likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, as the broad-sense heritability for root length was significantly larger, and primarily due to epistasis, we also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. Four interacting pairs of loci were revealed, involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. The genotype-phenotype maps for these pairs revealed epistasis that cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. The statistical epistatic analyses were thus indispensable for confirming known, and identifying new, candidate genes for root length in this population of wild-collected A. thaliana accessions. We also illustrate how epistatic cancellation of the additive genetic variance explains the insignificant narrow-sense and significant broad-sense heritability by using a combination of careful statistical epistatic analyses and functional genetic experiments.

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Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana

Cited by 24 publications

References 9 publications

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

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