@misc{matallana-ramirez_whetten_sanchez_payn_2021, title={Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Pinus taeda L.) in North America}, volume={12}, ISSN={["1664-462X"]}, url={https://doi.org/10.3389/fpls.2021.606908}, DOI={10.3389/fpls.2021.606908}, abstractNote={Earth’s atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taedaL.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Matallana-Ramirez, Lilian P. and Whetten, Ross W. and Sanchez, Georgina M. and Payn, Kitt G.}, year={2021}, month={Apr} }
 @article{kurt_matallana-ramirez_kohlway_whetten_frampton_2020, title={A fast, flexible and inexpensive protocol for DNA and RNA extraction for forest trees}, volume={29}, ISSN={["2171-9845"]}, DOI={10.5424/fs/2020292-16730}, abstractNote={Aim of the study: DNA and RNA extraction are still one of the most important and challenging steps of many molecular genetics applications such as Next-Generation Sequencing technologies. In this study, traditional laboratory preparation protocols and commercially available nucleic acids extraction kits’ features were combined into a procedure suitable for extraction of either DNA or RNA in 96-well plate format at high throughput.Area of study: The study covers forest tree species from the United States of America.Materials and methods: The DNA and RNA protocol were tested on 27 species, including especially recalcitrant forest tree species, from five angiosperm and three gymnosperm families. DNA was also extracted from stored (from 2 to 6 years) silica-dried samples of 11 species of Pinaceae.Main results: The spectrophotometric analysis of DNA and RNA showed that gymnosperms yielded lower quantity, but higher quality nucleic acids than angiosperms which have variable results among species. The quantity and quality of DNA from stored samples were generally lower than fresh silica-dried samples. The RNA results showed high-enough yield (6.6 to 8.8 RIN) for downstream analyses.Research highlights: It was demonstrated that high quality and high molecular weight nucleic acids for Next-Generation Sequencing applications can be isolated from hundreds of samples from a wide range of taxonomic groups. The new protocol has features similar to both traditional laboratory and commercial extraction kits; is easy to set up in any molecular research laboratory, can be applied to a large number of samples (hundreds) in a working day, uses inexpensive reagents and supplies, and is compatible with automation.Key words: Angiosperms; gymnosperms; isolation protocol; nucleic acids.}, number={2}, journal={FOREST SYSTEMS}, author={Kurt, Yusuf and Matallana-Ramirez, Lilian and Kohlway, William and Whetten, Ross and Frampton, John}, year={2020} }
 @article{matallana-ramirez_rauf_farage-barhom_dortay_xue_dröge-laser_lers_balazadeh_mueller-roeber_2013, title={NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis}, volume={6}, ISSN={1674-2052}, url={http://dx.doi.org/10.1093/mp/sst012}, DOI={10.1093/mp/sst012}, abstractNote={Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoter-reporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence.}, number={5}, journal={Molecular Plant}, publisher={Elsevier BV}, author={Matallana-Ramirez, Lilian P. and Rauf, Mamoona and Farage-Barhom, Sarit and Dortay, Hakan and Xue, Gang-Ping and Dröge-Laser, Wolfgang and Lers, Amnon and Balazadeh, Salma and Mueller-Roeber, Bernd}, year={2013}, month={Sep}, pages={1438–1452} }
 @article{rauf_arif_dortay_matallana-ramírez_waters_gil nam_lim_mueller-roeber_balazadeh_2013, title={ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription}, volume={14}, ISSN={1469-221X 1469-3178}, url={http://dx.doi.org/10.1038/embor.2013.24}, DOI={10.1038/embor.2013.24}, abstractNote={Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence‐associated genes. Here, we report that unexpectedly ORE1 interacts with the G2‐like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1.}, number={4}, journal={EMBO reports}, publisher={Wiley}, author={Rauf, Mamoona and Arif, Muhammad and Dortay, Hakan and Matallana-Ramírez, Lilian P and Waters, Mark T and Gil Nam, Hong and Lim, Pyung-Ok and Mueller-Roeber, Bernd and Balazadeh, Salma}, year={2013}, month={Mar}, pages={382–388} }
 @article{balazadeh_siddiqui_allu_matallana-ramirez_caldana_mehrnia_zanor_köhler_mueller-roeber_2010, title={A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence}, volume={62}, ISSN={0960-7412}, url={http://dx.doi.org/10.1111/j.1365-313X.2010.04151.x}, DOI={10.1111/j.1365-313X.2010.04151.x}, abstractNote={The onset and progression of senescence are under genetic and environmental control. The Arabidopsis thaliana NAC transcription factor ANAC092 (also called AtNAC2 and ORE1) has recently been shown to control age-dependent senescence, but its mode of action has not been analysed yet. To explore the regulatory network administered by ANAC092 we performed microarray-based expression profiling using estradiol-inducible ANAC092 overexpression lines. Approximately 46% of the 170 genes up-regulated upon ANAC092 induction are known senescence-associated genes, suggesting that the NAC factor exerts its role in senescence through a regulatory network that includes many of the genes previously reported to be senescence regulated. We selected 39 candidate genes and confirmed their time-dependent response to enhanced ANAC092 expression by quantitative RT-PCR. We also found that the majority of them (24 genes) are up-regulated by salt stress, a major promoter of plant senescence, in a manner similar to that of ANAC092, which itself is salt responsive. Furthermore, 24 genes like ANAC092 turned out to be stage-dependently expressed during seed growth with low expression at early and elevated expression at late stages of seed development. Disruption of ANAC092 increased the rate of seed germination under saline conditions, whereas the opposite occurred in respective overexpression plants. We also detected a delay of salinity-induced chlorophyll loss in detached anac092-1 mutant leaves. Promoter-reporter (GUS) studies revealed transcriptional control of ANAC092 expression during leaf and flower ageing and in response to salt stress. We conclude that ANAC092 exerts its functions during senescence and seed germination through partly overlapping target gene sets.}, number={2}, journal={The Plant Journal}, publisher={Wiley}, author={Balazadeh, Salma and Siddiqui, Hamad and Allu, Annapurna D. and Matallana-Ramirez, Lilian P. and Caldana, Camila and Mehrnia, Mohammad and Zanor, Maria-Inés and Köhler, Barbara and Mueller-Roeber, Bernd}, year={2010}, month={Jan}, pages={250–264} }