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Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

Current climate change constitutes a challenge for the survival of several drought-sensitive forests. The study of the genetic basis of adaptation offers a suitable way to understand how tree species may respond to future climatic conditions, as well as to design suitable conservation and management strategies. Here, we focus on selected genetic signatures of the drought-sensitive relict fir, Abies pinsapo Boiss. Field sampling of 156 individuals was performed in two elevation ecotones, characterized by widespread A. pinsapo decline and mortality. The DNA from dead trees was investigated and compared to living individuals, accounting for different ages and elevations. We studied the genes gated outwardly-rectifying K+ (GORK) channel and Plasma membrane Intrinsic Protein (PIP1) aquaporin, previously related to drought response in plant model species, to test whether drought was the main abiotic factor driving the decline of A. pinsapo forests. A combination of linear regression and factor models were used to test these selection signatures, as well as a fixation index (Fst), used here to analyze the genetic structure. The results were consistent among these approaches, supporting a statistically significant association of the GORK gene with survival in one of the A. pinsapo populations. These results provide preliminary evidence for the potential role of the GORK gene in the resilience to drought of A. pinsapo., Ministerio de Economía y Competitividad (MINECO), Universidad Complutense de Madrid (UCM), Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub

Increasing variability and uncertainty regarding future climate provide new challenges for understanding species adaptive capacity. Trees are especially concerning given their lower evolutionary rates and ecological importance. Thus, the knowledge of their intraspecific genetic diversity is crucial to predict the possible evolutionary consequences of global climate change and its long-term effects on biodiversity. Furthermore, since drought stress is among the first limitations for plants facing a changing climate, understanding the underlying mechanisms involved in drought stress response/resilience in trees constitutes one of the most valuable research objectives in evolutionary ecology. Relict species constitute reliable models given their reduced geographic range size, isolation and usually fragmented distribution, which subject them to many shifting genetic processes. Moreover, despite these theoretically limitant genetic characteristics for adaptation, empirical evidence frequently shows a lack of decreased fitness (Hampe and Jump 2011). A possible explanation can be that many of them originated from populations that overcome the cold stages of the Quaternary. Therefore, they might contain key genetic variants in ecologically relevant traits (Crawford 2008, Kawecki 2008, Hampe and Jump 2011). A particularly interesting group are those that now inhabit at southern locations since they can be potentially preadapted to environmental conditions expected in future in more northerly central areas in the future (Hampe and Petit, 2005). Here, we attempted to test the effect of these processes in the genetic diversity and genetic structure of trees, as well as determining their evolutionary potential under a climate change scenario, by using as experimental models two southern relict and climate changethreatened conifers, located in altitudinal ecotones and sharing a biogeographic origin: the Southernomost european fir (Abies pinsapo Boiss.), endemic to Southern Spain, Los cambios en las condiciones medioambientes como consequencia del cambio climático y la incertidumbre ante ellos suponen nuevos retos para la capacidad adaptativa de las especies. Los árboles son particularmente preocupantes, dadas su menor tasa evolutiva y su importancia ecológica. Por ello, el conocimiento de su diversidad genética es crucial para predecir las posibles consecuencias evolutivas frente al cambio climático y su efecto en la biodiversidad a largo plazo. Considerando que la sequía es uno de los principales factores limitantes para las especies vegetales afectadas por el cambio climático, el conocimiento de los mecanismos implicados en la respuesta y resiliencia a la sequía en árboles constituye uno de los objetivos de investigación más importantes en ecología evolutiva. Las especies relictas son excelentes modelos debido a sus reducidas distribuciones geográficas, su aislamiento y su distribución frecuentemente fragmentada, que las somete a diversos procesos de cambio genético. A pesar de que, en teoría, estas características dificultarían su adaptación, la evidencia empírica, en muchos casos, no muestra una menor eficacia biológica en estas especies (Hampe and Jump 2011). Una posible explicación sería que muchas de ellas tienen su origen en poblaciones que sobrevivieron las frías etapas del Cuaternario. Por lo tanto, podrían contener variantes genéticas clave en rasgos ecológicamente importantes (Crawford 2008, Kawecki 2008, Hampe and Jump 2011). Las especies relictas más meridionales son de especial interés, ya que podrían estar preadaptadas a las condiciones ambientales esperadas en el futuro en áreas más septentrionales como consecuencia del cambio climático (Hampe and Petit, 2005). En la presente tesis se ha probado el efecto de estos procesos en la diversidad y estructura genética de los árboles, así como su potencial adaptativo en un escenario de cambio climático, usando como modelos experimentales dos coníferas relictas y amenazadas por el ca

Increasing variability and uncertainty regarding future climate provide new challenges for understanding species adaptive capacity. Trees are especially concerning given their lower evolutionary rates and ecological importance. Thus, the knowledge of their intraspecific genetic diversity is crucial to predict the possible evolutionary consequences of global climate change and its long-term effects on biodiversity. Furthermore, since drought stress is among the first limitations for plants facing a changing climate, understanding the underlying mechanisms involved in drought stress response/resilience in trees constitutes one of the most valuable research objectives in evolutionary ecology. Relict species constitute reliable models given their reduced geographic range size, isolation and usually fragmented distribution, which subject them to many shifting genetic processes. Moreover, despite these theoretically limitant genetic characteristics for adaptation, empirical evidence frequently shows a lack of decreased fitness (Hampe and Jump 2011). A possible explanation can be that many of them originated from populations that overcome the cold stages of the Quaternary. Therefore, they might contain key genetic variants in ecologically relevant traits (Crawford 2008, Kawecki 2008, Hampe and Jump 2011). A particularly interesting group are those that now inhabit at southern locations since they can be potentially preadapted to environmental conditions expected in future in more northerly central areas in the future (Hampe and Petit, 2005). Here, we attempted to test the effect of these processes in the genetic diversity and genetic structure of trees, as well as determining their evolutionary potential under a climate change scenario, by using as experimental models two southern relict and climate changethreatened conifers, located in altitudinal ecotones and sharing a biogeographic origin: the Southernomost european fir (Abies pinsapo Boiss.), endemic to Southern Spain

Wood constitutes the unique source of DNA in dead trees, but extraction of adequate quality DNA from dry wood is usually challenging. However, many different molecular studies require the use of such DNA. We have standardized and validated a modified CTAB protocol to isolate DNA from dry wood from Abies pinsapo and Cedrus atlantica species. Due to the degradation and very little DNA that is normally present in the wood from dead trees we have developed a PCR based test to certify the quality of the extracted samples. In the present study, we have proved too the effectiveness of this methodology to isolate DNA from conifer dry wood samples of sufficient quality to perform further molecular genetic experiments., Depto. de Genética, Fisiología y Microbiología, Fac. de Ciencias Biológicas, TRUE, pub