Promises and challenges of eco-physiological genomics in the field: tests of drought responses in switchgrass

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass

“…Unfortunately, a large number of prior studies have ignored the importance of sampling time, especially in transcriptome analysis in various stress response studies (Li, Wang, Tang, Kakani, & Mahalingam, ; Miao, Han, Zhang, Chen, & Ma, ; Song et al, ; Tang et al, ; Wang et al, ). Our finding suggest that a time‐series experiment design will help to avoid this bias in future gene‐by‐environment research (Lovell, Shakirov, et al, ).…”

“…However, the current cost of RNA‐seq remains a barrier for high‐throughput applications. Alternatively, an emerging 3′‐Tag RNA‐seq (3′‐TagSeq) technology provides a solution allowing large‐scale experiments (Meyer, Aglyamova, & Matz, ), which has been successfully used in species with complex genomes (Kremling et al, ; Lovell et al, ). Given the nature of circadian rhythm, time‐series experiments coupled with transcriptome studies represent key steps towards understanding the complex sensing and signalling process of photoperiod changes (Doherty & Kay, ).…”

Gene expression differs in codominant prairie grasses under drought

“…The number of differentially expressed genes within species is small compared to other studies (e.g., Bushman et al., ; Dong, Fan, Deng, Xu, & Zhao, ; Meyer et al., ; Wilkins, Waldron, Nahal, Provart, & Campbell, ), indicating that our power to detect differential expression was low. Although care was taken to minimize differences among plants, we performed an uncontrolled drydown which often leads to variation in water content (Lovell et al., ) and has somewhat limited applicability to field studies. As is seen in Figure , there is variation among droughted plants.…”

“…Yet, detecting stress within individuals and in ecological communities remains a problem of scale (Levin, ), and selecting responses and tools that are most appropriate for measuring drought stress remains a challenge. Ecologists have grown increasingly interested in pairing the molecular responses to drought, such as gene expression and metabolite analysis, with morphological and physiological data (Lovell et al., ) in order to reveal underlying mechanisms. An understanding of gene expression is a critical hurdle revealing these stress response mechanisms (Johnson et al., ; Leakey et al., ; Meyer et al., ; Swarbreck et al., ).…”

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

“…Switchgrass is split into two locally adapted ecotypes, upland and lowland (Morris et al, 2011;Lowry et al, 2014;Milano et al, 2016). The upland ecotype is more common in northern North America, has a small stature (up to 190 cm), and has limited resistance to multiple pathogens, including rust and other fungal pathogens as well as viruses (Casler, 2012;Uppalapati et al, 2013;Milano et al, 2016;Lovell et al, 2016;Alexander et al, 2017). In contrast, the southern lowland ecotype is large (up to 285 cm) and is more resistant to fungal pathogens (Casler, 2012;Uppalapati et al, 2013;Milano et al, 2016;Lovell et al, 2016).…”