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

Author
item LOVELL, JOHN - University Of Texas
item SHAKIROV, EUGENE - Kazan Institute Of Economics, Management And Law
item SCHWARTZ, SCOTT - University Of Texas
item LOWRY, DAVID - Western Sydney University
item ASPINWALL, MICHAEL - Western Sydney University
item TAYLOR, SAM - University Of New Hampshire
item BONNETTE, JASON - University Of Texas
item PALACIO-MEJIA, JUAN - University Of Texas
item HAWKES, CHRISTINE - University Of Texas
item Fay, Philip
item JUENGER, THOMAS - University Of Texas

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/26/2016
Publication Date: 5/31/2016
Publication URL: https://handle.nal.usda.gov/10113/5695366
Citation: Lovell, J.T., Shakirov, E.V., Schwartz, S., Lowry, D.B., Aspinwall, M.J., Taylor, S., Bonnette, J., Palacio-Mejia, J.D., Hawkes, C., Fay, P.A., Juenger, T.E. 2016. Promises and challenges of eco-physiological genomics in the field: Tests of drought responses in switchgrass. Plant Physiology. 172:734-748. doi:10.1104/pp.16.00545.

Interpretive Summary: Stress tolerance is a critical trait in plants allowing them to maintain growth during periods of less favorable growing conditions, such as during drought or heat waves. Plants tolerate stress by several mechanisms, including maintaining adequate water levels in plant tissues, which maintains plant ability to continue gaining carbon through photosynthesis. Stress tolerance mechanisms depend on the presence and activity of many genes, and molecular biology now provides tools to measure expression in plants under stress, allowing the specific genes linked with stress tolerance to identified. This paper synthesizes several studies attempting to identify genes responsible for stress tolerance in switchgrass, a native grass widely considered as a bioenergy feedstock source. The synthesis finds that the number of genes identified as being linked to stress tolerance depends greatly on whether stress tolerance experiments are conducted in the greenhouse in pots or as naturally-growing plants in the field. More genes are associated with greenhouse studies, where much of the natural variation present in the field is avoided. This means that gene expression studies in greenhouse potted plants may identify genes potentially active in field-grown plants, but studies must be conducted in the field to identify the important genes against the background of natural environmental variability that plants face in actual production.

Technical Abstract: Knowledge of the physiological and genetic basis of stress tolerance has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in controlled conditions or laboratories, not in the field. To test the comparability of drought responses across experiments with different levels of control over soil and canopy conditions, we undertook three independent experiments using the switchgrass reference Alamo AP13. We analyzed physiological and gene-expression variation across four locations, two sampling times and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses to drought. Critically, a drought experiment with small pots in the greenhouse elicited nearly identical physiological changes as an experiment conducted in the field, but an order of magnitude more differentially expressed genes. The strong across-experiment correlations between physiological plasticity, but not differential gene expression, highlight the complex and diverse genetic mechanisms that can produce phenotypically similar responses to various soil water deficits.