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ARS Home » Pacific West Area » Maricopa, Arizona » U.S. Arid Land Agricultural Research Center » Water Management and Conservation Research » Research » Publications at this Location » Publication #323242
Title: Field-based high-throughput plant phenotyping reveals the temporal patterns of quantitative trait loci associated with stress-responsive traits in cotton

Author
item PAULI, DUKE - Cornell University
item ANDRADE-SANCHEZ, PEDRO - University Of Arizona
item CARMO-SILVA, A.ELIZABETE - Rothamsted Research
item French, Andrew
item HEUN, JOHN - University Of Arizona
item Hunsaker, Douglas
item LIPKA, ALEX - University Of Illinois
item SALVUCCI, MICHAEL - Retired ARS Employee
item SETTER, TIMOTHY - Retired ARS Employee
item STRAND, ROBERT - Retired ARS Employee
item Thorp, Kelly
item WANG, SAM - University Of Arizona
item White, Jeffrey
item GORE, MICHAEL - Cornell University

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/24/2016
Publication Date: 4/1/2016
Citation: Pauli, D., Andrade-Sanchez, P., Carmo-Silva, A., French, A.N., Heun, J., Hunsaker, D.J., Lipka, A., Salvucci, M., Setter, T.L., Strand, R., Thorp, K.R., Wang, S., White, J.W., Gore, M. 2016. Field-based high-throughput plant phenotyping reveals the temporal patterns of quantitative trait loci associated with stress-responsive traits in cotton. Genetics. 6:865-879.

Interpretive Summary: Heat and drought stress threaten US cotton production by reducing yield, fiber quality and profitability. Compensation for drought is feasible provided ample water supplies for irrigation, but supplies are scarce and increasingly costly. Compensation for heat is even more difficult as fundamental genetic changes to the plants themselves are needed to adapt cotton to an increasingly hostile environment. Discovering these needed changes will help solve both problems: cotton plants could maintain or increase yields under high temperatures with similar or reduced water requirements compared with current cotton cultivars. To make this discovery possible many cultivars need to be grown, measured and analyzed for genetic and physiological conditions in field-stressed conditions. In 2010-2012, 95 Upland cotton lines were tested in this way with water-limited and well-watered conditions. Using an innovative tractor platform instrumented with multiple sensors the lines were observed many times during a day and over the growing season. Cotton canopy heights, temperatures and light reflectance were measured. Standard agronomic data, including yield and fiber quality were collected. Genetic information for all lines was assembled and interpreted. Unprecedented results from the experiments showed that plant features such as growth stage, height and drought stress could be linked with specific genetic characteristics important for plant productivity. Results also showed that the ability to make these links depends strongly upon when the sensor data were collected. These results are important for cotton researchers because they show that a new field technique that collects biologically significant data that was previously inaccessible. The results are also important for all crop researchers seeking ways to understand the relationship between a plant's genetic makeup and its ability to adapt to harsh environments and a changing climate.

Technical Abstract: To dissect the genetic basis of dynamic adaptive traits under relevant growing conditions, we employed a field-based, high-throughput plant phenotyping (HTPP) system that deployed four sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across three years. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate to high broad-sense heritabilities as well as expected interactions among genotypes with water regime and time of day. Temporal patterns of quantitative trait loci (QTL) expression were mostly observed for the more dynamic HTPP canopy traits, canopy temperature and NDVI, and varied with plant developmental stages. In addition, the strength of correlation between HTTP canopy and agronomic traits such as lint yield displayed a time-dependent relationship. We found QTL for HTPP canopy traits also shared with agronomic and physiological traits and some of which were associated with candidate genes implicated in having a response to environmental stress. This work demonstrates the novel use of a field-based, HTPP system to study the genetic basis of stress-adaptive traits in cotton and the results from which have the potential to facilitate the development of environmentally-resilient cotton cultivars.