- Author: Kara Manke, UC Berkeley science writer
- Contact: Jeannette E. Warnert
Scorching temperatures and parched earth are no match for the sorghum plant — this cereal crop, native to Africa, will remain green and productive, even under conditions that would render other plants brown, brittle and barren.
A new study published this week in the journal Proceedings of the National Academy of Sciences provides the first detailed look at how the plant exercises exquisite control over its genome — switching some genes on and some genes off at the first sign of water scarcity, and again when water returns — to survive when its surroundings turn harsh and arid.
"With this research, we are laying the groundwork for understanding drought tolerance in cereal crops," said Jeff Dahlberg, UC Cooperative Extension sorghum specialist. Dahlberg, co-author of the study, is also director the UC Kearney Agricultural Research and Extension Center in Parlier, one of nine research and extension centers in California that are part of UC Agriculture and Natural Resources.
Dahlberg said researchers can use the knowledge gained from this project to search for drought genes in other cereal crops.
"That has implications for feeding the world, particularly considering changing climate and weather patterns," he said.
The massive dataset, collected from 400 samples of sorghum plants grown during 17 weeks at Kearney, reveals that the plant modulates the expression of a total of 10,727 genes, or more than 40% of its genome, in response to drought stress. Many of these changes occur within a week of the plant missing a weekly watering or after it is first watered after weeks of no precipitation or irrigation.
Kearney is a 330-acre agriculture research facility in the heart of California's Central Valley, where field-scale, real-world research can be conducted on drought impact on plants and soil microbial communities. The climate is naturally dry throughout the summer, making it ideal to mimic drought conditions by withholding irrigation water.
"People have really shied away from doing these types of experiments in the field and instead conduct them under controlled conditions in the laboratory or greenhouse. But I believe that the investment of time and resources that we put into it is going to pay off, in terms of the quality of the answers that we get, in terms of understanding real-world drought situations," said Peggy Lemaux, UC Cooperative Extension specialist in UC Berkeley's Department of Plant and Microbial Biology and co-author of the paper.
The data was collected as part of the Epigenetic Control of Drought Response in Sorghum, or EPICON, project, a five-year, $12.3 million study into how the sorghum plant is able to survive the stress of drought. The EPICON study is run as a partnership between UC Berkeley researchers and scientists at UC Agriculture and Natural Resources (UC ANR), the Energy Department's Joint Genome Institute (JGI) and that agency's Pacific Northwest National Laboratory (PNNL).
To conduct the research, the team cultivated sorghum plants under three different irrigation conditions — pre-flowering drought, post-flowering drought and controlled applications of water — over three consecutive years at Kearney.
Each week during the growing season, members of the research team carefully harvested samples from the leaves and roots of selected plants and set up a mobile lab in the field where they could rapidly freeze the samples until they were processed for analysis. Then, researchers at JGI sequenced the RNA in each sample to create the transcriptome data, which reveals which of the plant's tens of thousands of genes are being transcribed and used to make proteins at particular times.
Finally, statisticians led by UC Berkeley statistics professor Elizabeth Purdom parsed the massive transcriptome data set to pinpoint how gene expression changed as the plants grew and were subjected to drought or relief from drought conditions.
"We very carefully controlled the watering conditions, and we sampled over the entire developmental timeframe of sorghum, so [researchers] could actually use this data not only to study drought stress, but also to study plant development," Lemaux said.
The researchers noticed a few interesting patterns in the transcriptome data. First, they found that a set of genes known to help the plant foster symbiotic relationships with a type of fungus that lives around its roots was switched off in drought conditions. This set of genes exhibited the most dramatic changes in gene activity that they observed.
"That was interesting, because it hinted that the plants were turning off these associations [with fungi] when they were dry," said John Vogel, a staff scientist at JGI and co-author of the paper. "That meshed well with findings that showed that the abundance of these fungi around the roots was decreasing at the same time."
Second, they noticed that certain genes known to be involved with photosynthesis were also turned off in response to drought and turned up during drought recovery. While the team doesn't yet know why these changes might help the plant, they provide interesting clues for follow-up.
The data in the current paper show the plant's transcriptome under both normal conditions and drought conditions over the course of a single growing season. In the future, the team also plans to publish data from the other two years of the experiment, as well as proteomic and metabolomic data.
Nelle Varoquaux and Cheng Gao of UC Berkeley and Benjamin Cole of JGI are co-first-authors of the study. Other co-authors include Grady Pierroz, Christopher R. Baker, Dhruv Patel, Mary Madera, Tim Jeffers, Judith A. Owiti, Stephanie DeGraaf, Ling Xu, Krishna K. Niyogi, Devin Coleman-Derr and John W. Taylor of UC Berkeley; Joy Hollingsworth, Julie Sievert and Jeffery Dahlberg of UC ANR KARE; Yuko Yoshinaga, Vasanth R. Singan, Matthew J. Blow, Axel Visel and Ronan O'Malley of JGI; Maria J. Harrison of the Boyce Thompson Institute; Christer Jansson of PNNL and Robert Hutmacher of UC ANR.
This research was funded in part by the Department of Energy (DOE) grant DE-SC001408; the Gordon and Betty Moore Foundation grant GBMF3834; the Alfred P. Sloan Foundation grant
2013-10-27; L'Ecole NormaleSupérieure-Capital Fund Management data science chair and the DOE's Office of Biological and Environmental Research grant DE-SC0012460. Work conducted by the DOE Joint Genome Institute is supported by the Office of Science of the DOE contract DE-AC02-05CH11231.
UC Agriculture and Natural Resources brings the power of UC research in agriculture, natural resources, nutrition and youth development to local communities to improve the lives of all Californians. Learn more at ucanr.edu.
RELATED INFORMATION
- Dealing with Drought: Uncovering Sorghum's Secrets
- Berkeley to lead $12.3M study of crop drought tolerance
- Drought treatment restructures plants' microbiomes
- Microbes associated with plant roots could be a key to helping plants survive drought
CONTACTS
Jeff Dahlberg, UC Cooperative Extension specialist at the UC Kearney Agricultural Research and Extension Center, jadahlberg@ucanr.edu
Peggy Lemaux, cooperative extension specialist at UC Berkeley's Department of Plant and Microbial Biology, lemauxpg@berkeley.edu
John Vogel, staff scientist, DOE Joint Genome Institute, jpvogel@lbl.gov
- Author: Lynn M. Sosnoskie
2018 Alfalfa and Forage Field Day
Wednesday, September 19, 2018
Kearney Agricultural Research and Extension Center
9240 S. Riverbend Ave., Parlier, CA 93648
7:30 AM Registration
8:00 AM TRAM LEAVES FOR FIELD TOUR
Alfalfa Varieties for Pest and Disease Management – Shannon Mueller, Agronomy Advisor and County Director, UCCE Fresno
Low-Lignin Alfalfa Testing – Daniel Putnam, CE Agronomy & Forage Specialist, UC Davis
Sorghum Drought Stress – Jeffery Dahlberg, KAREC Director and Bob Hutmacher, WSREC Director & CE Extension Specialist
Weed ID Mobile App: Hands-On – Lynn Sosnoskie, Agronomy & Weed Science Advisor, UCCE Merced & Madera
9:50 AM TRAM RETURNS
10:00 AM Weed ID: Tools and Tricks of the Trade – Lynn Sosnoskie
10:15 AM Insect Pest Management in Alfalfa: State of IPM Address – Tim Hays, PCA, Buttonwillow Warehouse, Lancaster, CA
10:30 AM Discussion
10:45 AM Break
11:00 AM Introduction of Soil Quality Advisors – NRCS and Nutrient Mgmt./Soil Quality Advisors Anthony Fulford, UCCE Stanislaus, Merced, & San Joaquin, and Daniela Carrijo, UCCE Fresno, Madera, Kings, & Tulare
11:15 AM Salinity Management: Soil and Cropping Systems Strategies – Michelle Leinfelder-Miles, Delta Crops & Agronomy Advisor, UCCE San Joaquin
11:30 AM Sub-Surface Drip Irrigation and Deficit Irrigation in Alfalfa – Daniel Putnam
11:45 AM Manured Corn-Wheat N, P, & K Budgeting – Nick Clark, Agronomy & Nutrient Mgmt. Advisor, UCCE Kings, Tulare, & Fresno
12:00 PM Discussion
12:15 PM Lunch
DPR & CCA CEU hours have been applied for.
2018 Alfalfa Day - Kearney Agenda
- Author: Michelle Leinfelder-Miles
In recent years, the University of California Division of Agriculture and Natural Resources has augmented research efforts on growing grain and silage sorghum [Sorghum bicolor (L.) Moench] in California. The purpose of the Delta Sorghum Seeding Rate Trial was to better understand optimal seeding rates for grain sorghum grown in the Sacramento-San Joaquin River Delta. While such information exists for Midwest sorghum production, applied information is lacking for California, and more specifically for the Delta – a unique agricultural region known for its organic soils, shallow groundwater, and cooler climate conditions. This information is important because sorghum has similar growth habits as corn and is sometimes grown as a substitute for corn because of its tolerance of drought and low-input conditions. In the United States, sorghum is used in a wide array of feedstocks for biofuels, pet foods, dairy, cattle, pork and poultry feed, and more recently as a gluten-free cereal grain for human food systems.
The trial took place during the 2016 and 2017 growing seasons on Tyler Island in Sacramento County. The 2016 trial was planted on May 20th, and the 2017 trial was planted on May 25th using a John Deere cone planter. Seed was planted approximately 2 inches deep. We used the grower's varieties, which were Eureka Seeds 3292 in 2016 and Eureka Seeds 3325W in 2017. Both varieties were white sorghum varieties, had 16,000 seeds/lb, and 85 percent germination, according to the labels. Five seeding rate treatments (5, 6, 9, 12, and 15 lbs/acre) were tested. Each plot consisted of four rows (30-inch row spacing) that were 45 feet in length in 2016 and 50 feet in length in 2017. The fields were managed similarly in both years. Site characteristics, cultural practices, and statistical procedures are described in the full report.The plots were harvested on November 14, 2016 and October 12, 2017 using an Almaco research combine, harvesting the center two rows from the four-row plots. Trial results are presented as plant establishment characteristics (Table 1), plant maturity characteristics (tables available in the full report), and yield (Figure 1). The tables and figure present mean values for the four (2016) or five (2017) replicates. Differences among treatments are indicated by different letters following the mean.
The seeding rates are expressed as plant populations in Table 1. The number of sorghum seeds/lb is highly variable across varieties. For this reason, when determining seeding rates, growers should first determine their desired plant population. A worksheet in the full report provides equations for calculating seeding rate based on desired plant populations and percent germination for the variety. Stand counts were made as the number of plants/10-foot row length approximately two weeks and one month after planting. The counts were scaled up to plants/acre. Across both years, stands generally decreased from the first count date to the second. Stand counts were lower in 2017 compared to 2016, but this did not translate into lower yields. Weeds were also counted in the month after planting (data not shown), but overall weed pressure was very low in both years.
Table 1. Plant establishment characteristics of the 2016 and 2017 UCCE Delta sorghum seeding rate trial.
While there were no statistical differences in yield across treatments in either year, the take-home message of the trial is that there appears to be no benefit to planting the highest seeding rates. In both years, the trend was for the 15-lb seeding rate to have the lowest yield. In 2016, there was a lot of variability in the data. There was a trend for the 9-lb treatment to have higher yields; however, we suspect this was due to the experimental design. In 2016, by random chance, there were several 9-lb treatment plots next to the sub-irrigation ditches, which were exterior to the experiment on both sides. For this reason, the 9-lb treatment may have been inadvertently favored with better moisture conditions. To correct for this, the experimental design was changed in 2017 in order to better control field variability. The 2017 yields were consistent across treatments, around 7000 lbs/acre. The 2017 results best illustrate how planting the higher seeding rates provided no yield benefit, yet would incur a higher seed expense. We recognize that growers will need to consider site characteristics, like weed or wireworm pest pressure, when determining optimal seeding rates; nevertheless, this research indicates that good yields can result from seeding rates of 5 or 6 lbs/acre (estimated plant populations of 80-96,000 plants/acre), and that planting higher plant populations would not only cost growers more in seed expense but could also cost them in yield.
Figure 1. Yield at 13 percent moisture of UCCE Delta sorghum seeding rate trial. There were no significant differences among treatments in 2016 (P = 0.1278) or 2017 (P = 0.2419).
In summary, it is important to study sorghum cultural practices in the Sacramento-San Joaquin Delta region, and in California at-large, because currently, most applied information comes from the Midwest. California growers need information on sorghum cultivation because sorghum may be grown as a lower-input substitute for corn. Sorghum seeding rates were studied to assist growers with determining optimum rates for the Delta environment. The results indicate that there is no yield benefit to planting seeding rates greater than 6 lbs/acre (estimated plant population greater than 96,000 plants/acre), and that planting higher rates is just added expense for the grower. Future research should investigate these plant populations on narrower row spacing. Special thanks go to growers, Steve and Gary Mello, and to UC Kearney Research and Extension Center Director, Jeff Dahlberg, for providing equipment and information for the success the trial.
- Author: Michelle Leinfelder-Miles
(There was an error in the previous version of this blog post. The error has been corrected here and in the full report, available from my website.)
The purpose of this trial was to better understand optimal seeding rates for grain sorghum grown in the Sacramento-San Joaquin River Delta – a unique agricultural region known for its fertile, organic soils, shallow groundwater, and cooler climate conditions. The trial was planted in the Sacramento-San Joaquin Delta, on Tyler Island in Sacramento County. The soil is a Rindge mucky silt loam with approximately 20 percent organic matter in the top 15 inches of soil. The Rindge series is a mucky peat soil down to about 60 inches, and approximately 55,600 acres in the Delta are described by the Rindge classification. The plot was planted on May 20, 2016 using a John Deere cone planter. Seed was planted approximately 2 inches deep. The trial was a white sorghum variety, Eureka Seeds 3292, which was the grower's variety. The variety has 16,000 seeds/lb and 85 percent germination, according to the label. Five seeding rate treatments (5, 6, 9, 12, and 15 lbs/acre) were replicated over four blocks positioned down the rows. The seeding rates are expressed as plant populations in Table 1. (The number of sorghum seeds/lb is highly variable across varieties. For this reason, when determining seeding rates, growers should first determine their desired plant population. A worksheet for calculating seeding rate from desired plant population is available from the full report.) Each plot consisted of four rows (30-inch row spacing) that were 45 feet in length. The previous crop in the field was wheat. Subsurface irrigation by “spud ditch” sub-surface irrigation was employed twice. The field was fertilized at planting with 35 gallons/acre of 8-24-0 with ½ percent of zinc. The field was cultivated one time, and Maestro 4EC (8 oz/acre), AAtrex 4L (0.75 pint/acre), and Crosshair (4 oz/acre) were applied for post-emergence weed control in mid-June. The plot was harvested on November 14, 2016 using an Almaco research combine, harvesting the center two rows from the four-row plots.
Trial results are presented as plant establishment characteristics (Table 1), plant maturity characteristics (Table 2), and yield (Figure 1). The tables and figure present mean values for the four replicates. Tukey's range test was the statistical method used to compare the means. Varieties were considered statistically different if their P value was less than 0.05, or 5 percent. Differences between treatments are indicated by different letters following the mean.
The estimated plant populations for the treatment seeding rates were calculated using the number of seeds/lb and percent germination for this variety. Stand counts were made as the number of plants/10-foot row length on June 1st and June 16th, and these counts were scaled up to plants/acre. Stand counts were as expected - higher counts for the higher seeding rates. Stand counts for all treatments decreased from June 1st to June 16th, but stand counts remained on target with the estimated plant population for the 5 and 6-lb seeding rates. Weeds were also counted in the month after planting and in the month before harvest (data not shown), but overall weed pressure was very low at this location.
There were no differences in the number days to flowering among treatments; however, there were differences among treatments in the other maturity characteristics. The higher seeding rate plots had taller plants with longer panicle exsertion (the length of the stem from the top leaf to the bottom of the panicle), which may suggest that at these higher densities, plants were competing with each other and growing taller. Panicles were longest in the 5 lb seeding rate and statistically longer than the panicles in the 12-lb and 15-lb rates. There were no statistical differences in grain moisture at harvest.
The treatment yields do not provide a clear take-home message of the results, except perhaps to show that the highest seeding rate (15 lbs/acre) is not an optimum seeding rate. However, if the 9-lb treatment was ignored, there would be a trend for yield to decrease as the seeding rate increased. A possible explanation for the high yield of the 9-lb treatment is that there were three of these plots proximal to the sub-irrigation ditches, which were exterior to the experiment on both sides. The 9-lb treatment may have been inadvertently favored with better moisture conditions as a result of the experimental design. In hindsight, the experiment should have been blocked across the rows instead of down the rows to account for these field conditions which may have introduced variability in soil moisture. Blocking down the rows accounted for very little unexplained variability, and in future years, the experiment will be designed to account for the variability across the rows.
In summary, it is important to study sorghum cultural practices in the Sacramento-San Joaquin Delta region because crop acreage appears to be increasing, and the Delta is a unique growing region of California. Sorghum seeding rates as a function of plant population were studied to assist growers with determining optimum rates for the Delta environment. While results are somewhat inconclusive, there appears to be a trend for the lower seeding rates to yield the highest. If this trend is shown in future years, then Delta growers could have higher productivity with lower seed costs.
If you have insects invading your kitchen or pantry, or if you've ever opened stored food products and discovered pests inside, you'll want to watch this new video from UC IPM. It describes several types of pantry pests, foods they are attracted to, and includes steps on how to prevent, manage and eliminate them from your home.
For more detailed information, read the Pantry Pests Pest Note. You can also read an article about pantry pests in the Retail and Garden Center IPM News at http://ipm.ucanr.edu/PDF/PUBS/retailipmnews.2015.july.pdf
Did you know that UC IPM has over 35 helpful home and garden videos? Visit http://ipm.ucanr.edu/IPMPROJECT/videolibrary-ur.html to watch more.