Research Archives - Department of Soil and Crop Sciences

Department announces awards during annual meeting

20Jan

Ambika Chandra, Ph.D. (center) with her award. Standing with Chandra is B.B Singh, Ph.D. (left) and David Baltensperger, Ph.D., professor and department head.

Ambika Chandra, Ph.D. (center) receiving the B.B. Singh Award for Outstanding Research in Crop Sciences. Standing with Chandra is B.B Singh, Ph.D. (left) and David Baltensperger, Ph.D., professor and department head.

Congratulations to all our faculty, staff and students who received awards during the Soil and Crop Sciences’ annual meeting held on January 14 in College Station.

The department recognized the retirement of Dr. Jaroy Moore, Director, Texas A&M AgriLife Research and Extension Center in Lubbock. Moore has been with the Texas A&M AgriLife Extension Service for 53 years. He served as the station leader in Pecos in 1977, then became resident director in El Paso in 1995 before he became the director in Lubbock in 1998.

Fifteen faculty, staff, and students were also recognized and presented with the following awards:

Special Award

B.B. Singh Award for Outstanding Research in Crop Sciences: Ambika Chandra, Ph.D.

Administrative

Administrative Support: Alisa Hairston

Extension Awards

Extension Faculty Award: Scott Nolte, Ph.D.

Collaborating County Extension Agent: Shane McLellan, Ph.D.

Technical/Extension Staff Support: – Field Support: Kyle Turner

Special Service/Recognition: Texas Wheat Producers Board and Association, Amarillo, TX
Rodney Mosier, Executive Vice President and Ms. Steelee Fischbacher, Director of Policy

Research Awards

Research Faculty: Paul DeLaune, Ph.D

Graduate Student Research – Agronomy: Chengsong Hu

Graduate Student Research – Plant Breeding: Zhen Wang

Graduate Student Research – Soil Science: Harrison Cocker

Research Support – Field Support: Dale Mott

Research Support – Lab Support: Chantel Scheuring

Technical Staff Support: Vicki Gergeni

Postdoctoral Research: Heng-An Lin, Ph.D.

Teaching Awards

Teaching – Faculty: William (Bill) Rooney, Ph.D.

Graduate Student Teaching: Andrew Osburn

: Clayton Moore – Special Achievement Award – Undergraduate Student Support

: Jaroy Moore, Ph.D., left, with David Baltensperger, Ph.D.

: Alisa Hairston – Special Achievement Award for Administrative Support

: Vicki Gergeni – Special Achievement Award for Technical Staff Support – Lab

: Kyle Turner – Special Achievement Award – Technical Staff Support Field

: Scott Nolte, Ph.D. – Extension – Faculty

: Heng An Lin – Postdoctoral Research

: Harrison Cocker – Graduate Student Research in Soil Science

: Andrew Osburn – Graduate Student Teaching

: Chantel Scheuring – Research Support

: William (Bill) Rooney, Ph.D. – Teaching

: Shane McLellan, Ph.D. – Collaborating County Extension Agent

Redmon, Adak Receive Vice Chancellor’s Awards in Excellence

14Jan

Congratulations to Larry Redmon, Ph.D. and Ph.D student Alper Adak who received Vice Chancellor Awards in Excellence this year. These awards recognize the commitment and outstanding contributions displayed by faculty, students and staff members across Texas A&M AgriLife.

Extension Education Awards

The Extension Specialist or Program Specialist Award was presented to Larry Redmon, Ph.D., professor and associate department head and AgriLife Extension program leader. Redmon’s educational presentations and seminars bring participants into the conversation, along with his expertise and ability to entertain audiences. The Ranch Management University, which draws participants from around the world, is one example. Evaluations have proven the annual event is highly effective in helping people adopt ranch management practices and land stewardship with an economic impact of $84 million. Redmon also spearheads the Bennett Trust programs. One of these programs caters specifically to women, providing them with the knowledge needed to make land stewardship and natural resource management decisions. Many attendees are new landowners and have little knowledge of where to begin with land ownership.

Research Awards

The Graduate Student Research Award recipient was Alper Adak, a doctoral student in the Department of Soil and Crop Sciences. Since enrolling in his doctoral program in 2018, Adak has been the primary author of four peer-reviewed research articles, greatly exceeding the standard for students in his department. He has given invited talks at international conferences and been sought out as a peer reviewer for publications in his field. One of his accomplishments was to conceive of and create a way to utilize unmanned aircraft systems data from the corn breeding and quantitative genetics program to predict yield and flowering times. However, his primary project is to identify genes responsible for the late flowering of Texas A&M AgriLife germplasm in northern climates. His poster on that work won first prize in the largest division at the Crop Science Society International Meeting in 2019.

A full list of awards was announced in AgriLife Today.

Regenerative agriculture evaluation gets underway in Texas and Oklahoma

3Dec

Written by: Kay Ledbetter

From carbon sequestration to greenhouse gas emissions to cover crops, this fall a team of Texas A&M AgriLife faculty and others will begin evaluating the impacts of regenerative agriculture in semi-arid ecoregions in Texas and Oklahoma.

A small white piece of equipment sits in a field - it will measure greenhouse gas. A cart on bicycle tires hauls the equipment

Soil carbon capture and greenhouse gas emissions will be measured in the field in the sustainable agriculture study. (Texas A&M AgriLife photo by Katie Lewis)

The Texas A&M AgriLife-led team aims to further understand and encourage the widespread adoption of regenerative practices that increase agricultural production and profitability while reducing agriculture’s environmental footprint.

Katie Lewis, Ph.D., Texas A&M AgriLife Research soil scientist, Lubbock, who will lead the project, said relationships between soil health and implementation of regenerative practices, agricultural production, climate change and regional economics are complex and poorly understood, particularly in the Southern Great Plains.

Without this understanding, the adoption of regenerative practices across the region and in similar ecoregions will remain limited. This will increase the vulnerability of agricultural production to climate change and continued depletion of water resources while passing up opportunities for carbon sequestration, enhanced agricultural production and greater agricultural resiliency.

The five-year “Sustainable Agricultural Intensification and Enhancement Through the Utilization of Regenerative Agricultural Management Practices” project has been funded by a $10 million grant from the U.S. Department of Agriculture National Institute of Food and Agriculture.

“What’s so exciting about this research is it will be the first regenerative agriculture project to cover this large of an area across both Texas and Oklahoma,” Lewis said. “With carbon being such a hot topic, we want to take a closer look at carbon sequestration – what is being captured and what is being lost through greenhouse gas emissions.”

Region-specific research to address semi-arid issues

Cattle graze is a field of corn growing in wheat stalks that were left to biodegrade

The study will look at implementing and grazing cover crops during fallow periods to evaluate environmental, economic and agronomic sustainability of regenerative agricultural systems.. (Texas A&M AgriLife photo by Paul DeLaune)

Many times, talk of cover crops or regenerative agriculture in the U.S. refers to areas with 40 to 50 inches of rain per year. This amount of rain is not what typically occurs in Texas and Oklahoma, one of the largest cotton and livestock production regions in the nation.

But little research has been conducted to better understand how regenerative agricultural practices, when incorporated into a larger production system, perform under the varying precipitation of these regions.

“We want this to be as real as possible,” Lewis said. “There’s just so much information that is not suited for our regions. This project is going to result in the optimization of practices for semi-arid regions that will result in profitable and sustainable practices.”

The team’s approach will look at not just one practice in isolation but the entire agricultural production system that includes cover crops, crop rotations, grazing and other management techniques that can work on a farm-by-farm situation.

“Long-term, region-specific research, especially in semi-arid regions, is needed to better understand regenerative practices and the effects on soil health and water use in cotton agroecosystems,” Lewis said.

Determining ways to alleviate the risk involved in raising crops as well as protecting the environment and natural resources are among the main goals of the project. The project encompasses short-term, medium-term and long-term goals, which will enable continued improvement even after the project ends.

Two men stand beside a flume and gearbox at the edge of a field

Texas A&M AgriLife researchers Paul DeLaune and Srini Ale look at an edge-of-field automatic water sampler near Vernon that will evaluate the effects of soil health promoting practices. (Texas A&M AgriLife photo by Kay Ledbetter)

“We plan to identify the immediate challenges on the ground and reduce the risk that is associated with change when it comes to farming practices,” Lewis said. “It’s nothing but change from one year to the next in farming, but helping to alleviate that risk is one of our main goals as well as to protect the environment and natural resources.”

More than just a research project
Equally important as determining the most efficient agricultural practices, Lewis said, is the need for further outreach and education for producers and landowners in these regions. Part of the project is a careful examination of how producers interpret information the team presents.

“This is not just a research-based project,” Lewis said. “It includes research, extension outreach, education – there’s so much misinformation that is published and available to the general public.”

Meeting the short-, medium- and long-term goals of the project involves working directly with producers, she said, but it also includes reaching out to students and consumers.

“We wanted to be able to start young with our college-age students and the general public and let them make more informed decisions when it comes to things that impact farmers and rural communities.”

field showing crop rotation wheat and fallow

The wheat, cotton, fallow rotation will be studied to determine the impacts of different management strategies on soil properties and crop performance. (Texas A&M AgriLife photo by Paul DeLaune)

The team’s approach to Extension outreach and education will go beyond that of many traditional projects, which rely on field days, workshops and farmers asking specific questions when they encounter a problem.

“We’re going to have a hands-on approach with the creation of a Master Soil Steward Program that will allow farmers to see results on their farm,” Lewis said. “It will be much more personal, and we’ll be able to talk with them on a farm-by-farm basis.”

Additionally, undergraduate and graduate courses will be established in regenerative agriculture at Oklahoma State University, Texas A&M University, Texas Tech University and West Texas A&M University utilizing data collected from this research.

Conducting the research, education and outreach
Within the Texas A&M College of Agriculture and Life Sciences, the project will include team members from the Department of Soil and Crop Sciences, Department of Agricultural Economics, Department of Animal Science and Department of Biological and Agricultural Engineering, as well as the Texas Water Resources Institute. In addition to the Texas A&M flagship campus, these individuals are located at Texas A&M AgriLife Research and Extension Centers in Lubbock, Amarillo, Vernon and Overton and represent AgriLife Research and Texas A&M AgriLife Extension Service.

Additionally, team members represent the Soil Health Institute, Morrisville, North Carolina; Texas Tech University, Lubbock; West Texas A&M University, Canyon; Oklahoma State University, Stillwater, and Oklahoma Panhandle Research and Extension Center, Goodwell; and the Office of Education, Innovation and Evaluation, Kansas State University, Manhattan, Kansas.

The Team
Project Director:
Katie Lewis, Ph.D., AgriLife Research soil scientist, Lubbock.
Co-Project Directors:
Allen Berthold, Ph.D., Texas Water Resources Institute assistant director, Bryan-College Station.
Kevin Wagner, Ph.D., Oklahoma Water Resources Center director, Oklahoma State.
Jourdan Bell, Ph.D., AgriLife Extension agronomist, Amarillo.
Paul DeLaune, Ph.D., AgriLife Research soil scientist, Vernon.
Donna McCallister, Ph.D., Texas Tech University assistant professor, Lubbock.
Co-Investigators:
Ali Mirchi, Ph.D., assistant professor of water, Oklahoma State.
Alexandre Caldeira Rocateli, Ph.D., Extension forage systems specialist, Oklahoma State.
Bruce McCarl, Ph.D., AgriLife Extension agricultural economist, Bryan-College Station.
Dianna Bagnall, Ph.D., Soil Health Institute research soil scientist, Morrisville, North Carolina.
Wayne Keeling, Ph.D., AgriLife Extension cropping systems and weed specialist, Lubbock.
Gerald Smith, Ph.D., AgriLife Research plant breeder, Overton.
Monte Rouquette, Ph.D., AgriLife Research forage physiologist, Overton.
Jason Smith, Ph.D., AgriLife Extension beef cattle specialist, Amarillo.
Terry Gentry, Ph.D., AgriLife Research soil and aquatic microbiologist, Bryan-College Station.
Sumit Sharma, Ph.D., Extension irrigation management specialist, Goodwell, Oklahoma.
Briana Wyatt, Ph.D., assistant professor in soil science, Bryan-College Station.
Lucas Gregory, Ph.D., Texas Water Resources Institute assistant director, Bryan-College Station.
Jason Warren, Ph.D., soil conservation Extension specialist, Oklahoma State.
Srinivasulu Ale, Ph.D., AgriLife Research geospatial hydrologist, Vernon.
Murilo Maeda, Ph.D., AgriLife Extension cotton specialist, Lubbock.
Andrea Jilling, Ph.D., assistant professor in environmental soil chemistry, Oklahoma State.
Seth Byrd, Ph.D., Extension cotton specialist, Oklahoma State.
Bill Pinchak, Ph.D., AgriLife Research animal nutritionist, Vernon.
Emi Kimura, Ph.D., AgriLife Extension agronomist, Vernon.
Bridget Guerrero, Ph.D., agricultural economics/business associate professor, West Texas A&M.
Will Keeling, AgriLife Extension risk management program specialist, Lubbock
Cindi Dunn, director, Office of Education, Innovation and Evaluation, Kansas State

Adaptive swarm robotics could revolutionize smart agriculture

3Dec

Written by: Steve Kuhlmann, Texas A&M University College of Engineering

Texas A&M University System researchers are working to establish a configurable, adaptive and scalable swarm system consisting of unmanned ground and aerial robots designed to assist in collaborative smart agriculture tasks.

The use of adaptive swarm robotics has the potential to provide significant environmental and economic benefits to smart agriculture efforts globally through the implementation of autonomous ground and aerial technologies.

A rotary wing drone captures images over a weed research plot at Texas A&M University, College Station. (Texas A&M AgriLife photo by Dr. Muthu Bagavathiannan)

“Agricultural robots, when used properly, can improve product quantity and quality while lowering the cost,” said Kiju Lee, associate professor and Charlotte and Walter Buchanan Faculty Fellow in the Department of Engineering Technology and Industrial Distribution and the J. Mike Walker ’66 Department of Mechanical Engineering at Texas A&M.

A swarm robotics project is being led jointly by Lee, Muthukumar Bagavathiannan, Ph.D., Texas A&M AgriLife Research weed scientist in the College of Agriculture and Life Sciences Department of Soil and Crop Sciences; and Juan Landivar, Ph.D., center director at the Texas A&M AgriLife Research and Extension Center at Corpus Christi.

Other investigators on the team include John Cason, Ph.D., AgriLife Research peanut breeder, Stephenville; Robert Hardin, Ph.D., agricultural engineering assistant professor, Department of Biological and Agricultural Engineering; Luis Tedeschi, Ph.D., AgriLife Research ruminant nutritionist, Department of Animal Science; Dugan Um, Ph.D., associate professor, Texas A&M-Corpus Christi Department of Mechanical Engineering; and Mahendra Bhandari, Ph.D., AgriLife Research crop physiologist, Corpus Christi.

Funding is being provided by the U.S. Department of Agriculture National Institute of Food and Agriculture through the National Robotics Initiative 3.0 program.

Configurable, adaptive and scalable swarm
The entire multidisciplinary group is working to establish a configurable, adaptive and scalable swarm, CASS, system consisting of unmanned ground and aerial robots designed to assist in collaborative smart agriculture tasks.

“We will develop the technical and theoretical groundwork for the deployable, scalable swarm system consisting of a physical robotic swarm of both ground and aerial robots, a digital twin simulator for low- and high-fidelity simulations, and an easy-to-use user interface for farmers to put this CASS system into use,” Lee said.

This approach to smart agriculture, enabled by the CASS technology, could result in long-term benefits thanks to reduced waste through better logistics, optimal use of water and fertilizer and an overall reduction in the use of pesticides.

The research team believes that by utilizing smaller machines to reduce soil compaction and working to avoid herbicide-resistant weeds through nonchemical methods of control, significant ecological and environmental benefits can be achieved.

Recent trends in smart agriculture focused on the usage of large machinery have had the objective of maximizing product quantity and minimizing costs — an approach that has resulted in some economic and environmental concerns.

Lee said issues including soil compaction, a limited ability to address small-scale field variability and reduced crop productivity are some of the long-term issues that have emerged from this approach.

CASS offers flexibility in addressing challenges

By leveraging the flexibility of swarm robotics, the CASS system is intended to become a platform technology that can be configured to meet application-specific needs.

“Current trends in precision agriculture and smart farming mostly focus on larger machinery or a single or a small number of robots equipped and programmed to perform highly specialized tasks,” Lee said. “This project will serve as a critical pathway toward our long-term goal of establishing a deployable easy-to-use swarm robotic system that can serve as a universal platform for broad agriculture applications.”

Although other systems employing swarm robotics exist, they are typically designed to perform just one specific task rather than being adaptable to a variety of situations.

Moving forward, the team will have the opportunity to address several challenges related to the complex and varying scale of agriculture applications through the design and implementation of their system.

“Despite the great potential, swarm robotics research itself has been largely confined to low-fidelity simulations and laboratory experiments,” Lee said. “These rarely represent the intricacies of an agricultural field environment. Also, human-swarm collaboration has not been extensively explored, and user-in-the-loop development and evaluation approaches are needed, in particular for the target end-users — in our case, farmers.”

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Texas A&M AgriLife helping set gold standard greenhouse gas emissions measurements for Department of Energy

22Jun

By: Kay Ledbetter

Greenhouse gas emissions from sorghum fields in the Texas High Plains will be the focus of a Texas A&M AgriLife Research study funded by a U.S. Department of Energy grant through the Advanced Research Projects Agency-Energy, ARPA-E.

This $3.1 million collaborative project, led by Oklahoma State University, is funded through ARPA-E’s Systems for Monitoring and Analytics for Renewable Transportation Fuels from Agricultural Resources and Management, or SMARTFARM, program.

man in field with technology to capture nitrous oxide

Walker Crane, a member of Nithya Rajan’s team, measures nitrous oxide measurements from a young sorghum field. (Texas A&M AgriLife photo)

About one-third of the grant will be utilized in Texas by Nithya Rajan, Ph.D., crop physiology and agroecology associate professor, who is the lead investigator for AgriLife Research on this project. Rajan will be joined by Ronnie Schnell, Ph.D., Texas A&M AgriLife Extension Service cropping systems specialist for sorghum. Both are in Texas A&M University’s Department of Soil and Crop Sciences in College Station.

“We are excited about this multi-state SMARTFARM project,” said David Baltensperger, Ph.D., head of the Department of Soil and Crop Sciences. “This project strengthens our ties with Texas sorghum producers and supports the goal of sorghum production in an environmentally friendly manner.”

Goals of measuring greenhouse gas emissions

The SMARTFARM program’s objective is to bridge the data gap in the biofuel supply chain by funding technologies that can quantify feedstock-related emissions at the field level and enable new market incentives for efficiency.

Rajan said the ARPA-E project will utilize current technology and sensor networks to continuously quantify field-level emissions for major greenhouse gases. This is expected to provide a “gold standard” assessment of emissions from bioenergy feedstocks in the Southern Great Plains.

“With any agriculture production field, greenhouse gas emission is inevitable — typically carbon dioxide and nitrous oxide — and that increases with the application of fertilizer, manure and other management practices,” she said. “Nitrous oxide is a powerful greenhouse gas that can stay in the atmosphere for several decades and can cause environmental issues.”
Nitrous oxide emissions graph
Rajan’s current research shows that there is a daily pattern associated with nitrous oxide emissions in agricultural fields. Emissions usually happen after fertilizer application and rainfall, but such frequent measurements are rarely made by scientists in production conditions due to the cost of equipment needed for continuous monitoring.

Carbon source or sink

Agricultural fields also sequester carbon. Tracking both carbon sequestration and greenhouse gas emissions simultaneously is necessary to understand if the field is a carbon source or a sink, as greenhouse gas emissions are usually expressed in carbon dioxide equivalents.

Schnell said sorghum production systems in the Southern Great Plains have an opportunity to contribute sustainable energy production in the U.S. Production environments, water use and common management practices have the potential for lowering greenhouse gas emissions.

Rajan said the team is concentrating on grain sorghum initially, because Texas, Kansas and Oklahoma are three of the nation’s main sorghum-producing states. According to the U.S. Department of Agriculture’s National Agricultural Statistics Service, nationwide, about 5.07 million acres were planted to grain sorghum.

Grain sorghum acreage is beginning to replace some corn acreage in the Texas Panhandle because of its water efficiency, she said. The Texas portion of the project is designed to take measurements of greenhouse gases, especially carbon dioxide and nitrous oxide, at an 85-acre commercial production field, continuously using the state-of-the-art instrumentation and methodologies. Schnell will assist with spatial measurements of soil water, nutrient, and crop growth at the site.

“This is the first time anyone is trying to do it at this scale,” Rajan said. “We are using a farmer’s field in the Panhandle area. We will be setting up a lot of equipment to make these measurements.”

Nithya Rajan, Ph.D., in a sorgum field. (Texas A&M AgriLife photo)

She said the equipment will allow them to take greenhouse gas measurements continuously from the sorghum field. Additionally, soil temperature and moisture sensors will be installed on each sub-acre of the 85-acre field. Soil and plant samples will also be collected from each acre.

The end goal is to build a ‘gold standard’ data set. The data set then will be available for all researchers studying the life cycle analysis and modeling of greenhouse gas emissions.

The project will begin in October 2020 and continue for three years. While the data gathering will be automated and managed through the internet, Rajan said project participants will make frequent visits to the site for installation, equipment maintenance, and plant and soil sample collection. This is only one of Rajan’s projects with sorghum.

Gopal Kakani, Ph.D., from Oklahoma State University is the lead principal investigator of this three-state project. Other team members are: Oklahoma State University researchers Jason Warren, Saleh Taghvaeian, Paul Weckler and Ning Wang, all Ph.D.s; and Kansas State University researchers Peter Tomlinson, Eduardo Alvarez Santos and Lucas Haag, all Ph.D.s.

Genomes of five cotton species unveiled by Texas-rich research team

20Apr

By: Kay Ledbetter

Cotton – we touch it every day. From clothes to medical supplies to animal feed, cotton continues to increase in quality. A recent collaborative, including Texas A&M researchers, is making sure this amazing crop, and thus the products made from it, will continue to be efficiently bred, grown and produced.

New cotton gene sequencing will help researchers improve the valuable staple in our lives. (Texas A&M AgriLife photo by Beth Ann Luedeker)

The multi-institutional research team sequenced five cotton species, including Upland and Pima cotton grown here in Texas, as well as globally. Contributions to the effort from Texas involved Texas A&M University, Texas A&M AgriLife Research and the University of Texas – Austin.

The most recent issue of Nature Genetics reports on the results of this collaboration — high-quality genome-wide sequence assemblies for each of five 52-chromosome species of the cotton genus Gossypium, a member of the Malvaceae family, which also includes okra, kenaf, hibiscus, durian and cacao.

The overall project was funded primarily by the National Science Foundation, and led by Z. Jeffrey Chen, Ph.D., a former student and former faculty member of Texas A&M who now holds the D. J. Sibley Centennial Professorship in Plant Molecular Genetics at the University of Texas at Austin.

Breeding cotton typically increases economic yield through better productivity, better quality of products and improved sustainability by providing better pest resistance and drought resilience, David Stelly, Ph.D., a co-principal investigator in the National Science Foundation project and AgriLife Research cotton breeder in the Texas A&M Department of Soil and Crop Sciences, College Station.

“Globally, cotton is the premier natural fiber crop of the world, a major oilseed crop and an important feed crop,” Stelly said. “This report establishes new opportunities in multiple basic and applied scientific disciplines that relate directly and indirectly to genetic diversity, evolution, wild germplasm utilization and increasing the efficacy with which we use natural resources for provisioning society.”

The cotton genome research project

While fiber removed from the cotton seed is of greatest value, ginned seed also provides significant additional value as a source of vegetable oil and/or dairy cattle feed. The recent data and findings provide immediately accessible resources for basic and applied research, including breeding and gene editing.

The five cotton species (Graphic provided by David Stelly)

The other three species sequenced originate from Hawaii, the Galapagos Islands or Ecuador and Brazil. They remain undomesticated but are sources of prospectively useful genetic differences. The Nature Genetics report should facilitate use of all five species in genomics-aided cotton breeding programs.

Stelly said the importance of the assemblies may be accentuated by the extreme complexity of cotton’s genome. It contains a relatively large number of genes, about twice as many as occur in most flowering plants with simple genomes.

The researchers report that sequences of these five species’ genomes will provide long-needed genomics resources and insights that will facilitate genetic improvements needed to maintain economic yield from production, enhance quality and value of the fiber and seed products, and further improve sustainability-enhancing features, such as resistance to pests, pathogens, drought and heat-resilience.

Contributions from Stelly’s laboratory

Contributions from Texas A&M came through Stelly’s laboratory. A key finding by graduate student Luis De Santiago was the detection and mapping of numerous “haplotypic blocks” throughout the genome of Upland cottons.

Stelly explained these present a major challenge for breeding, because they are both non-recombinant and virtually uniform among cultivars. Evidence corroborating the haplotypic blocks was obtained from analyses of genetic recombination, also involving Yu-Ming Li and former student Amanda Hulse-Kemp, Ph.D.

Also, from Stelly’s laboratory, researchers Robert Vaughn, Ph.D., provided plant, seed and nuclei acid samples to the team, and Bo Liu, Ph.D., provided integrative molecular cytogenetic mapping data.

“This kind of mega-project takes a lot of time and effort, but can yield game-changing results, and this one certainly has done that,” Stelly said. “Already, we are seeing paradigm shifts in what we and others are doing and thinking about doing. These kinds of data are vital to our research and breeding efforts and open many doors for exploration.”

He also emphasized collaborations and individual contributions are instrumental to success.

“Research projects like this unlock agriculture’s potential,” said Patrick J. Stover, vice chancellor of Texas A&M AgriLife, dean of the College of Agriculture and Life Sciences and director of Texas A&M AgriLife Research. “By developing crops that enhance health and increase profitability, we not only improve cotton immediately, but the way we approach this data and findings provide direction for basic and applied research far into the future.”

“The Soil and Crop Sciences Department appreciates the leadership of Dr. Stelly in guiding this project to completion and providing the vision for implementing the results to benefit our cotton producers,” said David Baltensperger, Ph.D., department head, College Station.

Other members of the team

Other project members include:
– Chen’s functional genomics / epigenetics team at UT-Austin.
– Jane Grimwood, Ph.D., and Jeremy Schmutz, along with their HudsonAlpha/JGI structural genomics and bioinformatics teams, including Jerry Jenkins, Ph.D., and key bioinformatics contributor Avinash Sreedasyam, Ph.D.
– The U.S. Department of Agriculture genomics and bioinformatics teams of Brian Scheffler, Ph.D., Mississippi, and Hulse-Kemp, North Carolina.
– The Clemson genomics team of Chris Saski, Ph.D.
– Keith McGee, Ph.D., and his educational team at Alcorn State.
– Mississippi State genomics group of Dan Peterson, Ph.D.
– The Iowa State taxonomic genomics group involving Jonathan Wendel and Corrinne Grover, both Ph.Ds.
– Industry involvement through Don Jones, Ph.D., with Cotton Incorporated, a not-for-profit company that works with cotton scientists, the textile industry and consumers.

Other institutions involved in the research were Nanjing Agricultural University in China, and the U.S. Department of Energy Joint Genome Institute. The work was supported by grants from the U.S. National Science Foundation, U.S. Department of Agriculture and Cotton Incorporated. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy. The work was also supported by grants from National Natural Science Foundation of China, Jiangsu Collaborative Innovation Center for Modern Crop Production, and Natural Science Foundation of Zhejiang Province, China.

Genetic capabilities cut time for potential Texas wheat lines to make field appearance

16Dec

Writer: Kay Ledbetter

When new pests, diseases or environmental issues are identified in Texas wheat, expertise in doubled haploid development can help find solutions in less than half the time of traditional breeding practices.

Chenggen Chu, Ph.D., a geneticist, joined Texas A&M AgriLife Research’s wheat program at Amarillo two years ago, and his doubled haploid wheat pure lines are already making it to field yield trials this fall.

Since moving to Amarillo, Chu has built a wheat doubled haploid production pipeline from scratch that can be shared with AgriLife Research’s wheat breeding programs in both Amarillo and College Station. He is training other personnel on the process.

Chenggen Chu, Ph.D., Texas AM AgriLife Research geneticist, looks at the first crop of doubled haploid wheat pure lines in a yield field trial at Bushland. (Texas A&M AgriLife photo by Kay Ledbetter)

The major advantage of using doubled haploid plants is to shorten time in developing genetically pure lines from five to six years in a traditional winter wheat breeding scheme, to only two or three years, said Shuyu Liu, Ph.D., AgriLife Research wheat geneticist, Amarillo.

“Texas A&M’s wheat breeding programs are very strong, but did not include anyone with the skills Dr. Chu brought with him,” Liu said. “The wheat doubled haploid line development procedures require some skilled steps in the laboratory.

“It also requires a special growth room and lab equipment for inducing haploid embryos, growing plants from young haploid embryos, doubling chromosome numbers to bring back the fertility, and recovering plants to grow in soil for seed production.”

What is doubled haploid?

Traditional wheat two sets of chromosomes (genetic material from both parents). This is called a diploid. In the general procedure for wheat doubled haploid production, corn was used as the father to pollinate the mother wheat plants.

During embryo development, only the chromosomes from the wheat mother plant are kept. These embryos with a single set of chromosomes are haploids and are highly sterile, producing almost no seed.

However, through an induced chromosome doubling process – the skill that Chu brings to the program – the haploids can produce another copy of chromosomes in each cell, bringing the chromosome numbers back to the normal two sets per cell and fully restoring their fertility.

This doubled haploid process turns the haploid to the regular diploid with two sets of chromosomes that are identical. The identical sets of chromosomes in each cell makes doubled haploid lines 100% genetically stable, even after being reproduced for many generations.

“This genetic stability, regardless of time and location, makes trait evaluation more accurate and reliable for breeders,” Chu said.

Chenggen Chu works in the lab at the Texas A&M AgriLife Research and Extension Center in Amarillo. (Texas A&M AgriLife photo by Kay Ledbetter)

Doubled haploids in the field

Chu has been able to optimize the procedures to increase efficiencies on both haploid plant induction and chromosome doubling. He led the genetic team working with Texas A&M’s two wheat breeding programs in College Station and Amarillo, and he produced more than 1,300 doubled-haploid lines in the first season from about 40 crosses.

The team has now finished the second season and harvested over 700 lines. The first set of 550 lines were increased for seed in Yuma, Arizona, and have been planted in multiple locations this fall for yield trials.

Liu said the process isn’t without challenges, as with any crop. The 2018 summer was very good for growing doubled haploid plants in the greenhouse in Bushland, but this past summer many plants failed to produce enough tillers due to the stressful, hot environment.

Next steps

“We would like to keep the trained personnel and established procedures and a facility to continue doubled haploid production to meet the requirements from both breeding and genetic research,” Liu said. “But that takes funding.”

He said they are currently working on two U.S. Department of Agriculture-National Institute of Food and Agriculture projects where doubled haploids are involved to develop pure lines with target genes.

At the same time, Chu is working to optimize the procedures further to increase the efficiency of doubled haploid development.

“We greatly appreciate the funding support from the Crop Improvement Program of Texas A&M AgriLife Research during the last two years and the continuous support from Texas Wheat Producers Board,” Liu said.

Such funding, he said, will be key to keeping skilled technicians and a facility with controlled light and temperature conditions in place.

Texas A&M-bred sorghum now on the cereal aisle

24Sep

By: Kay Ledbetter

Texas A&M AgriLife sorghum research may be known for its development of sorghum for animal feed and energy sectors, but cereal eaters across the nation are learning about its contributions to healthier human foods.

Bill Rooney, Ph.D., looks at the back of a box of cereal that features the Onyx sorghum variety he bred as a part of Texas A&M AgriLife’s efforts to meet the needs of the food industry. (Texas A&M AgriLife photo by Kay Ledbetter)

“We were targeting the health-food market when we developed the black grain sorghum hybrid Onyx in 2012,” said Bill Rooney, Ph.D., AgriLife Research sorghum breeder and Borlaug-Monsanto Chair for Plant Breeding and International Crop Improvement in the Texas A&M University Department of Soil and Crop Sciences, College Station.

The Onyx hybrid was licensed to Silver Pallet Inc., which spent several years in seed increase and commercial production on the Texas High Plains before featuring the product in their Grain Berry cereals.

“Texas A&M AgriLife is working to improve the quantity and quality of food production to benefit human health and ultimately lower health care costs,” said Patrick J. Stover, Ph.D., director of Texas A&M AgriLife Research and vice chancellor and dean for the College of Agriculture and Life Sciences. “Dr. Rooney’s research is a great example of how we can enhance the nutritional quality of the food supply to help manage chronic diseases by targeting quality end-points with human nutrition in mind.”

Increased public interest in antioxidants

The cereal boxes highlight the Onyx connection, marketing it as an “all-natural new sorghum grain developed by Texas A&M University, based on ancient black and hi-tannin sorghum varieties that, together in one plant, contain a more powerful combination of antioxidants that combat a whole spectrum of free radical threats to our bodies.”

Texas A&M AgriLife’s sorghum breeding work is featured on the back of the cereal box, outlining the nutritional qualities of Onyx sorghum. (Texas A&M AgriLife photo by Kay Ledbetter)

Rooney is known for his conceptualization and development of bioenergy sorghum hybrids – sorghum is considered to be the leading feedstocks for the bioenergy industry.

But as the general public becomes more health conscious, growing attention is being directed at his new and novel sorghum types for specific and unique markets.

Based on research conducted by the Texas A&M AgriLife Cereal Quality Lab, Rooney knew sorghums with dark colors and tannins have higher concentrations of antioxidants. As such, in developing the Onyx sorghum hybrid, he selected for those types to meet the growing public interest in finding foods with high antioxidant capacity.

Onyx2

“This was the first material we licensed with that characteristic,” he said. “We licensed a new hybrid to Silver Pallet last year, Onyx2, and increased seed production this year. It will be grown commercially next year.”

Onyx2 has the same components but provides better yields for production purposes, Rooney said. He said an issue with the original Onyx was its yield potential was lower than commercial grain sorghum hybrids.

“We were able to increase the yields about 25% from the first hybrid to the second,” he said.

Human nutrition market

Rooney said his program will continue to reach the human nutrition market with new hybrids.

“We are working with some specialty grain types, looking at new combinations of characteristics such as grain color, tannin concentration and endosperm characteristics,” he said.

Muffins made with Texas A&M AgriLife-bred Onyx sorghum cereal were served at the recent AgriLife Extension sorghum field day. (Texas A&M AgriLife photo by Kay Ledbetter)

The higher tannins are reaching the same market as the Onyx, Rooney said, because they have increased antioxidant values. Specific grain colors are for the specialty food market and are valued for the inclusion of specific compounds associated with natural preservatives.

“The grain source of these natural preservatives, however, is unique because most of the time these natural preservatives are sourced from fruits and vegetables that require processing to extract the compounds,” he said. “The sorghum requires less processing to access and stabilize the useful attributes.”

The other area of research, waxy endosperm sorghums, has the most marketing potential and interest for producers, Rooney said.

“Inclusion of these hybrid characteristics can affect industrial, food and livestock feed applications, because the starch is modified and is easier to process or digest,” he said. “Ethanol can be made faster; livestock can digest the grain faster; and it is easier for human food processors to use.”

Texas A&M researchers to develop climate-smart sorghum

9Aug

By: Kay Ledbetter
Contacts: Dr. Nithya Rajan, nrajan@tamu.edu
Dr. Bill Rooney, wlr@tamu.edu
Dr. Ronnie Schnell, ronshcnell@tamu.edu

Improved yield, greenhouse gas mitigation, water quality are ultimate goals

Texas A&M researchers believe the development of climate-smart crops is the key to improving nitrogen-use efficiency and reducing fertilizer nitrogen loss in agricultural fields.

The crops would have the ability to suppress soil nitrification and have reduced nitrogen emissions, said Dr. Nithya Rajan, Texas A&M AgriLife Research crop physiologist and principal investigator in College Station.

Rajan initiated a project study, “Innovative Sorghum-Based Production Systems with Biological Nitrification Inhibition Property to Enhance Sustainability of Agroecosystems,” funded by a $500,000 grant through the Agriculture and Food Research Initiative – Foundational and Applied Science Program of the U.S. Department of Agriculture – National Institute for Food and Agriculture, USDA-NIFA.

She said nitrification and subsequent denitrification activities promote the loss of nitrogen from agricultural fields and largely is the underlying reason for low nitrogen-use efficiency in most field crops, including sorghum.

Dr. Nithya Rajan, left, with Dr. Guntur Subbarao, middle, and Dr. Santosh Deshpande, far right, at the BNI field test site at ICRISAT in Hyderabad, India. (Texas A&M AgriLife photo)

“Some plants can suppress nitrification by releasing inhibitors from their roots, a property known as biological nitrification inhibition (BNI),” Rajan said. “This will help with retention of nitrogen for longer periods of time to facilitate its uptake by crops and reduce the loss of nitrogen as nitrous oxide, a powerful greenhouse gas and ozone-depleting substance.”

Initial work supported by another USDA-NIFA exploratory grant involved screening for BNI properties of a range of diverse sorghum genotypes from the program of AgriLife Research sorghum breeder Dr. William Rooney.

This exploratory work was carried out in collaboration with Dr. Guntur Subbarao, principal scientist from the Japan International Research Center for Agricultural Sciences, JIRCAS, in Tsukuba, Japan. Subbarao is a pioneer and world-renowned BNI expert.

“We believe that BNI-enabled crops and production systems are part of innovative solutions for a genetic-mitigation strategy to address problems associated with nitrogen fertilizers in agriculture,” Subbarao said.

Subbarao leads a multi-institutional research group on BNI research in collaboration with several CGIAR institutes including the International Crops Research Institute for the Semi-Arid Tropics, ICRISAT, in Hyderabad, India.

Sorghum seedlings are grown in special boxes for BNI characterization. (Texas A&M AgriLife photo)

“By collaborating with international institutions such as JIRCAS and ICRISAT that are at the forefront of developing this technology, we can bring innovative solutions to benefit U.S. agriculture,” Rajan said.

The current NIFA project is a collaborative effort by AgriLife Research, Texas A&M Engineering Experiment Station and JIRCAS.

Tackling the project with Rajan are the following Texas A&M researchers in College Station and their specialties: Drs. Sakiko Okumoto, plant physiologist; Ronnie Schnell, agronomist; Jacqueline Aitkenhead-Peterson, urban nutrient and water runoff; Kung-Hui Chu, environmental microbiology; John Jifon, plant physiologist; Muthu Bagavathiannan, weed scientist; as well as Rooney and Subbarao.

They will spend the next two years quantifying and characterizing the BNI compound secretion in sorghum, and evaluating the release of BNI compounds and nitrification inhibition in soils.

“The possibility of BNI in sorghum is exciting and has the potential to fundamentally change the way nitrogen is managed in the future for sorghum as well as other crops,” Schnell said. “Improving nitrogen-use efficiency in grain crops will have substantial economic and environmental benefits for Texas and its farmers. However, there is a lot of research that needs to be done first to develop this technology.”

Beyond identifying elite sorghum cultivars with BNI properties, extensive field testing will be needed to develop cropping systems around this new technology, he said.

“The long-term goal of this program is to develop elite sorghum cultivars with enhanced BNI properties,” Rooney said. “Preliminary evidence indicates that variation exists among sorghum genotypes and it will be possible to improve this trait to have an impact in the future.”

TAMU Turfgrass team displays research to USGA

9May

By: Beth Ann Luedeker
Contact: Dr. Ben Wherley, b-wherley@tamu.edu

Ben Wherley (l) and Kevin McInnes (far right) discuss ongoing research with the USGA Green Section’s research committee before touring the research plots.

The Texas A&M Turfgrass Science team recently hosted members of the United States Golf Association Green Section’s research committee at the Scotts Miracle-Gro Center for Lawn and Garden Research.

During the visit, faculty and grad students from the Department of Soil and Crop Sciences provided updates on several multi-year research projects that are currently being funded by the USGA Green Section. Drs. Ben Wherley and Kevin McInnes, respectively Associate Professor and Professor in the Department of Soil and Crop Sciences, are conducting this research with the assistance of their graduate students.

Reagan Hejl explains the tools being used to determine best management practices for irrigation of sand-capped fairways to members of the USGA Green section. (Texas A&M AgriLife photo by Beth Ann Luedeker)

“Data-driven irrigation scheduling for managing sand-capped fairways”

This project, being conducted by Wherley, McInnes and Ph.D. student Reagan Hejl, is a follow-up to a previous USGA-funded study which determined there was no significant quality or performance differences between fairways irrigated 1 day per week vs. 2 days per week. The current study will use data-driven techniques, including wireless sensors and evapotranspiration rates, to help determine the best irrigation practices for sand-capped fairways.

Master’s student Garrett Flores visits with members of the USGA Green Section research committee about the spent coffee grounds being used in his research. (Texas A&M AgriLife photo by Beth Ann Luedeker)

“Evaluation of spent coffee grounds as a turf fertilizer and root zone amendment”

This study, being conducted by Wherley, McInnes and Master’s student Garrett Flores, is evaluating the use of spent coffee grounds as a more sustainable, environmentally friendly alternative to sphagnum peat moss as a soil amendment for golf courses.

Master’s student Will Bowling demonstrates the difference wetting agents can make in the mitigation of sodicity caused by poor quality irrigation water on sand-capped fairways. (Texas A&M AgriLife photo by Beth Ann Luedeker)

“Long-term dynamics and management requirements of sand-capped fairways”

A third project follows a previous USGA study which suggested an optimal sand capping depth of 8 inches. This study, being conducted by Wherley, McInnes and graduate student Will Bowling, will evaluate the long-term changes in performance, soil properties and management requirements created by the sand-capping.

USGA is also funding several warm-season turf breeding projects being conducted by Dr. Ambika Chandra and others at the Texas A&M AgriLife Research and Extension Center in Dallas.

The USGA research committee includes USGA agronomists from both the south-central and western U.S. regions as well as current and retired university faculty.

Since 1920, the USGA has funded more than $40 million on research projects conducted at universities across the country. Their research program facilitates collaboration with allied associations and government agencies to promote golf course contributions to the environment. The scientific results advance the long-term viability of the game through sustainable resource management and environmental protection.