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[AgriLife Today] As DNA tests become more common, researchers rapidly add equipment to keep up

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By: Kathleen Phillips

Writer: Kathleen Phillips, 979-845-2872, [email protected]

Contact: Dr. Charlie Johnson, 979-862-3287, [email protected]

(Editors: April 25 is National DNA Day commemorating the day in 1953 when scientists published papers in the journal Nature on the structure of DNA. Now, 64 years later, the concept is much more familiar to the average person.)

COLLEGE STATION — Unless your career wardrobe consists of multiple white lab coats and your office has a cache of test tubes, you probably don’t remember where you were when it was announced that the human genome had been sequenced.

But, if you know that you can now dish out $100 to map your ancestral migration through history, the term “DNA” may roll off the tongue like the ABCs.

The surge in genetic research and its increasing acceptance in the general public bodes well for health, agriculture and natural resources discoveries — not to mention genealogy enthusiasts. This has scientists scampering to keep up with the technology, according to Dr. Charlie Johnson, director of the Genomics and Bioinformatics at Texas A&M AgriLife Research in College Station.

It’s been a productive 20-plus years since two bacterial genomes were first sequenced in 1995, according to the National Institutes of Health-National Center for Biotechnology Information. Almost 125,000 organisms have been sequenced, including — to help pinpoint your ancestry — the human genome in 2003.

“The technology is relatively new. Before 2007, sequencing was very difficult, slow and laborious,” Johnson said. “The human genome project, for example, started in 1990 and took 13 years to complete at a cost of about $3 billion.”

Once science got a grasp of the technology, however, researchers from agriculture to zoology clearly saw how peering into the innermost level of an organism’s existence might help address issues such as disease, drought and pestilence.

One problem, however, was cost, Johnson noted.

“The kind of instruments needed to do sequencing are not affordable for a single lab to own,” he said. “On the average, they cost about $1 million apiece. And it would be hard for any one investigator to generate enough research work to justify that investment.”

AgriLife Research, with its extensive scientific network across Texas, envisioned a bigger picture. In 2010, the agency hired Johnson to establish a central core of equipment and a set of experienced genomics technology scientists who could support researchers in a cost-effective, efficient way. Even more, they provide their expertise to scientists throughout the Texas A&M University System.

“Our reputation for scientific excellence and high-quality data has led to collaborations with scientists around the world, including groups in 35 countries,” Johnson noted.  “Beginning in 2009 when the first next generation sequencing system was purchased and over the last eight years, AgriLife has continued to keep pace with a technology that is changing so fast. The cost of sequencing has dropped from $3 billion for the first human genome to less than $1,000 today and is expected to dip below $100 in the coming years.”

This month, the center will put in place an Illumina NovaSeq 6000, a machine Johnson said can yield the equivalent of 48 human-sized genomes in less than two days. This will significantly cut costs.

“Texas A&M AgriLife is one of the first academic institutions to have access to this technology,” Johnson said. “This is the right tool at the right time to face this new era of big agri-genomics, and we are thrilled to be part of it.”

In essence, like one’s cellphone, DNA sequencing technology is ever-evolving at a frantic pace, he said.

“If you are not constantly upgrading, you quickly fall behind. We work hard to get these new machines so we can continue to provide the highest quality data using the latest genomic technologies to give our collaborators the biggest bang for the buck,” he said.

The center has more than 350 principal investigators in collaboration and has grown from “essentially doing a few projects a year to now basically adding one project a day,” Johnson noted.

And genome sequencing is only part of the effort. Johnson’s team also has an active bioinformatics research program, providing data analysis for researchers.

https://youtu.be/8IsAQHKr6zk

“Genome sequencing produces a massive amount of data,” he said. “Imagine a library stack of encyclopedias. Grind them up in a paper shredder, and you end up with strings of letters. The challenge is to put all those back together into the book that describes what you sequenced. Then you can use that information to make some discovery or find out something useful.”

Researchers who collaborate with the center agree.

“Working with the center can be faster and cheaper than outsourcing to other labs,” said Dr. Bill Murphy, professor of veterinary integrative biosciences at Texas A&M. “The acquisition of the PacBio machine was instrumental because few if any core labs offer this type of sequencing as a service. The availability of the instrumentation at the core labs has helped in obtaining my lab’s funding from the National Science Foundation, Morris Animal Foundation and Winn Feline Foundation.”

Murphy, whose lab works on generating an accurate genome sequence for the domestic cat, said a genome sequence allows researchers and veterinarians to identify the genetic bases of diseases, which can lead to the development of genetic tests and therapeutics to reduce the incidence of specific diseases within pet breeds and across the random-bred population.

“AgriLife has also generated genome sequence data from more than a dozen wild cat species, which has helped improve our understanding of cat evolution, hybridization and measure of genetic diversity that are relevant to guiding conservation practices,” Murphy said.

“The scope of what we do across AgriLife, the veterinary school, the medical school and engineering is extremely broad,” Johnson said. “Being able to work with them on their projects and finding out all that is going on in research is incredible.”

 

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Farm & Ranch

Meanwhile, Back at the Ranch…

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By Rayford Pullen | [email protected]

When May arrives, we start thinking about weed control. With two years of drought under our belts, grass grazed short and hay stocks depleted, what we do now will influence our forage conditions for the entire year. With 75 percent of our annual warm season forages made by July 15 in North Texas, we need to get the grass growing while the sun shines.

Speaking of the sun shining, the biggest deterrent to growing lots of grass is restricted sunlight, and the biggest sun blockers we have are weeds.

Have you noticed weeds are normally just slightly taller than your grass and are probably blocking 90 percent of the sunlight from reaching the grass itself? So obviously, we need to improve conditions, so sunlight reaches the plants we want to grow.

With grass extremely short, more sunlight is hitting the soil surface now, which in turn results in more weed seed germinating. With the moisture we have received, we expect an abundance of weeds this year.

To read more, pick up a copy of the May issue of NTFR magazine. To subscribe by mail, call 940-872-5922.

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Farm & Ranch

Land Market Report: March Land Sales

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By Jared Groce

Rural land sales are continuing on a steady pace for early spring, with prices holding very strong with the sell-to-list price ratios remaining very high, even on properties that have been on the market for a longer than usual time period. The total number of transactions are picking up once again as the spring selling season kicks off, and the average acreage continues to decrease.

Larger acreage properties seem to be in higher demand than smaller properties currently, with many buyers simply parking cash in real estate to hedge against inflation. Interest rates seem to have settled down and most experts agree that rates will be reduced by the fed this year. Some lenders have programs in place that allow the buyer to reduce their rates without having to go through a full refinance ordeal.

To read more, pick up a copy of the May issue of NTFR magazine. To subscribe by mail, call 940-872-5922.

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Farm & Ranch

Texas FFA State Vice President Weston Parr

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Future Farmers of America was founded by a group of farmers in 1928 with the mission of preparing the next generation of agriculture. It has done just that during its 95-year history, as the organization works to give back to others by following its motto, “learning to do, doing to learn, earning to live, living to serve.”

FFA is an organization made up of state associations, and at the helm of the Texas FFA is a team of 12 officers representing their respective areas within the Lone Star State. These individuals dedicate a year of their lives as they serve members, provide leadership, and work together with the state staff and board of directors to develop policy and lead the organization of over 177,000 members.

North Texas is represented by Area IV and Area IV, stretching from Wilbarger County to Bell County and from Runnels County to Grayson County. This year, those chosen to lead this great area are State President Isaac Hawkins Jr., Area IV, and State Vice President Weston Parr, Area V.

Parr is from the Sam Rayburn FFA chapter and the Area V Association, but the leader who now serves more than 19,100 members of Area V entered the FFA organization as a shy teenager who sat in the back of the room.

“I didn’t talk to a whole lot of people. I didn’t know what I wanted to do with my life or where I could see myself, so I wasn’t involved on my high school campus,” Parr recalled.

“Then I started FFA and slowly but surely, my ag teachers worked me into attending more contests, meeting new people, and speaking. I remember the first time I gave an officer speech to my chapter. I can still remember how embarrassing it was. To see the progression from that moment to speaking on stage at the state convention in front of thousands of people. Now I feel like I can enter the industry I want and be successful all because of what FFA afforded me for five years.”

There is not much Parr did not do during his time in high school. His contest participation included chapter conducting, wool judging, cotton judging, wildlife, and job interview, but his favorite was extemporaneous speaking, which he did not start until his senior year of high school.

“I wish I could go back to my freshman, sophomore, and junior years and start that sooner. I think if I had more time, I would have been more successful than I already was, but that was something I didn’t realize I liked at the time. I’m not naturally somebody who likes to speak in public, but it was actually my favorite,” Parr said.

Parr won several awards during his time competing. In 2023 alone, Parr earned the Texas FFA Service-Learning Proficiency title, was a National FFA Service-Learning Proficiency finalist, and a Texas FFA Extemporaneous Speaking finalist. In addition to his CDE and LDE events during high school, he showed commercial steers at Houston, and boilers at most major shows, participated in the county show with projects in ag mechanics, showed goats from time to time, and showed heifers until graduation.

“FFA provides invaluable resources and knowledge to be successful once you leave high school and you are out of the blue jacket for the first time. I have been a part of a lot of great organizations over the years, and they are all great in their own way, but in my opinion, FFA is the most successful at producing members of society who want to go and do something with themselves,” Parr said.

He was halfway through his time as Area V Association President and attending the national convention when he began to ponder the idea of running for state office.

“This is around the time when you usually figure out if you want to go through and be a state officer or you decide that area officer is your last run. I was unsure of where I wanted to go, but I knew I didn’t want to be done with FFA. I decided maybe it would be a good opportunity not only for me to make more friendships and connections, but also to give back to the program that allowed me to be able to do what I can do today,” Parr explained.

To read more, pick up a copy of the May issue of NTFR magazine. To subscribe by mail, call 940-872-5922.

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