Muhammad Rizwan Tufail

New discoveries in identifying causes of bacterial blight in Pakistani cotton.

Muhammad Rizwan Tufail, UAF doctoral scholar in plant pathology.
Muhammad Rizwan Tufail, UAF doctoral scholar in plant pathology.

Muhammad Rizwan Tufail, UAF doctoral scholar in plant pathology.

Muhammad Rizwan Tufail, UAF doctoral scholar in plant pathology.

Muhammad Rizwan Tufail, a doctoral student from the Department of Plant Pathology at the University of Agriculture, Faisalabad, is investigating bacterial blight in cotton. Cotton is one of the major crops produced in Pakistan, which is the fifth-largest producer of cotton in the world. Bacterial blight in cotton was first reported in Multan, Punjab, in 1965, and can reduce crop yields by up to 50% in some instances. It is spread primarily through infected seeds, and seed quality concerns are a major issue within multiple areas of Pakistani agriculture.

In January, Mr. Tufail arranged to have his bacterial samples shipped to the laboratory of Dr. Douglas Cook, his exchange mentor in the Department of Plant Pathology at UC Davis. The plan was to analyze the samples to confirm the presence of Xanthomonas, a bacterial pathogen with 22 types found around the world.

Mr. Tufail collected cotton leaf samples from 5 cotton cultivating regions scattered throughout Punjab, isolated the bacterium from the cotton plants, and confirmed their genotype through morphology identification. He established a field trial, inoculated his cultures, and collected further data. Once he isolated his DNA samples and prepared a genomic library, Mr. Tufail and Dr. Cook submitted the samples to the UCD Genome Center for processing and analysis.

The results? No Xanthomonas was found in any of Mr. Tufail’s research. The bacterial blight he had collected was a different type than the one he had suspected.

Dr. Cook elaborates: “Rizwan came into the lab with a hypothesis, pretty sure that you were working with bacterial blight from Xanthomonas. It was at a lab meeting at Lake Tahoe where he received the data analysis that showed no presence of Xanthomonas, and his immediate reaction was depression—he thought for sure something had gone wrong!”

Instead, Mr. Tufail’s genomic analysis had reported the presence of four different types of Pantoea, a genus of gram-negative bacteria and opportunistic pathogen. The most prevalent of the types was Pantoea Agglomerans, which shows similar morphological traits to Xanthomonas, the original blight suspect. Luckily, the molecular analysis provided the correct identification.

While pantoea agglomerans has been reported as boll rot in other cotton crops, it had never been observed on cotton leaves, from which Mr. Tufail had collected all of his samples. It is also the first time reporting the presence of Pantoea Agglomerans and other varieties in Pakistan, demonstrating that the pathogen may be more virulent than previously thought.

“We talked about it and looked at his research, and we’re pretty sure it’s a new instance of disease,” says Dr. Cook. “It’s been previously reported, but only sporadically. If the additional work bears out this new hypothesis, it’s an important new observation that leads to all sorts of new applied questions on controlling and preventing this new discovery.”

Mr. Tufail plans to re-confirm the bacteria identity through Koch postulates and conduct a genomic analysis of Pantoea, evaluating its virulence in cotton. His research will continue to provide new insight into an emerging threat to Pakistan’s valuable cotton production.

The U.S.-Pakistan Center for Advanced Studies (USPCAS) is educating and training the next generation of scientists, engineers, and policy makers through innovative academic programs crucial for Pakistan’s development in agriculture and food security. Through applied research, academia-industry collaboration, and policy formation, USPCAS enhances Pakistan’s economic growth and prosperity. USPCAS was made possible by support from the American people through United States Agency for International Development (USAID).

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Profile written by Levi McGarry.