BRIDGEcereal is designed to take the process of identifying large DNA variations from tedious to efficient
Understanding and improving cultures based on the huge amount of data that has been generated has also created a challenge for researchers due to the lack of easy-to-use and efficient bioinformatics tools, especially those designed to handle large volume DNA variations. in a species. (Photo by Sasun Bughdaryan on Unsplash)
PULLMAN, Wash. – Scientists at the Agricultural Research Service and Washington State University have developed an innovative web app called BRIDGEcereal that can quickly and accurately analyze the vast amount of genomic data now available for cereal crops and organize the material in intuitive graphs that identify patterns that locate genes of interest.
With the rapid advances in genomics over the past 25 years, a game changer for crop improvement has emerged called the pan-genome, defined as the assembled genomic sequences from multiple varieties within a species. But understanding and improving cultures based on the massive amount of data that has been generated has also created a challenge for researchers due to a lack of easy-to-use and efficient bioinformatics tools, especially those designed to handle large DNA variations. volumes in one species.
Take wheat, for example. The standard reference wheat genome, which was made for the Chinese Spring wheat variety, is five times larger than the human genome. Additionally, researchers have long struggled with the wide variation in the locations of genes that control essential agronomic traits in wheat’s 21 chromosomes. Right now, a dozen wheat genomes are publicly available.
This adds up to a huge amount of data, making their analysis a tedious process even for researchers with advanced bioinformatics skills. It is particularly difficult to sort through all the data to identify similar stretches of DNA that can control the same stretch, no matter where they are on a chromosome.
BRIDGEcereal is designed to take the process of identifying large DNA variations from tedious to efficient.
“Simply providing BRIDGEcereal with the DNA sequence you are interested in, it will complete the search process in less than a minute.” explained ARS research biologist Xianran Li, leader of the BRIDGEcereal project. Li serves on the ARSWheat Health, Genetics, and Quality Research Unit in Pullman, Washington.
“And BRIDGEcereal will organize the data it finds and present it to you in easy-to-understand graphs that highlight any pattern of where that DNA is,” Li added.
It took BRIDGEcereal just a minute to identify a promising candidate gene as the controller of a wheat mutation that shortens the length of the barbs, the bristle-like extensions from the head of the wheat grain. It has been known since the 1940s that a gene on wheat chromosome 4A controls the development of the beard, which is an iconic wheat trait. But the exact gene that controls that trait has remained unknown.
“By searching dozens of potential genes through BRIDGEcereal, we were able to quickly identify a gene with large DNA variation as the one that eluded the researchers,” Li said.
The scientists also designed BRIDGEcereal to be self-learning, also called unsupervised machine learning, meaning that BRIDGEcereal can independently learn to recognize new patterns without needing explicit instructions to follow.
“So what we have developed is a one-stop gateway to efficiently extract publicly accessible pan-genomes of cereals that will become more and more efficient as the data continues to grow,” said Li.
Bosen Zhang, a postdoctoral research associate at Washington State University and co-developer of the web app, added, “Researchers will find BRIDGEcereal an invaluable tool for selecting and prioritizing candidate genes that control specific traits in cereal crops.” .
BRIDGEcereal was initially developed to work with wheat. It has already been adapted to analyze similar data from barley, corn, sorghum and rice. This research was published in the journalMolecular plant.
The Agricultural Research Service is the primary internal scientific research agency of the United States Department of Agriculture. Every day, ARS focuses on solutions to agricultural problems affecting America. Every dollar invested in US agricultural research translates into a $20 economic impact.
#BRIDGEcereal #accelerates #analysis #genomic #data #cereal #crops