By Male Allan Ssekamatte

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the fundamental molecules present in all living organisms that control all hereditary characteristics of cells. While DNA serves as the genetic blueprint of life, encoding the instructions necessary for the growth, development, and functioning of every cell, RNA acts as a messenger, carrying those instructions from DNA to guide the synthesis of proteins, which are crucial for various cellular processes. Sequencing these molecules has become a powerful tool for answering a range of biological questions, from identifying pathogens to understanding genetic disease risks and uncovering the evolutionary history of organisms.

One of the most exciting advancements in sequencing technology is the MinION, a cutting-edge device developed by Oxford Nanopore. Unlike traditional sequencing methods that require large and expensive laboratory equipment, the MinION is portable and compact, making it accessible to a broader range of researchers and institutions. This device uses a flow cell containing an array of nanopores — tiny holes embedded in an electro-resistant membrane. Each nanopore is linked to a channel and sensor chip, which measures the electric current that flows through the pore. As DNA or RNA molecules pass through these nanopores, they disrupt the current, creating a unique ‘squiggle’ pattern. These patterns are then decoded in real-time using sophisticated base calling algorithms to reveal the precise sequence of genetic material.

Components of the MinION. left-empty MinION, middle- flow cell, right-loaded MinION – Photo by Male Allan Ssekamatte

The potential applications of MinION are vast, and it is already being employed in groundbreaking research around the world. At the Alliance of Bioversity and CIAT at Kawanda in Uganda, scientists have recently acquired a MinION for their work on common bean genomics. The excitement surrounding the device is palpable, as researchers plan to harness its capabilities for critical studies on common beans, one of the world’s most important food crops.

Following this, the common bean breeding team led by Dr. Clare Mukankusi, is eager to use this MinION to identify robust, accurate, and highly specific molecular markers in beans. Molecular markers are specific DNA sequences that serve as identifiable landmarks within an organism’s genome. They are invaluable tools in breeding programs, enabling scientists to select plants with desirable traits more efficiently. With the MinION, researchers will be able to conduct high-throughput sequencing, enabling faster and more accurate identification of these markers.

Mukankusi said: “The MinION will significantly enhance our ability as scientists to identify robust and highly specific molecular markers in common beans, allowing us to accelerate the breeding process and select plants with desirable traits more efficiently.”

MUKANKUSI – The device will help accelerate the breeding process – Photo Courtesy of Alliance of Bioversity International & CIAT

Additionally, this MinION will be used to probe deeper into the genomic makeup of two significant pathogens that affect common beans: E. phaseoli, which causes scab disease, and the bean stem maggot (BSM). By sequencing the genomes of these pathogens, researchers hope to gain a better understanding of their biology and behavior, which will, in turn, inform the development of more effective diagnostic tools. These advancements could be pivotal in improving the health and yield of common beans, which are a vital source of nutrition and income for millions of people around the world.

Setting up of the MinION in a lab for a sequencing run – Photo by Male Allan Ssekamatte

The work in Kawanda will be a part of a larger collaborative effort involving several partners across East Africa. Collaborations with the Kenya Agriculture and Livestock Research Organization (KALRO), Uganda’s National Agricultural Research Organization (NARO), and member countries of the Pan-Africa Bean Research Alliance (PABRA) are central to these initiatives. Together, these organizations aim to use the MinION to enhance bean production in Africa and beyond, combating the challenges posed by pests, diseases, and climate change.

As the MinION becomes an integral part of the research process in Kawanda, scientists are hopeful that its portability and efficiency will transform the way genomic research is conducted in the region. With its ability to produce real-time sequencing data, the MinION holds the promise of accelerating scientific discoveries and empowering researchers in their quest to tackle some of the most pressing agricultural challenges of our time.

By unlocking the secrets of the common bean’s genome and the pathogens that threaten it, the MinION is paving the way for more sustainable and resilient agricultural systems. With continued collaboration and innovation, this technology could have far-reaching implications for food security and the health of millions of people globally.