‘Model’ plant, a breeder’s treasure found | Crops

At a laboratory at the University of Bonn, Laibach dyeed the plant’s cells and examined them under a microscope. He found that the cells had only five chromosomes. That discovery is said to have attracted the attention of his advisor because it was the lowest odd number of chromosomes known to science at the time.

Today Laibach is credited with making Arabidopsis thaliana, a nondescript member of the mustard family, a model organism. It has long been used to study basic biological functions, which may be more widely applicable.

Researchers use the plant because of its small chromosome number as well as its compact size, rapid life cycle and prolific seed generation. It does not require much laboratory space and multiple generations can grow quickly, saving time and resources.

In 2000, Arabidopsis thaliana was one of the first organisms – and the first plant – to have its genome sequenced. The seven-year, $ 70 million Arabidopsis Genome Initiative includes multiple labs in Europe, Japan and the United States working together to determine the deoxyribonucleic acid – DNA – sequence of all five Arabidopsis chromosomes. That is the exact string of chemical building blocks – known as As, Ts, Cs and Gs – that specify the plant’s genetic code.

Joanne Chory and Joseph Ecker, professors at the Salk Institute, were instrumental in leading the initiative in the United States. They rallied support from influential researchers for the genome sequencing of Arabidopsis.

That led to significant funding, with the National Science Foundation as the lead agency. Ecker was at the University of Pennsylvania at the time and started working at the Salk Institute in 2000.

Ecker co-led a team of researchers to sequence chromosome 1, the largest of the five Arabidopsis chromosomes. The other four chromosomes were sequenced by teams from the United States, Japan and the European Union.

Years ago Chory had discovered DET1, an Arabidopsis mutant that could grow in the dark. She was asked to be a member of the Arabidopsis Genome Initiative Scientific Advisory Committee.

The mutant could grow in the dark even though it was not exposed to any light.

“What was unique about our study was the application of genetic techniques to a problem that has only been studied by plant physiologists,” she said. “It was the beginning of a revelation of how complex the pathways are that allow a plant to respond to light. It was difficult to identify a gene with the tools that we had then, and no overall sequence. “

Deciphering the Arabidopsis genome was revolutionary for both plant biology and genetics. Before that plant biologists who had an interesting mutant could not understand the clone genes how such a mutation in a gene could cause a dramatic phenotype – such as growing in the dark or tiny leaves. In genetics such known mutations are called markers.

The frequency with which mutations show up together – such as dark-growing plants with tiny leaves – can be used offspring to map genes relative to each other. Although it takes many crosses when breeding plants with multiple markers – to pinpoint the gene of interest. In this way – and with a molecular technique called restriction fragment length polymorphism analysis – Chory was able to localize the DET1 gene to the top of the chromosome 4.

Identifying the gene’s chromosome was just the first step. Determining the sequence and the exact location in the genome was another undertaking, which Chory completed for DET1 in 1994.

That related searching a DNA fragment of a library for one that overlapped the nearest marker. Then the non-overlapping end was used to search the library for another overlapping fragment. Repeated again and again, the process – known as chromosome walking – could eventually reach the gene of interest. Identifying and mapping a single gene within the genome could require a significant amount of time.

The Arabidopsis Genome Initiative made it possible for researchers to locate genes more easily within the Arabidopsis genome. They could, for example, look for DNA sequences that tell telltale signs of genes. Or they could look for gene sequences already known from other plants and see if they were also present in the Arabidopsis genome.

Importantly researchers could use plant mutations to identify unknown genes in the genome. One of the keys to that method is a bacterium called Agrobacterium tumefaciens, which infects plants. The bacterium does so randomly to insert its own DNA, in the form of a circular structure called a plasmid, into the plant’s genome. The bacterial DNA causes the plant to form a crown gall or tumor.

Scientists have determined how to replace bacterial DNA with custom DNA – known as a T-DNA insertion line. Agrobacterium transports custom DNA into the plant. Viruses are used in a similar way to deliver gene therapies into human cells.

If a gene in the T-DNA lands, it can cause a mutation – for example, a plant that produces petals where the stamens would usually be. Then scientists can locate their genome within T-DNA and know that it must land in a gene related to flower development. They can sequence that region and identify the gene.

With that approach, hundreds of thousands of T-DNA insertion lines, scientists have managed to identify – to some degree – all of Arabidopsis’ 28,000 genes.

One of the scientific community’s most important T-DNA insertion collections – or sequence-indexed insertion mutant libraries – was created by Ecker and other Salk researchers. The insertions are known as “Salk lines,” which can be ordered from a Salk website. To date the database has been accessed more than 11 million times, typically 4,000 times per month. Salk also provides seeds to the global Arabidopsis research community through two seed banks. Visit signal.salk.edu for more information.