New technique helps find valuable crop trait genes

MutChromSeq combines chromosome flow sorting with classical mutagenesis to pinpoint desirable crop traits faster.

Scientists at the John Innes Centre in Norwich, U.K., have applied an innovative technique to the wheat and barley genomes that makes it easier to pinpoint specific genes that might be used in crop improvement programs, according to a news release.

Plant breeders are on a mission to develop new and improved crop varieties that can better cope with the effects of climate change, new pests and diseases and produce higher yields to feed a growing human population. To do this, it is useful to know exactly where the genes are located that are responsible for advantageous traits, such as disease resistance genes, for example, or genes that help plants withstand drought.

Locating the gene for a particular plant trait, however, can be like trying to find a needle in a haystack: It's a small, specific sequence of DNA mixed up in a jumble of other genes, regulatory sequences and non-coding DNA. For some plants, like the model plant Arabidopsis, or rice, the genomes are like small "hay bales," so the gene's "needles" are somewhat easier to find, but for wheat and barley, two of the most important cereal crops across the globe, the genomes are so large that it's like searching a whole barn full of haystacks, the news release explained.

Working with colleagues in Switzerland and the Czech Republic, Dr. Brande Wulff and his team from the John Innes Centre have succeeded in applying an innovative technique called MutChromSeq to the wheat and barley genomes. The technique reduces the complexity of the search for a gene by eliminating parts of the genome where it is known that the gene will definitely not be found.

So, how does MutChromSeq work?

"It is based on a known technique called chromosome flow sorting in which we can separate chromosomes one from the other by tagging them with fluorescent markers," Wulff explained. "Take the bread wheat genome, for example: This has 21 chromosomes, so with flow sorting, we can separate chromosome 1 from chromosome 2 and from chromosome 3 and so on. If we know that a particular gene is located on, say, chromosome 21, but we don't know precisely where, then we can filter out chromosomes 1-20 to narrow down the search. It's much quicker, easier and cheaper to sequence just one chromosome than all 21."

In MutChromSeq, chromosome flow sorting is combined with classical mutagenesis. Seeds from a plant with the trait of interest are subjected to a chemical that disrupts their DNA, and mutants that have lost the trait are identified by screening. Then, by running the MutChromSeq analysis on these mutant plants, the sequence of the mutated chromosomes can be compared with the non-mutated chromosome.

"By looking for the differences in sequence between the mutated and wild-type chromosomes, we can identify genes without knowing anything about their structure beforehand," Wulff said. "So long as we already know which chromosome a particular gene is on, this technique is going to make it much easier to clone any wheat or barley gene of interest, which is great news for researchers."

The paper, "Rapid Gene Isolation in Barley & Wheat by Mutant Chromosome Sequencing," was published Oct. 31 in Genome Biology.

This research was funded by JIC Innovation Fund, Biotechnology & Biological Sciences Research Council, Swiss National Science Foundation grants, Czech Science Foundation, Czech Republic National Program of Sustainability and Plant Fellows Program.

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