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Epigenetic-related Genes Modulate Early Germination of Wheat, Study Finds

NEW YORK (GenomeWeb News) – Genetic and epigenetic factors may be behind why some wheat strains begin to sprout prematurely under high humidity and rainfall conditions, researchers from McGill University reported in PLOS One yesterday. One gene in particular — AGO802B — appears to play a role in premature sprouting by modulating DNA methylation.

Broadly, seed germination relies on antagonist interactions between abscisic acid and gibberellic acid, but the McGill team led by Jaswinder Singh noted that there has been increasing evidence that epigenetic factors also influence when plants sprout. To further investigate that link, they examined the role of ARGONAUTE4_9 genes, which are part of the RNA-dependent DNA methylation pathway, in wheat development.

"The complex RdDM machinery is composed of several proteins that guide the genome in response to growth, developmental, and stress signals. It's a bit like the plant's brain," Singh, a professor of plant sciences, said in a statement. "Although in the past scientists have identified it as the pathway that regulates the way a variety of genes are expressed, until now no one had made the link with [pre-harvest sprouting]."

According to McGill, pre-harvest sprouting can cost the wheat industry as much as $1 billion a year as plants that sprout before they are fully mature have a lower yield as well as produce an inferior quality of grain.

In plants, ARGONAUTE proteins, particularly AGO4_9 class ones, are involved in DNA silencing through the RNA-dependent DNA methylation pathway. In barley, the researchers noted, there are two AGO4_9 class genes, and wheat, as a related allohexaploid species with three genomes, has three homoeolog genes that correspond to those barley genes. One of those homoeologs, AGO802 was in the chromatin database ChromDB. The others, AGO804 homoelogs, were uncovered by Singh and his colleagues using Blast searches of three different wheat databases.

The three AGO802 homoeologs, the researchers found, were nearly identical, and the AGO804 ones also appeared to be highly similar.

In addition, the six AGO4_9 genes mapped to chromosomes 3S and 1S.

To examine the expression of these six genes in developing seeds, the researchers used homoeolog-specific primers and performed QRT expression analysis at different post-fertilization stages. While expression patterns varied, the researchers noted that AGO802 expression was between two times and three times higher than AGO804 expression levels. Expression levels also varied due to which genome encoded the gene — the A, B, or D wheat genome.

Focusing on AGO802B transcripts, the researchers examined how a number of Canadian wheat varieties, both resistant and susceptible to pre-harvest sprouting, expressed AGO genes.

Interestingly, they found a polymorphism in the fragment lengths of the AGO802B transcripts — seven of the 10 varieties contained an insertion in the 3' UTR that appeared to be a short, interspersed nuclear element.

That insertion, the researchers found, is present in all but one of the resistant varieties and is absent in the susceptible ones.

Using DNA blot analysis, Singh and his colleagues examined DNA methylation patterns in six wheat varieties, five with the insertion and one without it. The resistant varieties with the insertion had reduced levels of methylation as compared to the susceptible variety. The sixth variety, which has a moderate pre-harvest sprouting reaction, fell in between those methylation levels.

In addition, the resistant varieties had low levels of AGO4 protein as compared to the susceptible varieties.

"The strong correlation of the insertion in AGO802B with the PHS resistant genotypes suggests that it may be involved in modulating seed dormancy in these genotypes," the study authors said.

The researchers noted that this work could be applicable to other cereal crops, and could help find ways to minimize crop losses due to humid conditions.

"This discovery is important for other cereals like barley as well as for wheat," Surinder Singh, an author on the paper and a PhD student in Jaswinder Singh's lab, said in a statement released by McGill. "This means that not only should we be able to avoid the ugly bread and sticky crumbs produced by PHS wheat in [the] future, we should also end up with better beer."

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