QnAs with Blake C. Meyers

Over his career, Blake C. Meyers has worked on short-read nucleic acid sequencing and applied it to the analysis of small RNA molecules. His research has advanced researchers’ understanding of the biological functions of small RNAs. He identified mechanisms and pathways through which small RNAs in plants are produced and function and characterized the effects of small RNAs on gene expression and genome biology. Meyers has explored a class of small RNAs that includes trans-acting small interfering RNAs (tasiRNAs) and phased, secondary siRNAs (phasiRNAs), focusing on the reproductive phasiRNAs found in anthers—the male reproductive organs—of many flowering plants. In his Inaugural Article (1), Meyers describes his findings on phasiRNAs in wheat. A professor of plant sciences at the University of California, Davis, Meyers was elected to the National Academy of Sciences in 2022.

Blake C. Meyers. Image credit: Blake C. Meyers (University of California, Davis, CA).

PNAS: How did you become interested in small RNAs in plants?

Meyers: When I first started as an assistant professor at the University of Delaware in the early 2000s, I was working on a technology that ultimately evolved into next-generation sequencing. The lab next door was that of a plant RNA biochemist, Pamela Green. We realized that the technology could be adapted for deeply sequencing small RNAs. The breadth of microRNA regulation in animals and plants was becoming clear, along with clues of other small RNA pathways involved in silencing. Armed with this new technology and a few completely sequenced plant genomes, it was fertile ground for discovery.

We worked on diverse aspects of small RNA discovery and we applied the technology to plant genomes as they were newly sequenced. We collaborated to analyze the genetic pathways that lead to the production of plant small RNAs, including microRNAs, heterochromatic siRNAs, and the phasiRNAs—a class of secondary siRNAs triggered by a primary microRNA.

My lab’s small RNA interests continued to evolve. In 2009, a team described an unusual abundance of phasiRNAs in anthers of rice and maize (2). A unique feature of one class of these phasiRNA is their 24-nucleotide (nt) spacing. I started collaborating with a colleague at Stanford University, Virginia Walbot, whose lab focuses on the development of anthers. Our work with Ginny’s group showed that these reproductive phasiRNAs are extremely abundant at specific stages and cell types in anthers of maize. Since that time, we’ve been working to understand the biogenesis, the localization, the evolution, and the function of these reproductive phasiRNAs.

PNAS: How did your Inaugural Article come about?

Meyers: In wheat and other related crops, such as barley and rye, there are few, if any, scalable methods for producing hybrid seeds. Controlling pollen flow is the basis for the production of hybrid corn, a major agricultural advancement because of the yield gains achieved through heterosis in hybrid plants. In corn, we have shown that knocking out a gene called Dicer-Like 5 (DCL5) eliminates a pathway for 24-nt phasiRNA production and confers male sterility. We demonstrated that this sterility is conditional, i.e., it is a reversible phenotype dependent on the environment, a trait potentially useful for hybrid seed production.

We decided to test and compare the phenotype in wheat, as wheat is the interest of the Inaugural Article’s first author, Sébastien Bélanger. To obtain a wheat dcl5 mutant, we worked together with a group at the John Innes Center in the United Kingdom. The characterization of this mutant and the reproductive phasiRNAs gave us some surprising results that we describe in the article. The article thus represents a comparative genetic and genomic analysis.

PNAS: What were the surprising findings?

Meyers: From the work of many groups, we know that phasiRNAs require a microRNA “trigger.” Yet we had previously described—in tomato and petunia—reproductive phasiRNA loci for which the microRNA trigger was not identified. This was puzzling, but it seemed like it could have been a lineage-specific oddity. With the current work in wheat, we investigate these “triggerless” phasiRNAs in more detail, produced from well over 1,000 loci. We demonstrate that there’s no evidence of microRNA-induced cleavage at these loci, consistent with our inability to find a microRNA that matches the motif at the start of the phasiRNAs. This has left us with more questions than answers.

The other thing that surprised us are the conditions that restore fertility in the dcl5 mutant. Since wheat is closely related to maize, we thought the phenotype would be regulated in the same way, i.e., at normal temperatures, it would be male sterile, but if we lower the temperature, we could recover male fertility. This conditionality was already a striking result for maize, as the phasiRNAs are still missing at the lower, permissive temperatures. Surprisingly, the temperature to induce male fertility is the opposite in wheat relative to maize: In our wheat mutant, male fertility is recovered by higher temperatures but also without small RNA recovery. This again left us with more questions than answers.

With only the maize result, we had hypotheses about how a lower temperature might stabilize biochemical processes to compensate for the loss of these small RNAs. But those hypotheses don’t work with a higher temperature recovery, so we’re back to the drawing board. There’s certainly something interesting going on at the molecular level.

PNAS: What are the potential applications of these findings?

Meyers: Our work investigates a pathway that we hope could ultimately contribute to hybrid wheat production, boosting yields. Yield gains are important for such widely grown crops as wheat, given growing global demands on agriculture. The basic biology insights are exciting too, and these questions should keep us busy for a few years. We are in an era of plant biology when there are many molecular and genomic discoveries that are being made about the diverse ways and processes by which plants reproduce, and I’m happy to be a part of it.