Impact of gene on crop development could boost cereal yields

The productivity of major crops such as barley could get a boost in the future thanks to discoveries in the inner workings of genes and how they influence crop development, a new study from the James Hutton Institute and the University of Dundee has shown.

Scientists from both institutions have carried out the first study to demonstrate that a gene encoding a protein called HvAPETLA2 (HvAP2) controls how closely grains are packed on the top of the barley stem or spike, an important agronomic trait called spike density. Dr Kelly Houston, a molecular geneticist at the James Hutton Institute and co-author of the study, led the effort to pinpoint HvAP2 as a key gene influencing spike density.

“We examined the HvAP2 gene sequence in hundreds of barley lines showing differences in spike density,” Dr Houston said. “We were fascinated to observe that dense spike lines always had mutations in one small region of the HvAP2 gene – the micro RNA binding site. Micro RNAs (miRNA) normally block gene function by binding to specific sites like the one found in HvAP2.

This concentration of functional mutations highlighted to us the potential importance of this region in determining spike density, which led to further experiments to understand the exact mechanism regulating HvAP2.” The effort to identify HvAP2 as regulating spike density was aided by genomic resources which scientists at the James Hutton Institute have been instrumental in developing, such as the barley genome assembly published last year in Nature.

Co-author Sarah McKim, from the Division of Plant Sciences at the University of Dundee, found that these mutations prevented mRNAs from blocking HvAP2 function. “We essentially had an overabundance of HvAP2 activity in the extreme dense spike line, showing that more HvAP2 led to more grain packing on the spike,” she said, “and as a developmental biologist, I was keen to examine the mechanism behind this control.”

Conducting a fine-scale microscopic analysis of growing spikes in normal and extreme dense spike barleys, Dr McKim found that loss of miRNA-regulation of HvAP2 caused spike growth to pause early in development and grow more slowly afterwards, leading to denser spikes. “This study reveals how control of specific phases of developmental timing by miRNAs influences important agronomic traits in some of the world’s most economically, sociologically and ecologically relevant crops,” she commented.

This collaborative and interdisciplinary project between researchers at the James Hutton Institute and the University of Dundee demonstrates how barley research is moving beyond gene discovery into the mechanisms of gene action, which will allow breeders to be more predictive and sophisticated in their breeding strategies.

Dr Houston and Dr McKim suggest a future scenario where “through crossing, barley breeders could achieve a stacking of desirable traits such as increased grain density with longer spikes to increase yield.” The paper "Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence" is published in the Early Edition area of the journal Proceedings of the National Academy of Sciences of the United States of America (PNAS), and is available online at

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