In a new study published in the journal Science on March 24, 2022 (“Convergent selection of a WD40 protein that enhances grain yield in maize and rice“), researchers have compared a genetic region in two of the world’s most economically important crops, corn and rice, that regulates a quantitative trait─ the number of rows of kernels on an ear of corn or a stalk of paddy.

As humans domesticated the ancestors of today’s popular cereal crops, specific human needs and agricultural practices have selected certain genes and genetic pathways over time. This is an instance of convergent selection, where distinct species evolve comparable traits in response to similar environmental pressure.  A few instances of convergently selected genes in cereal crops have been identified in past studies, but little is known about the extent and frequency of molecular convergence at a genome-wide scale in cereal crops.

Although corn and rice were domesticated independently nearly 100,000 years ago, agriculturally desirable traits such as ease of cultivation, high grain yield and nutrient richness, are shared between them. While these traits appear to have undergone convergent selection in distinct lineages, it is unknown if they were driven by conserved genes. Targeting such conserved genes in breeding programs could provide a way to develop improved cereal varieties.

“We found that the quantitative trait locus KRN2 in maize [corn] and its rice ortholog, OsKRN2, experienced convergent selection,” the authors note. These genes in corn and rice produce WD40 proteins that interact with other gene products to decrease grain number in both crops.

First author of the paper, Wenkang Chen, PhD, a scientist at the State Key Laboratory of Plant Genomics at the Chinese Academy of Sciences in Beijing and his colleagues probed the genomes of corn and its evolutionary ancestor, teosinte, for evolutionary signals of selection and identified a quantitative trait locus (QTL) associated with an increased number of kernels. Through fine mapping of this genomic region, the team located KRN2 in corn and its ortholog OsKRN2 in rice.

Since both KRN2 in corn and OsKRN2 in rice negatively regulate grain number, the researchers investigated the effects of knocking out the genes in the respective species, through gene editing experiments and controlled field trials. They found this genetic manipulation increased the yield in corn by nearly 10% and the yield of rice by nearly 8%, “with no apparent trade-offs in other agronomic traits.”

In addition, through genome-wide scans the authors have identified 490 pairs of orthologous genes that have undergone convergent selection during the evolution of corn and rice. They show these genes include several that belong to two shared molecular pathways.

“A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. KRN2, together with other convergently selected genes, provides an excellent target for future crop improvement,” the authors note.

Exploring the role of genes orthologous to KRN2 and OsKRN2 across cereal crops like wheat could provide opportunities for developing new global food crops with enhanced production, the authors say.