Convergent selection of a WD40 protein that enhances grain yield in maize and rice

A better understanding of the extent of convergent selection among crops could greatly improve breeding programs. We found that the quantitative trait locus KRN2 in maize and its rice ortholog, OsKRN2, experienced convergent selection. These orthologs encode WD40 proteins and interact with a gene of unknown function, DUF1644, to negatively regulate grain number in both crops. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-offs in other agronomic traits. Furthermore, genome-wide scans identified 490 pairs of orthologous genes that underwent convergent selection during maize and rice evolution, and these were enriched for two shared molecular pathways. KRN2, together with other convergently selected genes, provides an excellent target for future crop improvement. Description Amazing grains Maize and rice are important sources of human calories and have been, mostly independently, subject to human selection for thousands of years, often for similar traits such as grain yield. W. Chen et al. examined the genomes of accessions of domestic maize and its wild relative, teosinte, for evolutionary signals of selection. From these sequences, the authors identified a quantitative trait locus in maize that increased kernel row number. Fine mapping determined that this locus contains a candidate gene, KRN2. Gene-editing experiments of KRN2 and its homolog in rice determined that a similar phenotype increasing grain number per plant could be recapitulated. Thus, identifying genes under selection in one cereal provides useful fodder for crop improvements. —LMZ Convergent selection of KRN2 and other genes in maize and rice provide insight for crop improvement. INTRODUCTION During the independent process of cereal evolution, many trait shifts appear to have been under convergent selection to meet the specific needs of humans. Identification of convergently selected genes across cereals could help to clarify the evolution of crop species and to accelerate breeding programs. In the past several decades, researchers have debated whether convergent phenotypic selection in distinct lineages is driven by conserved molecular changes or by diverse molecular pathways. Two of the most economically important crops, maize and rice, display some conserved phenotypic shifts—including loss of seed dispersal, decreased seed dormancy, and increased grain number during evolution—even though they experienced independent selection. Hence, maize and rice can serve as an excellent system for understanding the extent of convergent selection among cereals. RATIONALE Despite the identification of a few convergently selected genes, our understanding of the extent of molecular convergence on a genome-wide scale between maize and rice is very limited. To learn how often selection acts on orthologous genes, we investigated the functions and molecular evolution of the grain yield quantitative trait locus KRN2 in maize and its rice ortholog OsKRN2. We also identified convergently selected genes on a genome-wide scale in maize and rice, using two large datasets. RESULTS We identified a selected gene, KRN2 (kernel row number2), that differs between domesticated maize and its wild ancestor, teosinte. This gene underlies a major quantitative trait locus for kernel row number in maize. Selection in the noncoding upstream regions resulted in a reduction of KRN2 expression and an increased grain number through an increase in kernel rows. The rice ortholog, OsKRN2, also underwent selection and negatively regulates grain number via control of secondary panicle branches. These orthologs encode WD40 proteins and function synergistically with a gene of unknown function, DUF1644, which suggests that a conserved protein interaction controls grain number in maize and rice. Field tests show that knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-off in other agronomic traits. This suggests potential applications of KRN2 and its orthologs for crop improvement. On a genome-wide scale, we identified a set of 490 orthologous genes that underwent convergent selection during maize and rice evolution, including KRN2/OsKRN2. We found that the convergently selected orthologous genes appear to be significantly enriched in two specific pathways in both maize and rice: starch and sucrose metabolism, and biosynthesis of cofactors. A deep analysis of convergently selected genes in the starch metabolic pathway indicates that the degree of genetic convergence via convergent selection is related to the conservation and complexity of the gene network for a given selection. CONCLUSION Our findings show that common phenotypic shifts during maize and rice evolution acting on conserved genes are driven at least in part by convergent selection, which in maize and rice likely occurred both during and after domestication. We provide evolutionary and functional evidence on the convergent selection of KRN2/OsKRN2 for grain number between maize and rice. We further found that a complete loss-of-function allele of KRN2/OsKRN2 increased grain yield without an apparent negative impact on other agronomic traits. Exploring the role of KRN2/OsKRN2 and other convergently selected genes across the cereals could provide new opportunities to enhance the production of other global crops. Shared selected orthologous genes in maize and rice for convergent phenotypic shifts during domestication and improvement. By comparing 3163 selected genes in maize and 18,755 selected genes in rice, we identified 490 orthologous gene pairs, including KRN2 and its rice ortholog OsKRN2, as having been convergently selected. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by increasing kernel rows and secondary panicle branches, respectively.