Genes confer the primary traits that are passed on from generation to generation in plants and animals. Where, when and how new genes arise are far-reaching biological questions with practical implications. If scientists could identify emergent genes that confer new traits, the breeding potential for crops could be greatly expanded. During the quest for understanding where new genes come from, it is now known that genes can arise anew from regions of the genome where there were none previously. These so-called "orphan genes" may be key ways that species can evolve and adapt to challenging environments through the expression of new traits. To uncover orphan genes, this project taps into the sequenced genomes of maize, a major crop of worldwide importance, and Brassica, another model crop. Both species have major genomic resources available for orphan gene discovery. The research will identify orphan genes and evaluate traits possibly conferred by the genes in maize lines adapted to particular conditions. Candidate orphan genes that influence agronomically important traits will be selected and functionally analyzed. Computational tools will be developed to mine the sequence datasets and the resulting data will be integrated into community databases. At all stages, students will be trained in computational and genomic science. To reach high school students and early undergraduate students, new computer games modules are being developed and tested with the intention of increasing an understanding of the function and potential of orphan genes. A long-term outcome is that researchers and society will be able to design new solutions to improving crops through harnessing orphan genes.
The premise that new genes can arise from non-genic DNA sequences is borne out from massive DNA and RNA sequencing data. This concept sharply contrasts with the long-accepted view that novel gene functions primarily arise from a slow process of accumulated mutations and rearrangements of already-established genes. A hypothesis is that a major role of orphan genes is to regulate the defense and metabolic responses that enable evolutionary adaptation to new environments. This research will identify orphan genes of major agronomic species, focusing first on maize and Brassica. These results will inform a systematic analysis of orphan genes at the level of subspecies, thus categorizing orphan genes in the context of the adaptation and selection that has occurred as the result of human intervention for improved agronomic traits. Based on the resultant data, specific orphan genes will be selected for experimental functional analysis. Data will be integrated into community databases, and code will be available to the public. New computer game modules will be targeted to high school and early undergraduate students. The goal is to develop data and computational tools that facilitate predictive understanding of the function of orphan genes in driving evolutionary adaptation, to harness these resources for improving crops, and to disseminate the information to researchers and students. These capabilities will empower researchers to explore the significance of recently-emerged orphan genes, and transform fundamental knowledge into innovative solutions that improve crop traits.