Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: a case study in Pyrus architecture genes

Authors: ZHANG, HUITING - Washington State University; WAFULA, ERIC - Pennsylvania State University; Eilers, Jon; HARKESS, ALEX - Pennsylvania State University; RALPH, PAULA - Pennsylvania State University; TIMILSENA, PRAKASH RAJ - Pennsylvania State University; DEPAMPHILIS, CLAUDE - Pennsylvania State University; Waite, Jessica; Honaas, Loren

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/21/2022
Publication Date: 11/14/2022
Citation: Zhang, H., Wafula, E., Eilers, J.R., Harkess, A., Ralph, P., Timilsena, P., Depamphilis, C., Waite, J.M., Honaas, L.A. 2022. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: a case study in Pyrus architecture genes. Frontiers in Plant Science. 13. Article 975942. https://doi.org/10.3389/fpls.2022.975942.
DOI: https://doi.org/10.3389/fpls.2022.975942

Interpretive Summary: The “genome” is the collection of all an organism’s genetic material that includes all of its genes. We are in the age of plant genomics – new plant genomes are published every month. In plants there are typically tens of thousands of genes in the genome. As the genomes are sequenced and published, they are made publicly available for researchers to use, thus enabling genetic studies. Often a starting point for a genetic study is learning about genes that influence traits of interest. For instance, in peach and plum trees, some genes that influence their architecture (for example, branch angle, branching pattern, plant height) have been identified – tree architecture is an important consideration in commercial orchards. Because peach and plum are related to other important tree fruit species (e.g., cherry, apple, & pear) researchers hope to be able to transfer some of our knowledge about their genes to other trees. This is a challenging task – in part because sorting through tens of thousands of genes is daunting, but also because genomes are large and complex, and therefore require sophisticated software and powerful computers to analyze. Here we present a computational workflow that helps us more easily transfer genetic knowledge between plant species. Using this approach, we identified and fixed issues with a current pear genome (hidden genes in the ‘Bartlett’ cultivar genome). We also identified a list of genes shared by pears and other tree fruit species for further studies that are aimed at understanding the genes that influence architecture in fruit trees, namely European pears like ‘Bartlett.’

Technical Abstract: Recent years have witnessed the rapid development of sequencing technologies and their impact on understanding horticultural plant genomes. However, experimental evidence connecting agronomic genes to important traits is still lacking in most non-model organisms. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruits, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks, in European pear. Curating a list of architecture genes with high-confidence gene models across various pome fruit species and cultivars can serve as an important first step towards identifying key genetic factors for these desirable traits. Here we present a draft genome of P. communis ‘d’Anjou’ and an improved annotation of the latest P. communis ‘Bartlett’ genome. To study gene families involved in tree architecture in European pear and other rosaceous species, we developed a workflow using a collection of bioinformatic tools towards curation of gene families of interest across genotypes. Our workflow can be adopted for new cultivars and other gene families. This work will allow us to lay the groundwork for future functional studies in pear architecture.