Plant Hormones: Gene Family Organization and Homolog Interactions of Genes for Gibberellin Metabolism and Signaling in AllotetraploidBrassica napus

Abstract

Gibberellins (GA) are phytohormones that regulate a number of key traits for crop performance, such as control of plant height, flowering time, and nitrogen use efficiency. We have curated gene family organization and expression of genes for GA biosynthesis, catabolism, and signaling in allopolyploid Brassica napus. Genes encoding early GA biosynthetic enzymes, including ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), and ent-kaurenoic acid oxidases (KAO), form small families that are composed of one or two homeologous gene pairs. Late GA biosynthesis, including GA 20-oxidase (GA20ox), and GA 3-oxidase (GA3ox) and GA catabolism GA 2-oxidase (GA2ox) enzymes, and signaling proteins, including GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptors, GID2/SLEEPY(SLY) F-box proteins, and DELLA repressors are encoded by larger families of 5–15 pairs of homeologs (i.e., 10–30 genes). Overall, families of GA metabolism and signaling genes are well maintained among ten Brassica napus accessions regarding the number of family members. However, this is achieved by the equilibrium between active gene duplications and losses. The BnaGA20ox, BnaGA2ox, and BnaGID2/SLY2 families show remarkable diversification within accessions. The BnaGA20ox and BnaGA2ox families show gene duplications and losses more frequently than other families, and a number of truncated genes are annotated for these genes. Truncated GA2ox were frequently found in Brassica oleracea, suggesting that active diversification of BnaGA2ox is derived from the progenitor. Gene duplications and losses are frequently observed for the pairs of homeologs. Moreover, homeolog exchanges are enriched for family members showing gene duplications and/or losses. These suggest that homeolog interaction is associated with gene family maintenance. Transcriptomes at various developmental stages in the ZS11 accession showed that most homeolog pairs are co-expressed, and gene expression divergence between homeologous genes is mostly tissue-specific. These analyses suggest that genomics-based breeding is suitable to effectively select GA-related traits from a limited source of genetic diversity in young polyploid B. napus.