Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.)

Author(s)

Cardoso-Silva, Claudio Benicio ; Aono, Alexandre Hild ; Mancini, Melina Cristina ; Sforca, Danilo Augusto ; da Silva, Carla Cristina ; Pinto, Luciana Rossini ; Adams, Keith L. ; de Souza, Anete Pereira

• Document type: Journal article
• Source: FRONTIERS IN PLANT SCIENCE; v. 13, p. 13-pg., 2022-06-30.

Abstract

Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes. (AU)

• FAPESP's process: 14/11482-9 - Evaluation of genomic synteny between sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum): comparision of genes involved in a QTL for Brix in sorghum to syntenic region in sugarcane
• Grantee: Melina Cristina Mancini
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 15/16399-5 - Balance between dosage and allelic expression to map the global gene expression profile in sugarcane
• Grantee: Cláudio Benício Cardoso da Silva
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 19/03232-6 - Genome wide selection in sugarcane using machine learning and complex networks for economically important traits
• Grantee: Alexandre Hild Aono
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 15/24346-9 - Allelic variation analysis in genes of economic importance among hom(oe)ologous regions of sugarcane (Saccharum spp.) genome
• Grantee: Carla Cristina da Silva
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 17/26781-0 - Transcriptome survey of sugarcane hybrids (Saccharum spp.) and ancestral species (S. officinarum and S. spontaneum) for gene expression pattern and homoeologous interaction studies
• Grantee: Cláudio Benício Cardoso da Silva
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Grantee: Anete Pereira de Souza
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants