Allele-specific hormone dynamics in highly transgressive F2 biomass segregants in sugarcane (Saccharum species)

Abstract

Abstract Background Sugarcane is a competitive candidate to serve as feedstock for biofuel production worldwide. Plant hormones play an important role in growth and development and regulate biomass yield. Understanding hormonal dynamics and their regulation is critical for increasing sugarcane biomass. To enhance our understanding of biological pathways involved in biomass accumulation, transcriptome analysis of highly segregating F2 introgression hybrids derived from the cross of Saccharum officinarum'LA Purple' and wild S. robustum 'MOL5829' was performed in this study. Recently sequenced information rich allele-specific genome of S. officinarumserved as a reference to identify differentially regulated genes in two groups of extreme segregants of biomass. Results Overall, 8059 differentially expressed genes (log2FC > 2) were grouped into distinct categories viz. Gene Models (21.5%) (GMs), alleles (68%), paralogs (10%) and tandemly duplicated genes (0.14%). KEGG analysis showed enrichment of auxin (IAA), jasmonic acid (JA) and abscisic acid (ABA) related pathways and interesting regulatory roles of three hormone repressor gene families (Aux/IAA, PP2C, and JAZ) of IAA, ABA and JA, respectively. Signaling pathways of these hormones indicated down-regulation of AUX/IAA and PP2C and up-regulation of JAZ repressor genes in high biomass group controlling the expression of downstream growth and development genes. Endogenous hormone levels show higher IAA and ABA contents in high biomass and vice versa for JA. Weighted co-expression network analysis (WGCNA) demonstrated high connectivity between identified hormones related key genes and cell wall structural genes in high biomass genotypes. FPKM and RT-PCR based expression analysis showed the up-regulation of carbohydrate structural genes and down regulation of inflorescence and senescence related genes, which indicated an extended vegetative growth phase in high biomass genotypes. Furthermore, high biomass group displayed modulated regulation of hormones which was achieved by the cumulative expression of Gene Models (GMs), dominant alleles, paralogs, and tandemly duplicated genes. Conclusion Our data revealed that activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties.