Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

Abstract

Sucrose is the key economic trait in sugarcane which is a highly polyploid multi-species hybrid and shows a complex pattern of trait inheritance. The excessively large genome of sugarcane is comparatively less explored through Next Generation Sequencing tools for creating superior varieties. In this study, RNAseq libraries of two extreme bulks from a segregating full-sib population and its parents were used to identify 9905 conditionspecific non-synonymous genetic variants (NSVs), out of which 43 had a very high degree of differential enrichment (∆f >0.5) for contrasting sucrose accumulating conditions. The statistical model used in this study which was able to quantify the relative effect of NSVs on the trait detected highly significant positive and negative effect NSVs located in the coding regions of genes involved in sucrose metabolism, photosynthesis, mitochondrial electron transport, glycolysis and transcription. In addition, a few differential pre-mature stop codons that could result in production of truncated proteins were also detected in genes coding for aquaporin, GAPDH, aldolase, cytochrome C-oxidase, chlorophyll synthase and plant plasma membrane intrinsic proteins. Additionally, a total of 2140 differentially expressed genes (DEGs) linked to high sucrose accumulation were identified. Among the DEGs, sucrose phosphate synthase III, genes involved in transport, auxin signal transduction, etc., were upregulated, while those involved in electron transfer, cytochrome P450, etc., were downregulated in high sucrose accumulation conditions. This study was able to give finer insights in to the role of allelic heterozygosity on sucrose accumulation and the identified NSVs and DEGs could be useful as candidate markers in marker-assisted breeding for developing high sugar varieties.