Abstract
BackgroundIn finger millet, calcium is one of the important and abundant mineral elements. The molecular mechanisms involved in calcium accumulation in plants remains poorly understood. Transcriptome sequencing of genetically diverse genotypes of finger millet differing in grain calcium content will help in understanding the trait.Principal FindingIn this study, the transcriptome sequencing of spike tissues of two genotypes of finger millet differing in their grain calcium content, were performed for the first time. Out of 109,218 contigs, 78 contigs in case of GP-1 (Low Ca genotype) and out of 120,130 contigs 76 contigs in case of GP-45 (High Ca genotype), were identified as calcium sensor genes. Through in silico analysis all 82 unique calcium sensor genes were classified into eight calcium sensor gene family viz., CaM & CaMLs, CBLs, CIPKs, CRKs, PEPRKs, CDPKs, CaMKs and CCaMK. Out of 82 genes, 12 were found diverse from the rice orthologs. The differential expression analysis on the basis of FPKM value resulted in 24 genes highly expressed in GP-45 and 11 genes highly expressed in GP-1. Ten of the 35 differentially expressed genes could be assigned to three documented pathways involved mainly in stress responses. Furthermore, validation of selected calcium sensor responder genes was also performed by qPCR, in developing spikes of both genotypes grown on different concentration of exogenous calcium.ConclusionThrough de novo transcriptome data assembly and analysis, we reported the comprehensive identification and functional characterization of calcium sensor gene family. The calcium sensor gene family identified and characterized in this study will facilitate in understanding the molecular basis of calcium accumulation and development of calcium biofortified crops. Moreover, this study also supported that identification and characterization of gene family through Illumina paired-end sequencing is a potential tool for generating the genomic information of gene family in non-model species.
Highlights
Calcium is an important essential element, acts as secondary messenger in various biological processes
Identification of calcium sensor genes The rice calcium sensor genes were used as reference for identification of their homologues in finger millet transcriptome
The contig sequences which are repeated more than one time were used for open reading frame (ORF) selection
Summary
Calcium is an important essential element, acts as secondary messenger in various biological processes. Daily consumed cereals are poor in calcium, biofortification of these cereals for calcium and understanding molecular basis of its accumulation is in need. Earlier studies suggested the roles of various calcium transporters in the accumulation of calcium in plants [5] but the role of calcium sensor genes in regulating calcium transportation has not been reported till date. Transcriptome sequencing of genetically diverse genotypes of finger millet differing in grain calcium content will help in understanding the trait. Principal Finding: In this study, the transcriptome sequencing of spike tissues of two genotypes of finger millet differing in their grain calcium content, were performed for the first time. Validation of selected calcium sensor responder genes was performed by qPCR, in developing spikes of both genotypes grown on different concentration of exogenous calcium
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