Transcriptome wide identification and validation of calcium sensor gene family in the developing spikes of finger millet genotypes for elucidating its role in grain calcium accumulation

• Published in: PloS one 2014-08, Vol.9 (8), p.e103963-e103963
• Main Authors: Singh, Uma M, Chandra, Muktesh, Shankhdhar, Shailesh C, Kumar, Anil
• Format: Article
• Language: English
• Subjects: Accumulation; Amino Acid Sequence; Arabidopsis; Arabidopsis thaliana; Barley; Biology and Life Sciences; Calcium; Calcium - metabolism; Calcium content; Calmodulin; Cereals; Data processing; Eleusine - chemistry; Eleusine - genetics; Eleusine - metabolism; Eleusine coracana; Finger; Gene expression; Gene Expression Regulation, Plant; Gene sequencing; Genes; Genes, Plant; Genetic aspects; Genetically altered foods; Genomics; Genotypes; Grain; Kinases; Metabolic Networks and Pathways; Millet; Molecular biology; Molecular modelling; Molecular Sequence Data; Oryza; Oryza - genetics; Phylogeny; Plant biology; Plant Proteins - chemistry; Plant Proteins - genetics; Plant Proteins - metabolism; Potassium; Proteins; Rice; Seeds; Sensors; Spikes; Tissues; Transcriptome
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0103963

In 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. 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. 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. Through 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.