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Transcriptomic approach for understanding the role of calcium signaling and transport genes in relation to grain calcium content and calcium responsiveness in finger millet

KrishiKosh

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Title Transcriptomic approach for understanding the role of calcium signaling and transport genes in relation to grain calcium content and calcium responsiveness in finger millet
 
Creator Singh, Uma Maheshwar
 
Contributor Anil Kumar
 
Subject transcriptomes, calcium, signals, transport, genes, nutrient content, finger millet
 
Description Thesis-PhD
Finger millet is a plant with exceptionally high seed Ca content. Little is known about the genetic and epigenetic basis of calcium accumulation in seed. In order to understand the mechanisms of high seed Ca accumulation, two genotypes of finger millet differing in seed Ca content i.e. GPHCPB-1 (low Ca) and GPHCPB-45 (high Ca) were selected in present study. Through PCR based approach a total of 8 genes of Calcium regulated protein kinases were isolated, but these were quite few to be able to explain the exact mechanism of high seed Ca accumulation. Therefore, to cover all Ca signalling and transport genes expressed during seed development, the transcriptome of developing spike of both GPHCPB-1 and GPHCPB-45 genotypes were sequenced. A total of 55 and 52 Ca signaling and transport genes were identified in GPHCPB-1 and GPHCPB-45 genotype respectively. On the basis of phylogeny, per cent sequence identity, and conserved sequence analysis all the genes were classified into Ca sensor and transporter gene families. Differential expression analysis showed that 15 genes were highly expressed in GPHCPB-45, 7 were highly expressed in GPHCPB-1 and remaining 32 had very less (FPKM4) were studied towards exogenous application of Ca in both GPHCPB-1 and GPHCPB-45 genotypes. The overall high expression of most of the Ca sensor genes i.e., EcCDPK16, EcCDPK19, EcCIPK2, EcCIPK9, and EcCIPK11 were observed in GPHCPB-45 genotype in later stages of spike development, in a concentration dependent manner. Similarly, the overall high expression of Ca transporter genes i.e., EcPM3ATPase2, EcPM4ATPase8, EcPM12ATPase4, EcER3ATPase3 and EcCaX3 were observed in GPHCPB-45 in later stages of spike development, in a concentration dependent manner. The expression of two genes EcCIPK19 and EcPM8ATPase was comparatively higher in GPHCPB-1 as compared to GPHCPB-45 genotype. The exceptionally higher expression of EcCaX3 in response to exogenous Ca and at later stages of spike development in high Ca containing genotype establishes this gene as a strong candidate for higher seed Ca accumulation and its further use for Ca biofortification. However, exploration of its spatial distribution within seed, over expression and knockout studies will help in understanding the exact role of this gene in high seed calcium accumulation. Finally, transcriptome based functional annotation provides a greater insight into the mechanisms related to seed calcium accumulation and would help to accelerate future research in this very important area of seed biology.
 
Date 2016-11-04T14:30:20Z
2016-11-04T14:30:20Z
2013-08
 
Type Thesis
 
Identifier http://krishikosh.egranth.ac.in/handle/1/83943
 
Language en
 
Format application/pdf
 
Publisher G.B. Pant University of Agriculture and Technology, Pantnagar - 263145 (Uttarakhand)