Designing and Validation of Primers for High grain number for use in Molecular Breeding in rice  

Pranati Swain , Lambodar Behera
Central rice research institute, India
Author    Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 12   doi: 10.5376/cmb.2014.04.0012
Received: 24 Nov., 2014    Accepted: 25 Dec., 2014    Published: 29 Dec., 2014
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Pranati Swain and Lambodar Behera, 2014, Designing and Validation of Primers for High grain number for use in Molecular Breeding in rice, Computational Molecular Biology, Vol.4, No.12, 1-8 (doi: 10.5376/cmb.2014.04.0012)


Improvement of rice grain yield is an important goal in rice breeding. Yield improvement efficiency depends upon yield related components like grain number per panicle, grain weight, tillers number per plant, etc. Of these factors, grain number per panicle was shown to be highly correlated with yield. Pyramiding genes for grain number is highly indispensable in rice improvement programs. The high grain number genes, Apo1, Dep1, Ghd7are responsible for more seed production leading to increase in grain yield in rice. The length, sequence ID, chromosomal position and protein evidences of these genes were found from Orzabase, RAP-DB and Gramene database. The promoter, poly-A signal, DNA strand, open reading frame, initial signal/3’ splice site score, 5’ splice site, coding region, probability of exon and intron of high grain number genes under study were found out. These informations were used to design primers for these high grain number genes. The similarity search of designed primers showed 100% similarity with respective high grain number genes. The secondary structure prediction along with the comparative structural analysis of their respective proteins were performed. Three deigned primers for Dep1gene, one for Ghd7 gene and one for Apo1 gene were tested for amplification from high and low grain rice varieties, HGN1 and Heera, respectively. Two primers, Dep1-1 (promotor) for Dep1gene and Ghd7-2(Exon1) for Ghd7 gene amplified fragments from high grain variety, HGN1 while failed to amplify from low grain variety, Heera, indicating that these primers would be useful for introgression of genes from high grain varieties into low grain varieties to improve yield potential in rice through molecular breeding approach in future.

High grain number genes; Comparative structural analysis of high grain number proteins; Primer designing; Amplification of genes
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