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Computational Molecular Biology 2014, Vol. 4, No. 12, 1-8
http://cmb.biopublisher.ca
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Research Article Open Access
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
Corresponding author email
Computational Molecular Biology, 2014, Vol.4, No.12 doi: 10.5376/cmb.2014.04.0012
Received: 10 Dec., 2014
Accepted: 25 Dec., 2014
Published: 29 Dec., 2014
© 2014
Swain, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use,
distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
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
Abstract
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, Ghd7
are 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
Dep1
gene, 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
Dep1
gene 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.
Keywords
High grain number genes; Comparative structural analysis of high grain number proteins; Primer designing;
Amplification of genes
Introduction
Rice is cultivated in more than 100 countries
worldwide on approximately 150 million hectares of
land. Among the rice growing countries in the world,
India has the largest area under rice crop and ranks
second in production next to China. In India, it is
grown in 44 million hectares accounting for 43% of
food grain production and 46% of the total cerea
production. Even though rice covers largest area under
cultivation, the potential of rice production till has to
be exploited. Rice productivity has more than doubled
since the green revolution in the 1960s. Thus, further
improving rice yield potential has posed tremendous
challenges to rice breeders. Recent estimation
suggests that a 40% increase in the production of rice
is must by 2030 to meet the demands of the ever
increasing population (Khush, 2003). The cultivated
rice (
Oryza sativa
L.) is rich in genetic diversity apart
from highly diverse 21 wild progenitors and the
African cultivated rice,
Oryzaglaberrima
Steud
.
In
addition to staple food, rice has extensive protective
and curative properties against human ailments like
epilepsy, chronic headache, rheumatism, paralysis,
skin diseases, diabetes, arthritis, indigestion, blood
pressure, colon cancer, internal rejuvenation of tissues
and overcoming postnatal weaknesses (Kirtikar and
Basu, 1935). Identification and pyramiding of
favorable/superior alleles for yield and its component
traits would make a significant contribution to
breeding high-yielding rice varieties.Improvement of
rice grain yield is an important goal in rice breeding.
Unfortunately, yield improvement efficiency is not