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NISCAIR ONLINE PERIODICALS REPOSITORY (NOPR) >
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Research Journals >
Indian Journal of Biotechnology (IJBT) >
IJBT Vol.09 [2010] >
IJBT Vol.09(2) [April 2010] >
| Title: | Use of in silico and semiquantitative RT-PCR approaches to develop nutrient rich rice (Oryza sativa L.) |
| Authors: | Banerjee, Shubha
Sharma, D J
Verulkar, S B
Chandel, G |
| Keywords: | Expression analysis
in silico
iron zinc protein rich rice
MGS
MTS
RT-PCR |
| Issue Date: | Apr-2010 |
| Publisher: | CSIR |
| Abstract: | Inspite of
striking agricultural progress and adequate food grain production, protein
energy and micronutrient malnutrition are widespread among rural and poor
population. The pharmaceutical and diet diversification based approaches have
achieved little success due to poverty and educational unawareness.
Biofortification of staple food crop rice, which is consumed in large amounts
daily, will serve as an important vector to combat malnutrition. The possible
approach to improve nutritive value of rice involves exploitation of available
genetic variability for grain protein and Fe/Zn contents with conventional and
modern biotechnological tools. We have analysed variability in grain protein and
Fe/Zn levels in rice, and factors affecting them for identification of rice
genotypes with higher nutritive value. Wide variation for grain protein and
micronutrient levels were recorded among the tested rice genotypes, which
ranged from 6.19 to 10.75% for grain protein content, 4.82 to 22.69 μg/g for
grain Fe and 13.95 to 41.73 μg/g for grain Zn content. Significant effect of
nitrogenous fertilizer dose and native soil properties were observed on grain
protein content, whereas grain Fe and Zn levels were more significantly
affected by native soil properties and showed non-significant effect of
nitrogen applied. Three genotypes, R-RF-31, Lalmati and R 1033-968-2-1 were identified
as high protein and Fe/Zn containing rice lines. In view of our findings and
previous studies, where significant Gene  Environment (G E)
effect has been reported on grain nutritive traits, molecular markers are of
great use for intensive screening of large populations and identification of
environmentally stable outperforming genotypes. The genomic sequence of
candidate genes governing micronutrient content in rice were, thus, analysed in
silico for identification of novel gene specific markers (SSRs and SNPs)
and expression sequence tags (ESTs and MPSS) to understand putative expression
pattern. Further, to confirm in silico
expression results and functionally characterized Fe and Zn homeostasis related
genes, root and shoot transcriptome analysis of a set of 12 diverse rice
genotypes was carried out for expression of 21 metal homeostasis related genes
belonging to OsYSLs, OsFROs, OsZIPs, OsNRAMPs and OsFERs families, and OsNAAT1,
OsVIT1, OsNAC and OsNAS2 genes. A total of 176 novel SNPs and 39 novel SSRs
were identified within metal related genes, which can be used for developing
gene specific markers. The ESTs and MPSS tag based in silico expression analysis results were in consistency to the
semi-quantitative RT-PCR based transcriptome analysis. Expression profiling of
rice root and shoot transcriptome at maximum tillering and mid-grain filling
stages revealed high level of expression of most of the Fe and Zn uptake and
transport related genes in genotypes showing higher grain Fe and Zn
concentrations. The rice genotypes with high grain protein and micronutrients,
identified in this study, will provide the basis of bioavailability assay and
will also serve as potential genetic material for molecular breeding of
nutrient rich rice. |
| Page(s): | 203-212 |
| ISSN: | 0975-0967 (Online); 0972-5849 (Print) |
| Source: | IJBT Vol.09(2) [April 2010]
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