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Yemane Girma,Dadakhalandar Doddamani,Rajkumar,Sadik Ahmed Wasik Ahmed,Sheweta Gujar,Suvarna Patil,Gurusiddesh Hiremath,Bashasab Fakrudin 한국작물학회 2014 Journal of crop science and biotechnology Vol.17 No.3
Single Nucleotide Polymorphisms (SNPs) are the commonest type of nucleotide variation distributed throughout thegenome and have enormous potential to saturate genetic maps. However, their identification is constrained by the huge investmentrequired for their detection. In this study, we used publicly available EST (Expressed Sequence Tag) sequences to identifySNPs in Sorghum bicolor. A total of 12,421 putative SNPs were identified from 2,921 contiguous transcripts leading to anaverage SNP interval of one putative SNP for every 275.26 bp. The proportion of transition type mutations (0.598) was largerthan transversion types conforming to biological expectations. In order to demonstrate the utility of the SNPs for developmentof markers with relatively cheap assays, we experimentally validated SNPs using Single Strand Conformation Polymorphism(SSCP) technique in sorghum accessions, which are used as parents for development mapping populations. Genotyping theseparents of mapping populations with SSCP markers showed up to 33% polymorphism in the markers suggesting that the SNPscan be used as potential resource for S. bicolor crop improvement programs
Nagaraja Deeplanaik,Krishna Venkatarangaiah,Ramesh Chapeyil Kumaran,Santosh Kumar Hulikal Shivashankar,Dadakhalandar Doddamani,Sandeep Telkar 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.4
Pigeonpea, a drought tolerant, semi-arid pulse crop has been investigated for the expression of differentially expressed genes(DEGs) under drought stress. The cDNA library of soybean leaf tissue retrieved from the Unigene database of the NCBI, were comparedfor in silico expression using IDEG6 web statistical tool. A list of 52 non-redundant DEGs consisting of 11 up-regulated and41 down-regulated was obtained. Among these, more photosynthesis and light harvesting proteins were down-regulated in droughtstress conditions. Pathways were assigned based on KEGG database, revealing 32 genes involved in 17 metabolic pathways. Homologous sequences of six up-regulated genes namely, ADF3, APB, ASR, DLP, LTP1, and UGE5 were then used for quantitativereverse transcription PCR (qRT-PCR) in pigeonpea. The qRT-PCR result revealed the significant up-regulation of dehydrin-like protein(DLP) (5.02 log2 fold) and down-regulation of acid phosphatase class B family protein (APB) (9.43 log2 fold) and non-specificlipid transfer protein 1-like (LTP1) (18.81 log2 fold) in pigeonpea water-stressed leaf sample compared to well-watered leaf samples. No significant difference was observed in the stressed root compared to the stressed pigeonpea leaf sample except that APB showedan up-regulation of 11.35 log2 fold change
Deeplanaik, Nagaraja,Kumaran, Ramesh Chapeyil,Venkatarangaiah, Krishna,Shivashankar, Santosh Kumar Hulikal,Doddamani, Dadakhalandar,Telkar, Sandeep 한국작물학회 2013 Journal of crop science and biotechnology Vol.16 No.4
Pigeonpea, a drought tolerant, semi-arid pulse crop has been investigated for the expression of differentially expressed genes (DEGs) under drought stress. The cDNA library of soybean leaf tissue retrieved from the Unigene database of the NCBI, were compared for in silico expression using IDEG6 web statistical tool. A list of 52 non-redundant DEGs consisting of 11 up-regulated and 41 down-regulated was obtained. Among these, more photosynthesis and light harvesting proteins were down-regulated in drought stress conditions. Pathways were assigned based on KEGG database, revealing 32 genes involved in 17 metabolic pathways. Homologous sequences of six up-regulated genes namely, ADF3, APB, ASR, DLP, LTP1, and UGE5 were then used for quantitative reverse transcription PCR (qRT-PCR) in pigeonpea. The qRT-PCR result revealed the significant up-regulation of dehydrin-like protein (DLP) (5.02 log2 fold) and down-regulation of acid phosphatase class B family protein (APB) (9.43 log2 fold) and non-specific lipid transfer protein 1-like (LTP1) (18.81 log2 fold) in pigeonpea water-stressed leaf sample compared to well-watered leaf samples. No significant difference was observed in the stressed root compared to the stressed pigeonpea leaf sample except that APB showed an up-regulation of 11.35 log2 fold change.