IN SILICO DEVELOPMENT OF CONSERVED INTRON SCANNING PRIMERS (CISPs) FOR THE DETECTION OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) IN PIGEONPEA (Cajanus cajan L.)
| dc.contributor.advisor | LOHITHASWA, H. C. | |
| dc.contributor.author | SHILPA, H. B. | |
| dc.date.accessioned | 2017-06-16T08:34:39Z | |
| dc.date.available | 2017-06-16T08:34:39Z | |
| dc.date.issued | 2010-07-25 | |
| dc.description.abstract | Pigeonpea (Cajanus cajan. L), a member of fabaceae is a nutritious tropical and subtropical crop. It is often considered as an ‘orphan crop’ due to limited resources for genome characterization. With the availability of complete genome sequence information of Medicago truncatula, Conserved Intron Scanning Primer (CISP) approach was used for targeted discovery of functional and anonymous Single Nucleotide Polymorphisms (SNPs) in pigeonpea. A total of 307 candidate Cajanus-Medicago CISPs were developed by BLAST aligning 10,000 pigeonpea ESTs downloaded from NCBI database, with the Medicago genome. Random 192 CISPs representing loci distributed over eight chromosomes of Medicago were tested on ten members of legume family. Total amplification of CISP loci was ranged from 70.83% (Urdbean, TAU 1) to 96.88% (Medicago, EC 547749). Very low and high rate of single copy amplification was observed in groundnut (TMV 2, 25.52 %) and Medicago (EC 547749, 75.52%). The study demonstrated the success of cross taxon primers such as CISPs suggesting their potential use in comparative legume genomics. Among 192 CISPs, selected 118 primers which produced prominent single copy amplification in BRG 2 were used to genotype other varieties of pigeonpea. Out of 118 CISPs, 96.61 % of amplification was observed in ICP 7035, BRG 1and GS 1, where as 98.30 % amplification was observed in BRG3. With respect to single copy amplification among the selected pigeonpea genotypes, the success rate of 77.97% (ICP 7035) – 83.89% (BRG 3, ICPL 87119) was observed. Sequencing of single copy amplicons from 36 CISPs produced across 8 pigeonpea varieties revealed 42 SNPs and 7 INDELs. We designed 16 SNAP primer pairs corresponding to 8 SNP sites using Web SNAPER (http://ausubellab.mgh.harvard.edu/). Development of more CISPs are required for molecular genetic diversity study in pigeonpea. | en_US |
| dc.identifier.other | Th-9642 | |
| dc.identifier.uri | http://krishikosh.egranth.ac.in/handle/1/5810020909 | |
| dc.language.iso | en | en_US |
| dc.pages | 142 | en_US |
| dc.publisher | University of Agricultural Sciences GKVK, Bangalore | en_US |
| dc.sub | Genetics and Plant Breeding | en_US |
| dc.subject | null | en_US |
| dc.theme | IN SILICO DEVELOPMENT OF CONSERVED INTRON SCANNING PRIMERS | en_US |
| dc.these.type | M.Sc | en_US |
| dc.title | IN SILICO DEVELOPMENT OF CONSERVED INTRON SCANNING PRIMERS (CISPs) FOR THE DETECTION OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) IN PIGEONPEA (Cajanus cajan L.) | en_US |
| dc.type | Thesis | en_US |