Browsing by Author "SHILPA, H. B."
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ThesisItem Open Access IN SILICO DEVELOPMENT OF CONSERVED INTRON SCANNING PRIMERS (CISPs) FOR THE DETECTION OF SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) IN PIGEONPEA (Cajanus cajan L.)(University of Agricultural Sciences GKVK, Bangalore, 2010-07-25) SHILPA, H. B.; LOHITHASWA, H. C.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.ThesisItem Open Access MARKER-ASSISTED BREEDING FOR TOLERANCE TO BIOTYPE-4 OF BROWN PLANTHOPPER (Nilaparvata lugens Stal.) AND MANDYA ISOLATE OF BLAST (Magnaporthe grisea Hebert.) IN RICE (Oryza sativa L.)(University of Agricultural Sciences GKVK, Bangalore, 2014-11-10) SHILPA, H. B.; Shivakumar, N.The present investigation was carried out to transfer major resistance gene Pil conferring resistance to blast (Magnaporthe grisea L.) and bph4 for brown planthopper (BPH, Nilaparvata lugens Stal.) in the genetic background of rice cultivar Jaya through marker-assisted backcross breeding at Zonal Agricultural Research Station, V. C. Farm, Mandya from 2011-2014. The donors ClOlLAC for blast and CR271 l -76 for BPH resistance were crossed with Jaya and the F 1s derived were identified through polymorphic markers. Selected F 1 s were backcrossed with Jaya to raise BC1 F 1, BC2F 1, BC3F1 (separate transfer crosses i. e., Jaya x ClOlLAC and Jaya x CR2711-76) and intercrossed to obtain TC-F2s [(Jaya x ClOlLAC) X (Jaya x CR2711-76)]. The BC 1 F 1s were also selfed to develop segregating BC 1F2 populations. Marker analysis of 101 BC 1F2 plants from (Jaya x ClOlLAC) X Jaya cross, using RM224 marker yielded 32 plants having Pil gene while, from 112 BC 1 F2 plants of (Jaya x CR2711-76) X Jaya cross evaluated, using RM586 and RM589 markers for bph4 gene, 57 plants were found to be homozygous. Out of 111 TC-F2s, 30 plants selected genotypically and 33 phenotypically, had Pil gene. Thirty three pyramided progenies with Pil and 44 with bph4 gene were identified after genotypic and phenotypic evaluation of BC 1 F2s. Totally ten plants having both Pil and bph4 genes were selected. Among them, eight have showed better grain yield/plant (-21.08 g) compared to Jaya (13 g). Plant number 13, 14, 24, 31, 49, 86 and 109 were early to flower (89-99 days) compared to Jaya (11 Odays ). They recorded higher number of filled grains/panicle (58.2-101.67) and spikelet fertility (55.68-64.38%) as compared to Jaya (51.8 and 24.98%). Among the three markers validated, RM224 for blast and RM586 for BPH showed significant association with the pyramided genes.