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Professor Jayashankar Telangana State Agricultural University, Hyderabad (Telangana State)
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ThesisItem Open Access BIOCHEMICAL AND MOLECULAR CHARACTERIZATION OF RICE (Oryza sativa L.) GENOTYPES FOR HIGH IRON AND ZINC LEVELS(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY RAJENDRANAGAR, HYDERABAD, 2010) SRIDEVI, R.N.V.S.; MANORAMA, KRice (Oryza sativa L.) is the most important staple food grain with regard to human nutrition and calorie intake providing more than one-fifth of the calories consumed worldwide by the human beings. Biofortification of staple food crops has thus been considered as a sustainable strategy to overcome the problem of micronutrient deficiencies. The present study was conceptualized and executed with the prime objectives of screening of rice cultivars for micronutrients (iron and zinc) content and identification of SSR (Simple Sequence Repeats) DNA markers closely associated with high micronutrient content in rice cultivars. The powdered brown rice samples were estimated for iron and zinc content by Atomic Absorption Spectrophotometry. Based on the results obtained on iron and zinc contents, the rice varieties were classified under high, medium and low categories for both iron and zinc contents separately. Out of the 54 rice samples used in the study, the iron content of different rice cultivars ranged from 0.95 to 74.75 mg/kg. Six varieties had high iron content ranging from 51.35 to 74.75 mg/kg. Around 21 varieties had medium iron content ranging from 20.15 to 36.55 mg/kg and another 27 varieties had low iron content ranging from 0.95 to 16.35 mg/kg. With respect to zinc content, it was observed that there was not that much variation between varieties as observed for iron content. Out of the 56 rice samples used for the study, the zinc content varied from 9.42 to 27.86 mg/kg. Higher zinc content was observed in 19 varieties, from 20.13 to 27.86 mg/kg. The remaining cultivars had a zinc content ranging from 9.42 to 19.58 mg/kg. A total of twenty-nine SSR markers distributed over five chromosomes of rice were used for PCR amplification for identifying the primers closely associated with genomic regions associated with high micronutrient content. These SSR markers were selected for the study as they are located in the iron and zinc QTL regions on the rice chromosomes. Three high iron content and three low iron content varieties were selected, and, similarly three high zinc content and three low zinc content rice varieties were chosen for amplification of their DNA by PCR using all the twenty-nine SSR markers selected. Out of the twenty-nine markers used, the marker RM 12263 was observed to amplify bands which were polymorphic between the six high and low iron content rice varieties. A band of lower size (around 146 bp with AAG repeat) was amplified in the three high iron content varieties namely MTU-7029, Sumati and MTU-2067 and one low iron content variety, MTU 1001 among the low iron containing varieties. The other two low iron containing varieties, MTU-2077 and NLR-28600 showed a band of a slightly higher size of around 155 bp. This marker RM 12263 was then used for amplification of DNA of all the 54 rice varieties, which were arranged in the decreasing order of iron content. The amplified PCR products of these rice varieties were loaded in this order in the agarose gel to assess whether the polymorphism observed could be attributable to high/low iron contents. A 100 bp ladder was used as the marker. The gel was observed for polymorphism between high and low iron containing varieties. There was no definite trend of polymorphism that could be attributable to high or low iron content in the rice grains to clearly differentiate the rice varieties with high and low iron content and even the variation in band size could not be able to distinguish the rice varieties with either high or low iron contents. None of the other markers used in the present investigation showed any polymorphism between the rice varieties with high and low iron or zinc contents.ThesisItem Open Access BIOCHEMICAL AND MOLECULAR CHARACTERIZATION OF MAIZE ( Zea mays L.) GENOTYPES FOR HIGH IRON CONTENT(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY RAJENDRANAGAR, HYDERABAD, 2010) NAGALAKSHMI, S; MANORAMA, KMaize (Zea mays L.) is one of the food grains with regard to human nutrition and calorie intake, providing more than one-fifth of the calories consumed worldwide by the human species. Biofortification of staple food crops has thus been considered a sustainable strategy to overcome the problem of micronutrient deficiencies. The present study was conceptualized and executed with the prime objective of screening maize genotypes for micronutrient (iron) content and identification of SSR (Simple Sequence Repeats) markers closely associated with high and low micronutrient content in maize genotypes. The powdered yellow maize samples were estimated for iron content by Atomic Absorption Spectrophotometry (AAS). Based on the results obtained on iron content, the maize genotypes were classified under high, medium and low categories. Out of the 14 maize samples used in the study, the iron content of different maize genotypes ranged from 9.81 to 80.47 mg / kg. Four genotypes had high iron content ranging from 42.08 to 80.47 mg / kg. Six genotypes had medium iron content ranging from 22.01 to 26.08 mg / kg and remaining four genotypes had low iron content ranging from 9.81 to 19.85 mg / kg. A total of eighty SSR markers distributed over ten chromosomes of maize were used for PCR amplification for identifying the primers closely linked with genomic regions associated with micronutrient content. Four high and four low iron containing genotypes were selected for amplification with all the eighty SSR primers. Out of the eighty markers used, the markers umc1982, umc1353, umc1008 and umc1349 exhibited polymorphism between the four maize genotypes with high iron content and three genotypes with low iron content. These markers umc1982, umc1353, umc1008 and umc1349 were then used for amplification of DNA of all the fourteen maize genotypes, which were arranged in the decreasing order of iron content in the agarose gel, to assess whether the polymorphism observed could be attributable to high and low iron contents. 50-100 bp DNA ladder were used to determine the size of the bands. The gel was observed for polymorphism between high and low iron containing genotypes. There was a definite trend of polymorphism that could be attributable to high and low iron content in the grains to clearly differentiate the maize genotypes with high and low iron content, using umc1008, which is located on chromosome 4. A 200bp band could be associated with high iron content and a 150bp band could be associated with mediam and low iron content. None of the other markers used in the present investigation showed any polymorphism between the maize genotypes with high and low iron content.ThesisItem Open Access TAGGING OF GENE FOR RESISTANCE TO POST FLOWERING STALK ROT IN MAIZE(Zea mays) CAUSED BY Macrophomina phaseolina(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY RAJENDRANAGAR, HYDERABAD, 2010) SUNEETHA, P; ANURADHA, GMaize is one of the most important economic cereal crops and an ideal forage crop. It occupies a prominent position in global agriculture. 67% of maize is used for live stock feed and 25% of maize for human consumption, industrial purposes and the balance is used as seed.The productivity of maize is influenced by both biotic and abiotic factors. Maize suffers from about 110 diseases on a global basis. In India there are four downy mildews, four stalk rots, three foliar diseases, root rots and other diseases affecting kernel and other aerial parts. Disease spectrum varies in different agro climatic zones. More serious diseases are leaf blight, stalk rots, downy mildews and rusts. Stalk rots take a heavy toll, among which stalk rots caused by Macrophomina phaseolina (Tassi) Goid and Fusarium moniliformae results in 30-40% losses. Post flowering stalk rot (PFSR) is the complex disease caused by three fungi,viz., Cephalosporium acremonium, Macrophomina phaseolina, Fusarium moniliformae and one bacterium Erwinia carotovora var zeae. Out of these, post flowering stalk rot caused by Macrophomina phaseolina is the important disease of maize in the state of Andhra Pradesh. Author : P.SUNEETHA Title of the thesis : “TAGGING OF GENE FOR RESISTANCE TO POST FLOWERING STALK ROT IN MAIZE(Zea mays) CAUSED BY Macrophomina phaseolina” Degree to which it is submitted : MASTER OF SCIENCE IN AGRICULTURE Faculty : AGRICULTURE Department : AGRICULTURAL BIOTECHNOLOGY Major Advisor : Dr. G.ANURADHA Principal Scientist (Breeding) Biotechnology Unit Agricultural Research Institute Rajendranagar, Hyderabad – 30. University : ACHARYA N. G. RANGA AGRICULTURAL UNIVERSITY Year of submission : 2010 In order to tag the post flowering stalk rot resistant gene maize inbred lines BPPTI-34 (resistant) and BPPTI -66(Susceptible), were crossed to produce F1. F1’s were selfed as well as back crossed to the susceptible parent to derive F2 and BC1F1 populations respectively. Parents P1 and P2, F1 and two mapping populations F2 and BC1F1 were artificially inoculated with the Macrophomina phaseolina culture. F1s inoculated with the culture showed resistant reaction revealing for that resistance for post flowering stalk rot is governed by dominant gene. F2 population segregated in 3:1 ratio i.e 87 resistant: 27 susceptible and BC1F1 population segregated in the ratio of 1:1 i.e 26 resistant: 24 susceptible showing that resistance to post flowering stalk rot is governed by single dominant gene. A total of 150 microsatellite markers distributed on entire genome were used to screen the parents. Of these, 54 SSR markers from ten chromosomes were found polymorphic in the parents. These fifty four markers were used to screen the bulk DNAs prepared from 10 plants each of resistant and susceptible plants from F2 and BC1F1 populations to find the markers linked to the resistance gene. By bulked segregant analysis (BSA) the marker umc 1269 clearly distinguished resistant and susceptible bulks as that of resistant and susceptible parents indicating that this marker is tightly linked to the gene for resistance to post flowering stalk rot.ThesisItem Open Access IMPACT OF BIOFERTILIZERS ON NUTRIENT CONTENT AND ANTIOXIDANT ACTIVITY OF AMARANTHUS(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) RAVI SHANTHI KUMARI, A; SUMATHI, SAmaranth greens, are common leafy vegetables available throughout the tropics and in many warm temperate regions. It is remarkably rich in vitamin C, iron, calcium and folate. However, there is very little information on the use of biofertilizers and organic manures alone or in combination with chemical fertilizers on Amaranthus yield and quality. Thus this study is desgined to evaluate the impact of biofertilizers on nutrient content and antioxidant activity of Amaranthus. The experiment was conducted in complete randomized design with 12 treatments and three replications. Vermicompost, chemical fertilizers and biofertilizers were applied to the soil according to the treatments imposed. Amaranthus seeds were sown in poly bags with different treatments. The crop was harvested at 30 days (first picking), 45 days (second picking), 60 days (third picking) DAS. At each picking, yield was noted. Fresh leaf samples were used for estimation of vitamin C content and total carotene content. Dry powdered leaf samples were used for estimation of total antioxidant activity, total phenols and mineral content. The physico-chemical properties of soil and microbial population of soil was estimated before sowing and after harvesting of crop. The shelf life was assessed after harvesting at room temperature and refrigeration temperature. There were significant differences in yield, vitamin C content, carotene content, minerals, phenols and antioxidant activity of Amaranthus. Among treatments significantly higher yield was recorded with the application of 50% RDF+NBF+PSBF. Total dry weight differed significantly among the treatments at all stages. Higher total dry weight was recorded with the application of 50 % RDF+NBF+PSBF. The quality parameters viz., vitamin C content, carotene content, minerals, phenols and antioxidant activity were significantly higher with the application of 50% RDF+NBF+PSBF. The shelf life of Amaranthus was significantly better with the application of 50% RDF+NBF+PSBF and the lowest shelf life was recorded in 100% RDF. The results from this study demonstrated that yield and quality parameters will be improved by combined application of chemical fertilizers and biofertilizersThesisItem Open Access MOLECULAR TAGGING OF GENE FOR BPH RESISTANCE IN RICE (Oryza sativa L.) cv. BM71(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) SREEVANI, B; BALRAM, MRice is cultivated in more than 100 countries around the globe and its significance as food crop is ever increasing as the world population continues to explode. Insects are a serious threat to cereal crops and cause significant damage to crop production annually. Rice crop is host to a large number of insects that feed on rice. Of the six kinds of planthoppers, brown planthopper (BPH; Nilaparvata lugens Stål) (Homoptera: Delphacidae) is the most damaging insect pest of rice in Asia. Earlier studies documented tremendous genetic variation for BPH resistance existing in rice germplasm. Knowledge on the molecular markers linked to genomic regions associated with BPH resistance to enable marker assisted selection in breeding programmes. In this study, an attempt was made to trace BPH resistance loci from BM 71, a derivative of MTU4569/ARC6650//Bunnan///IR64, a medium duration, high yielding culture resistant to BPH using simple sequence repeat (SSR) markers. MTU 3626, a semi dwarf, medium duration, high tillering, coarse grain, high yielding variety susceptible for BPH developed from the cross IR8/MTU3 was crossed to BM71 to produce F2:3 population. A total of 170 F2:3 population were used for screening against BPH using Standard Seed Box method. The parents, BM 71 showed moderate resistance (damage rating of 3.3) to BPH when MTU 3626 showed complete susceptibility (damage rating of 9). The damage rating of F2:3 population ranged from 2.69 to 9.0 with an average of 6.36. Genetics of BPH resistance in the cross MTU 3626/ BM 71 did not show Mendelian segregation. Quantitative and transgressive nature of BPH resistance was observed in the F2:3 segregating population. Parental polymorphism survey was conducted between the parents MTU 3626 and BM 71. A total 235 markers were tested, of which, 46 (19.57%) of the markers showed polymorphism. Bulked segregant analysis using phenotypic extremes was carried out by using 46 polymorphic SSR primer pairs in bulks (resistant and susceptible) made based on F2:3 phenotypic extremes. Out of 46 polymorphic primer pairs, 2 primer pairs i.e., RM 19660 (chromosome 6) and RM 20037 (chromosome 6) were polymorphic in bulks. Single marker analysis was done by using genotypic and phenotypic data of entire population and found that the markers RM 19660 and RM 20037 were significantly associated with BPH resistance at <0.01 probability and contributing 40.1 % and 25.7% of total phenotypic variation. Linkage analysis of two polymorphic marker data showed significant linkage between RM19660 and RM20037 at <0.001 probability and the distance between markers was 28.5 cM. In simple interval mapping, the threshold LOD for BPH resistance at 0.05 and 0.01 levels are 8.28 and 11.78 respectively. Simple interval mapping has identified a major QTL between RM 19660 and RM 20037 with a LOD value of 54.39 at a peak position 15 cM distance. The QTL is placed at 12 cM away from left side of RM19660 and 11cM away from right side of RM20037. This QTL has explained 32% of total phenotypic variation with additive and dominance variance of 1.33 and 1.75 respectively. Overall results of the study suggested the possibility of a genetic locus on chromosome 6 significantly associated with BPH resistance in the mapping population of the cross MTU 3626/ BM 71. Fine mapping of the genomic region influencing BPH resistance in the present study may be taken up by developing RILs for identification of closely linked markers which can be used in Marker Assisted Breeding programmesThesisItem Open Access IDENTIFICATION OF MOLECULAR MARKERS FOR GENOMIC REGIONS ASSOCIATED WITH HIGH IRON AND ZINC CONCENTRATION IN RICE GRAINS(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) ROJA, V; SARLA, NRice (Oryza sativa L.) is a widely adapted cereal crop grown almost throughout the world. Rice is the most important staple food grain with regard to human nutrition and calorie intake providing more than one-fifth of the calories consumed worldwide. Biofortification of staple food crops has been considered a sustainable strategy to overcome the problem of micronutrient deficiencies. The present study was carried out at Directorate of Rice Research (DRR), Rajendranagar using an advanced back cross population derived from four consecutive back crosses of a recipient parent Samba Mahsuri (BPT 5204), an elite indica cultivar and common wild rice Oryza rufipogon with the prime objective of screening brown rice for micronutrient (iron, zinc) concentration and identification of SSR (Simple Sequence Repeats) DNA markers closely linked with high micronutrient content. 128 BC4F4 lines were estimated for iron and zinc concentration using atomic absorption spectrophotometry. The iron and zinc concentration of 128 rice lines ranged from 6.4 to 106.6 μg g-1 and 15.5 to 52.05 μg g-1, respectively. The top ten lines showed iron and zinc ranging from 24 to 106.6 μg g-1 and 31.5 to 52 μg g-1, respectively. In most of the lines, iron ranged between 13-24 μg g-1 and zinc ranged from 26 to30 μg g-1. Interestingly, the top five high iron lines showed high zinc also but the reverse was not true. Grain Fe and Zn contents exhibited non-significant association among themselves and also with other grain traits. Parental polymorphism survey was conducted to identify the polymorphic markers between the parents. Out of 188 rice micro satellite markers 51 (27 %) were polymorphic and among 36 gene specific markers 3 (8%) were polymorphic. Out of 128 lines only 5.2 % plants were homozygous for O. rufipogon alleles and 9.5 % were heterozygous. Introgression from O. rufipogon ranged from 0 % to 66.7 % with an overall mean introgression of 14.7 %. Highest introgression (%) was observed in line no. 6 (66.7 %). The percentage introgression for the locus RM279 on chromosome 2 was 47 %, while the percentage of introgression of the gene specific primer ZIPRM5511 was 14.8 % in the mapping population. The marker RM5699 on chromosome 2 was linked to iron concentration in brown rice and RM448 on chromosome 3 was linked to zinc concentration in brown rice. Earlier studies on the linkage analysis showed that these two markers were linked to important agronomic traits such as yield, biomass, heading dates, harvest index, panicle characteristics and also to the salt and salinity tolerance in rice. This study demonstrated that introgressions of the O. rufipogon alleles can increase the Fe and Zn concentration in brown rice of indica cultivar Samba Mahsuri significantly. This is an acceptable non-transgenic way of increasing iron and zinc concentration in brown rice.ThesisItem Open Access CONFIRMATION AND FINE MAPPING OF MAJOR QTL FOR GRAIN SIZE IN BASMATI RICE(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) ANNE KITTY DEBORAH, D; ANURADHA, GBasmati rice is a unique varietal group that has gained wider acceptance as a speciality rice all over the world by virtue of its unique quality traits. Grain size plays a crucial role in determining the grain quality in Basmati rice. Genetic control of basmati grain quality traits is quite complex, but breeding of new varieties having Basmati grain quality characters can be greatly facilitated by the use of molecular markers tightly linked to these traits. Hence, in the present investigation 155 recombinant inbred lines (RILs) developed from a cross between Basmati370 and Jaya were used for confirmation and fine mapping of a major QTL for grain size in Basmati rice using SSR markers derived from inside and near the genomic region associated with grain size in the marker interval of RM289 and RM18600 on chromosome 5, that was already identified by Vemireddy (2008) using F2 population developed from the same cross. The parents used for mapping, Basmati370 and Jaya differed significantly with respect to all the three traits viz., grain length (GL), grain breadth (GB) and Length- Breadth ratio (LBR). Transgressive segregation of 45.8 % in grain length, 21.93 % in grain breadth and 12.25 % in LB ratio was observed in the RILs. All the three traits exhibited normal distribution in the RIL population indicating quantitative inheritance of these traits. Correlation analysis among the grain characters studied in RILs revealed a highly significant negative association of LB ratio with grain breadth and significant positive correlation with grain length. Out of 52 SSR and 1 INDEL markers used, 23 (43.40 %) were polymorphic, 27 (39.62 %) were monomorphic and 9 (16.98 %) were not amplified between Basmati370 and Jaya. The RILs were genotyped for these 23 polymorphic markers and the linkage map employing phenotypic and genotypic data of the RILs was constructed using MAPMAKER v 3.0. The QTLs were identified using interval mapping (IM) and composite interval mapping (CIM) methods of QTL Cartographer v 2.5 software with 2.5 as LOD threshold for detecting a QTL. A minor QTL for grain length qGL5.1 was identified by IM in the marker interval of RM6024 and RM1237 with Phenotypic Variance (PVE) of 3.7 %. A single QTL designated as qGB5.1 was detected for grain MAPMAKER v 3.0. The QTLs were identified using interval mapping (IM) and composite interval mapping (CIM) methods of QTL Cartographer v 2.5 software with 2.5 as LOD threshold for detecting a QTL. A minor QTL for grain length qGL5.1 was identified by IM in the marker interval of RM6024 and RM1237 with Phenotypic Variance (PVE) of 3.7 %. A single QTL designated as qGB5.1 was detected for grain breadth in the marker interval of RM1237 and RM18582 with PVE of 3.58 % in CIM and 4.51 % in IM and a QTL qGLB5.1 for Length- Breadth Ratio was identified with PVE of 11.8 %. The genetic distance of the flanking markers harbouring QTL cluster in the previous study conducted by Vemireddy (2008) was 26.5 cM whereas in the present study it was narrowed down to 15.7 cM. The physical distance also has come down from 11,128 kb to 685 kb. Comparision of rice genome database revealed that LOC_OS05g31920 (zinc ion binding protein), LOC_OS05g31930 (retrotransposon protein, putative, unclassified), LOC_OS05g31940 (retrotransposon protein, putative, unclassified), LOC_OS05g31950 (retrotransposon protein, putative, Ty3-gypsy subclass), LOC_OS05g31959 (hypothetical protein) and LOC_OS05g31970 (expressed protein) genes are present at this region. Interestingly, two predicted genes closure to this region viz., AP2 transcription factor and RING E3 ligase were reported to be involved in controlling the seed size and weight by earlier studies. In the present study, one microsatellite marker i.e., RM18582 showed close association with the grain size QTLs. This marker has potential to be used in markerassisted improvement of the grain size in Basmati rice. Though the present study was carried out in single environment, together with the results of F2 population of the same cross, it could be concluded that these three QTLs associated with grain size traits of Basmati could be considered as stable QTLs. These QTLs, apart from their suitability in improvement of the traits concerned, can also serve as potential candidates for fine mapping. These stable QTLs also facilitate development of Near‐isogenic lines and advanced breeding lines.ThesisItem Open Access MARKER ASSISTED BREEDING (MAB) FOR SHOOT FLY TOLERANCE IN SORGHUM (Sorghum bicolor (L.) Moench(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) LAKSHMIDEVI, G; JANILA, PThe yield potential of NTJ 2, a popular rabi season sorghum variety of Andhra Pradesh can be enhanced by improving it for shoot fly resistance. This can be achieved through introgression of a QTL on SBI 05 governing leaf glossiness from the donor, J 2779-P4, obtained from ICRISAT using marker assisted backcrossing (MABC). In the present study, foreground and background markers were identified, F1 plants (of the cross, NTJ 2 X J 2779-P 4) were confirmed for hybridity using markers, and 12 F2 plants that are homozygote’s for the target QTL were selected. Thus, the results from this study have set a stage for the proposed MABC program. A set of 17 and 170 SSR primer pairs were evaluated in the parents for identification of foreground and background markers, respectively. Five foreground markers for the target QTL and 35 background markers that distinguish the genome of recipient and donor parent were polymorphic. These polymorphic markers can be used in the MABC. The background markers were distributed on all the 10 chromosomes. The F1 plants derived from the cross, NTJ 2 x J 2779-P4 were confirmed for hybridity using five foreground markers and the confirmed F1 plants were both selfed and backcrossed to NJT 2. A total of 12 plants, homozygotes for the target QTL were selected among 83 F2 plants using the identified foreground markers. The F2 plants were selected, if only all foreground markers tested amplified the donor type alleles (B-type). Further phenotypic selection of these 12 F2 plants is under progress to identify the segregants that are close to NTJ 2 phenotype; they will be advanced to derive both, F3 progenies by selfing and BC1F1 generation by backcrossing to NJT 2.ThesisItem Open Access PARENTAL POLYMORPHISM SURVEY BETWEEN DONOR RICE LINES WITH BIOTIC STRESS RESISTANCE GENES AND ELITE RECIPIENT VARIETIES USING SSR MARKERS(ACHARYA N.G. RANGA AGRICULTURAL UNIVERSITY, 2011) KISHORE KUMAR, Y; SUNDARAM, R. MThe present investigation entitled “Parental polymorphism survey between donor rice lines with biotic stress resistance genes and elite recipient varieties using SSR markers” was undertaken with the objectives to study the polymorphism existing between biotic stress Brown Plant Hopper, Gall midge, Bacterial Leaf Blight, Blast resistant donor parents and recipient elite varieties by screening with 150 Hyper variable SSR markers and to find markers which are showing high polymorphism for their use in background selection of recurrent parents. The study also attempted to compare the genetic relatedness among the donor and elite recipient parents. A total of 150 Hypervariable SSR markers were analyzed with sixteen parental lines and of which 105 markers showed polymorphism. Among 105 markers, 85 markers are polymorphic to some of the genotypes and 20 markers are highly polymorphic to all the genotypes. The markers HRM 10167, HRM11111, HRM11570, HRM12469, HRM14250, HRM15727, HRM16649, HRM400, HRM19697, HRM5720, HRM6697, HRM6699, HRM22977, HRM23146, HRM24217, HRM25796, HRM26086, HRM26213, HRM28157, HRM28580 were observed to be highly polymorphic. The target chromosomes where the resistance genes are located in donor rice genotypes are chromosome 6, 7, 8, 9, 11, 12. Of the 20 polymorphic markers, 12 markers were lying on target chromosomes. These include HRM400 and HRM19697 on chromosome 6, HRM5720 and HRM6697 on chromosome 7, HRM6699, HRM22977 and HRM23146 on chromosome 8, HRM24217 on chromosome 9, HRM26086 and HRM26213 on chromosome 11, HRM28157 and HRM28580 on chromosome12. The data obtained from SSR markers were utilized for calculation of Jaccard’s similarity co-efficient using UPGMA cluster analysis. The similarity co-efficient ranged from 0.15 to 1 and genotypes were grouped into two major clusters. The Polymorphic information Content (PIC) values of 20 polymorphic primers ranged from 0.33 to 0.75 with a mean PIC value of 0.551 and it is considered informative for genetic studies and the polymorphism shown by the markers can be used for background selection of the recurrent parents.