Linkage disequilibrium among modern sugarcane cultivars

Modern sugarcane cultivars are derived from a few interspecific hybrids created early in this century. Linkage disequilibrium was investigated in a population of 59 cultivars representing the most important commercial clones bred in Mauritius as well as a few old cultivars involved in their genealogy. Thirty-eight probes scattered over the sugarcane genome map were used to reveal RFLPs. Forty-two cases of bilocus associations were observed involving a total of 33 loci. Most of them are separated by less than 10 cM. All the corresponding allele couples were found in at least 1 of the originally created cultivars, suggesting that they depict ancient associations. This global disequilibrium is interpreted as the result of the foundation bottleneck related to the first interspecific crosses; the preferential allele associations thus created have been maintained through subsequent crosses when the loci were closely linked. This phenomenon is likely also to apply to genes of agricultural interest. A practical consequence is that markers can be used to track known QTLs in modern breeding materials without the necessity to repeatedly study segregating progenies. This structure gives high value to the correlation between molecular markers and agricultural traits among cultivars. Received: 6 March 1999 / Accepted: 25 March 1999     

Evaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP markers

 Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity. Genetic variability was estimated with 18 primers and 43 RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins. The majority of the RFLP probes issued from low-copy DNA sequences. On the basis of on the genetic distance matrices, the two molecular methods gave related estimates of the genetic relationship between genotypes. Although an influence of cocoa morphological groups and geographical origins of trees was observed, a lack of gene differentiation characterized the T. cacao accessions studied. The continuous RFLP variability observed within the species may reflect the hybridization and introgressions between trees of different origins. Nevertheless, the Nacional type was detected to be genetically specific and different from well-known types such as Forastero, Criollo and Trinitario. Some of those genotypes were characterized by a low heterozygosity rate and may constitute the original Nacional pool. These results also provide information for the constitution of a cocoa tree core collection. Received: 10 June 1996/Accepted: 11 October 1996     

A bacterial artificial chromosome library for sugarcane

Modern cultivated sugarcane is a complex aneuploid polyploid with an estimated genome size of 3000 Mb. Although most traits in sugarcane show complex inheritance, a rust locus showing monogenic inheritance has been documented. In order to facilitate cloning of the rust locus, we have constructed a bacterial artificial chromosome (BAC) library for the cultivar R570. The library contains 103,296 clones providing 4.5 sugarcane genome equivalents. A random sampling of 240 clones indicated an average insert size of 130 kb allowing a 98% probability of recovering any specific sequence of interest. High-density filters were gridded robotically using a Genetix Q-BOT in a 4 × 4 double-spotted array on 22.5-cm² filters. Each set of five filters provides a genome coverage of 4x with 18,432 clones represented per filter. Screening of the library with three different barley chloroplast gene probes indicated an exceptionally low chloroplast DNA content of less than 1%. To demonstrate the library’s potential for map-based cloning, single-copy RFLP sugarcane mapping probes anchored to nine different linkage groups and three different gene probes were used to screen the library. The number of positive hybridization signals resulting from each probe ranged from 8 to 60. After determining addresses of the signals, clones were evaluated for insert size and HindIII-fingerprinted. The fingerprints were then used to determine clone relationships and assemble contigs. For comparison with other monocot genomes, sugarcane RFLP probes were also used to screen a Sorghum bicolor BAC library and two rice BAC libraries. The rice and sorghum BAC clones were characterized for insert size and fingerprinted, and the results compared to sugarcane. The library was screened with a rust resistance RFLP marker and candidate BAC clones were subjected to RFLP fragment matching to identify those corresponding to the same genomic region as the rust gene. Received: 12 September 1998 / Accepted: 12 March 1999     

Application of synteny across Poaceae to determine the map location of a sugarcane rust resistance gene

A major rust resistance gene has been identified in a self-progeny of the sugarcane cultivar R570. Until now, this gene was known to be linked to a marker revealed by the sugarcane probe CDSR29 but unassigned to any linkage group of the current genetic map. We used synteny relationships between sugarcane and three other grasses in an attempt to saturate the region around this rust resistance gene. Comparison of sugarcane, sorghum, maize and rice genetic maps led to the identification of homoeologous chromosome segments at the extremity of sorghum linkage group D, rice linkage group 2, maize linkage group 4 and in the centromeric region of maize linkage group 5. One hundred and eighty-four heterologous probes were selected and tested for cross-hybridization with sugarcane DNA; 106 produced a good hybridization signal and were hybridized on 88 individuals of the R570 selfed progeny. Two hundred and seventeen single-dose markers were added to the R570 genetic map, of which 66% mapped to linkage group VII, together with the rust resistance gene. This gene has now been mapped to the end of a co-segregating group consisting of 19 RFLP markers. None of the mapped loci were located closer to the gene than CDSR29. The gene thus appears to reside at the edge of a ’’synteny cluster’’ used to describe the different grass genomes. Received: 12 January 2000 / Accepted: 21 March 2000     

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid

 A sorghum composite linkage map was constructed with two recombinant inbred line populations using heterologous probes already mapped on maize and sugarcane. This map includes 199 loci revealed by 188 probes and distributed on 13 linkage groups. A comparison based on 84 common probes was performed between the sorghum composite map and a map of a sugarcane (Saccharum spp.) cultivar being developed and presently comprising 10 tentative linkage groups. A straight synteny was observed for 2 pairs of linkage groups; in two cases, 1 sorghum linkage group corresponded to 2 or 3 sugarcane linkage groups, respectively; in two cases 1 sugarcane link- age group corresponded to 2 separate sorghum linkage groups; for 2 sorghum linkage groups, no complete correspondance was found in the sugarcane genome. In most cases loci appeared to be colinear between homoeologous chromosomal segments in sorghum and sugarcane. These results are discussed in relation to published data on sorghum genomic maps, with specific reference to the genetic organization of sugarcane cultivars, and they, illustrate how investigations on relatively simple diploid genomes as sorghum will facilitate the mapping of related polyploid species such as sugarcane. Received: 12 August 1996 / Accepted: 30 August 1996     

Molecular diversity in pineapple assessed by RFLP markers

Pineapple, Ananas comosus (L.) Merr, is the third most important tropical fruit cultivated in all tropical and subtropical countries. Pineapple germplasm includes all seven species of the genus Ananas and the unique species of the related genus Pseudananas. A knowledge of its diversity structure is needed to develop new breeding programs. Restriction fragment length polymorphism (RFLP) was used to study molecular diversity in a set of 301 accessions, most of which were recently collected. This sample was analysed using 18 homologous genomic probes. Dissimilarities were calculated by a Dice index and submitted to Factorial Analysis. The same data were represented as a diversity tree constructed with the score method. Pseudananas sagenarius displayed a high polymorphism and shares 58.7% of its bands with Ananas. Within Ananas, variation appears continuous and was found mostly at the intraspecific level, particularly in the wild species Ananas ananassoides and Ananas parguazensis. As for the cultivated species, Ananas comosus appears relatively homogeneous despite its wide morphological variation and Ananas bracteatus, which is grown as a fence and for fruit, appears still much less variable. By contrast Ananas lucidus, cultivated by the Amerindians for fiber, displays a high polymorphism. This tree displayed a loose assemblage of numerous clusters separated by short distances. Most species were scattered in various clusters, a few of these being monospecific. Some accessions which had not been classified, as they shared morphological traits typical of different species, re-group with one or the other, and sometimes with both species in mixed clusters. No reproductive barrier exists in this germplasm and these data indicate the existence of gene flow, enhancing the role of effective sexual reproduction in a species with largely predominant vegetative mutiplication. Received: 8 March 2000 / Accepted: 14 April 2000     

Molecular analysis of plants regenerated from embryogenic cultures of hybrid sugarcane cultivars (Saccharum spp.)

Summary The genomic stability of tissue culture regenerants of sugarcane (Saccharum spp. hybrids, cvs CP721210, CP68-1067 and B43-62) was analyzed by DNA restriction fragment length polymorphism (RFLP). Plants regenerated from calli, cell suspensions, cryopreserved cell suspensions and protoplasts were used. Total DNA isolated from 19 different sources was digested with EcoRI, HindIII, BamHI, BamHI, EcoRI and PstI and probed with six known maize mitochondrial genes (coxI, coxII, atpA, atp6, atp9 and rrn18-rrn5), three random maize mitochondrial cosmid clones, two random maize chloroplast cosmid clones and a wheat Nor locus clone. Hybridization patterns indicated that the variation observed was minor and appeared only in the secondcycle regenerants. No differences were observed among the three cultivars and the regenerants from calli, suspension culture, cryopreserved suspension culture and protoplasts. Mitochondrial DNA (mtDNA) isolated from CP72-1210 plants and its embryogenic cell suspensions, and bulk samples from all CP72-1210 regenerants pooled together were digested with EcoRI, HindIII, PstI, BamHI and SalI and probed with three recombinationally active wheat mtDNA clones, K, K3 and X2. No variation in the mtDNA restriction patterns was observed between the CP72-1210 plants and its regenerants. However, restriction pattern variation was observed only from EcoRI digestion, and hybridization patterns of K3, K and X2 revealed minor variations in the mtDNA of cell suspensions when compared with the DNA of the CP72-1210 plant. Except for a qualitative variation detected by the X2 probe and minor stoichiometric variations detected by the K3 probe, sugarcane DNAs were found to be stable after plant regeneration.Florida Agriculture Experiment Station Journal Series No. R-02703     

Genetic basis of resistance to sugarcane mosaic virus in European maize germplasm

 Sugarcane mosaic virus (SCMV) causes considerable damage to maize (Zea mays L.) in Europe. The objective of the present study was to determine the genetic basis of resistance to SCMV in European maize germplasm and to compare it with that of U.S. inbred Pa405. Three resistant European inbreds D21, D32, and FAP1360A were crossed with four susceptible inbreds F7, KW1292, D408, and D145 to produce four F₂ populations and three backcrosses to the susceptible parent. Screening for SCMV resistance in parental inbreds and segregating generations was done in two field trials as well as under greenhouse conditions. RFLP markers umc85, bnl6.29, umc10, umc44, and SSR marker phi075 were used in F₂ populations or F₃ lines to locate the resistance gene(s) in the maize genome. Segregation in the F₂ and backcross generations fitted to different gene models depending on the environmental conditions and the genotype of the susceptible parent. In the field tests, resistance in the three resistant European inbreds seems to be controlled by two to three genes. Under greenhouse conditions, susceptibility to SCMV in D32 appears to be governed by one dominant and one recessive gene. Allelism tests indicated the presence of a common dominant gene (denoted as Scm1) in all three resistant European inbreds and Pa405. Marker analyses mapped two dominant genes: Scm1 on chromosome 6S and Scm2 on chromosome 3. Received: 17 November 1997 / Accepted: 25 November 1997     

Assessment of genetic diversity in Azadirachta indica using AFLP markers

 Genetic diversity was estimated in 37 neem accessions from different eco-geographic regions of India and four exotic lines from Thailand using AFLP markers. Seven AFLP selective primer combinations generated a total of 422 amplification products. The average number of scorable fragments was 60 per experiment, and a high degree (69.8%) of polymorphism was obtained per assay with values ranging from 58% to 83.8%. Several rare and accession-specific bands were identified which could be effectively used to distinguish the different genotypes. Genetic relationships within the accessions were evaluated by generating a similarity matrix based on the Jaccard index. The phenetic dendrogram generated by UPGMA as well as principal correspondence analysis separated the 37 Indian genotypes from the four Thai lines. The cluster analysis indicated that neem germplasm within India constitutes a broad genetic base with the values of genetic similarity coefficient ranging from 0.74 to 0.93. Also, the Indian genotypes were more dispersed on the principal correspondence plot, indicating a wide genetic base. The four lines from Thailand, on the other hand, formed a narrow genetic base with similarity coefficients ranging from 0.88 to 0.92. The lowest genetic similarity coefficient value (0.47) was observed between an Indian and an exotic genotype. The level of genetic variation detected within the neem accessions with AFLP analysis suggests that it is an efficient marker technology for delineating genetic relationships amongst genotypes and estimating genetic diversity, thereby enabling the formulation of appropriate strategies for conservation and tree improvement programs. Received: 20 October 1998 / Accepted: 28 November 1998     

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers

Sugarcane cultivars are polyploid, aneuploid clones derived from interspecific hybridization between Saccharum officinarum and S. spontaneum. Their genome has recently started to be unravelled as a result of the development of molecular markers. We constructed an AFLP genetic map based on a selfing population of a specific cultivar, R570.Using 37 AFLP primer pairs, we detected 1,185 polymorphic markers of which 939 were simplex (segregated 3:1); these were used to construct the map. Of those 939, 887 were distributed on 120 cosegregation groups (CGs) based on linkages in coupling, while 52 remained unlinked. The cumulative length of all the groups was 5,849 cM, which is probably around one-third of the total genome length. Comparison with reference S. officinarum clones enabled us to assign 11 and 79 CGs to S. spontaneum and S. officinarum,respectively, whereas 11 CGs were probably derived from recombination between chromosomes of the two ancestral species. The patchy size of the groups, which ranges from 1 to 232 cM, illustrates the difficulty to access large portions of chromosomes, particularly those inherited from S. officinarum. Repulsion phase linkages suggested a high preferential pairing for 13 CG pairs. Out of the 120 CGs, 34 could be assigned to one of the 10 homo(eo)logy groups already defined in a previous RFLP map owing to the use of a small common marker set. The genome coverage was significantly increased in the map reported here. Implications for quantitative trait loci (QTL) research and marker-assisted breeding perspectives are discussed. Received: 31 August 2000 / Accepted: 16 October 2000     

Molecular marker diversity among current and historical maize inbreds

Advanced-cycle pedigree breeding has caused maize (Zea mays L.) inbreds to become more-elite but more-narrow genetically. Our objectives were to evaluate the genetic distance among current and historical maize inbreds, and to estimate how much genetic diversity has been lost among current inbreds. We selected eight maize inbreds (B14, B37, B73, B84, Mo17, C103, Oh43 and H99) that largely represented the genetic background of current elite inbreds in the U.S. seed industry. A total of 32 other inbreds represented historical inbreds that were once important in maize breeding. Cluster analysis of the inbreds, using data for 83 SSR marker loci, agreed well with pedigree information. Inbreds from Iowa Stiff Stalk Synthetic (BSSS), Reid Yellow Dent, and Lancaster clustered into separate groups with only few exceptions. The average number of alleles per locus was 4.9 among all 40 inbreds and 3.2 among the eight current inbreds. The reduction in the number of alleles per locus was not solely due to sample size. The average genetic distance (D _ij ) was 0.65 among the eight current inbreds, 0.67 among the 32 historical inbreds, and 0.67 among all 40 inbreds. These differences were statistically insignificant. We conclude that genetic diversity among current inbreds has been reduced at the gene level but not at the population level. Hybrid breeding in maize maintained, rather than decreased, genetic diversity, at least during the initial subdivision of inbreds into BSSS and non-BSSS heterotic groups. We speculate, however, that exploiting other germplasm sources is necessary for sustaining long-term breeding progress in maize. Received: 21 August 2000 / Accepted: 5 January 2001     

Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers

Forty fourth single-copy RFLP markers were used to evaluate the genetic diversity of 122 accessions of common wild rice (CWR, Oryza rufipogon Griff.) and 75 entries of cultivated rice (Oryza sativa L. ) from more than ten Asian countries. A comparison of the parameters showing genetic diversity, including the percentage of polymorphic loci (P), the average number of alleles per locus (A), the number of genotypes (Ng), the average heterozygosity (Ho) and the average genetic multiplicity (Hs) of CWR and indica and japonica subspecies of cultivated rice from different countries and regions, indicated that CWR from China possesses the highest genetic diversity, followed by CWR from South Asia and Southeast Asia. The genetic diversity of CWR from India is the second highest. Although the average gene diversity (Hs)of the South Asian CWR is higher than that of the Southeast Asian CWR, its percentage of polymorphic loci (P), number of alleles (Na) and number of genotypes (Ng) are all smaller. It was also found that the genetic diversity of cultivated rice is obviously lower than that of CWR. At the 44 loci investigated, the number of polymorphic loci of cultivated rice is only 3/4 that of CWR, while the number of alleles, 60%, and the number of genotypes is about 1/2 that of CWR. Of the two subspecies studied, the genetic diversity of indica is higher than that of japonica. The average heterozygosity of the Chinese CWR is the highest among all the entries studied. The average heterozygosity of CWR is about two-times that of cultivated rice. It is suggested that during the course of evolution from wild rice to cultivated rice, many alleles were lost through natural and human selection, leading to the lower heterozygosity and genetic diversity of the cultivated rice. Received: 19 May 1999 / Accepted: 26 April 2000     

Molecular analysis of Ascochyta rabiei (Pass.) Labr., the pathogen of ascochyta blight in chickpea

Genetic diversity in Ascochyta rabiei (Pass.) Labr., the causative agent of ascochyta blight of chickpea, was determined using 37 Indian, five American (USA), three Syrian, and two Pakistani isolates. A total of 48 polymorphic RAPD markers were scored for each isolate and the data used for cluster analysis. Most of the isolates clustered in the dendrogram essentially according to geographic origin. Based on the two major clusters A and B, Indian isolates were grouped into two categories, type-A and type-B. Isolates of A. rabiei within the Punjab state were more diverse than isolates from other states in northwestern India. A DNA marker (ubc756_{1.6 kb}), specific to Indian isolates was identified. This is the first report of a molecular diversity analysis of Indian isolates of A. rabiei. The information may assist Indian chickpea breeders in the proper deployment of blight-resistant cultivars and in disease management. Received: 25 April 2000 / Accepted: 11 July 2000     

Comparison of the genetic maps of Brassica napus and Brassica oleracea

 The genus Brassica consists of several hundreds of diploid and amphidiploid species. Most of the diploid species have eight, nine or ten pairs of chromosomes, known respectively as the B, C, and A genomes. Genetic maps were constructed for both B. napus and B. oleracea using mostly RFLP and RAPD markers. For the B. napus linkage map, 274 RFLPs, 66 RAPDs, and two STS loci were arranged in 19 major linkage groups and ten smaller unassigned segments, covering a genetic distance of 2125 cM. A genetic map of B. oleracea was constructed using the same set of RFLP probes and RAPD primers. The B. oleracea map consisted of 270 RFLPs, 31 RAPDs, one STS, three SCARs, one phenotypic and four isozyme marker loci, arranged into nine major linkage groups and four smaller unassigned segments, covering a genetic distance of 1606 cM. Comparison of the B. napus and B. oleracea linkage maps showed that eight out of nine B. oleracea linkage groups were conserved in the B. napus map. There were also regions in the B. oleracea map showing homoeologies with more than one linkage group in the B. napus map. These results provided molecular evidence for B. oleracea, or a closely related 2n=18 Brassica species, as the C-genome progenitor, and also reflected on the homoeology between the A and C genomes in B. napus. Received: 14 June 1996 / Accepted: 11 October 1996     

Molecular mapping of the photoperiod response gene ea7 in barley

 The gene ea ₇ determining photoperiod insensitivity under short day length was mapped on the short arm of chromosome 6H near the centromere. The gene was linked to the two flanking markers Xmwg2264 and Xmwg916 by 6.7 and 13.0 cM, respectively. Compared to Ppd-H1 (chromosome 2H) and Ppd-H2 (chromosome 1H), ea ₇ determines the strongest effect on flowering time with 55 and 18 days difference compared to photoperiod sensitive genotypes grown under short and long photoperiods, respectively. Allelic and homoeologous relationships to major genes and quantitative trait loci controlling flowering time in barley and wheat are discussed. Received: 10 March 1998 / Accepted: 7 April 1998     

Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon

Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis performed with the three types of markers separated the genotypes into two main groups: (1) the sweet type, cultivated melons and (2) the exotic type, not cultivated melons. While the data obtained suggest that all three types of markers are equally informative, AFLPs showed the highest efficiency in detecting polymorphism. Received: 30 December 1999 / Accepted: 24 January 2000     

Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to assess the geographic origin of cultivars

Nine microsatellite markers (VVMD5, VVMD7, VVS2, ssrVrZAG21, ssrVrZAG47, ssrVrZAG62, ssrVrZAG64, ssrVrZAG79 and ssrVrZAG83) were chosen for the analysis of marker information content, the genetic structure of grapevine cultivar gene pools, and differentiation among grapevines sampled from seven European vine-growing regions (Greece, Croatia, North Italy, Austria and Germany, France, Spain and Portugal). The markers were found to be highly informative in all cultivar groups and therefore constitute a useful set for the genetic characterization of European grapevines. Similar and high levels of genetic variability were detected in all investigated grapevine gene pools. Genetic differentiation among cultivars from different regions was significant, even in the case of adjacent groups such as the Spanish and Portuguese cultivars. No genetic differentiation could be detected between vines with blue and white grapes, indicating that they have undergone the processes of cultivar development jointly. The observed genetic differentiation among vine-growing regions suggested that cultivars could possibly be assigned to their regions of origin according to their genotypes. This might allow one to determine the geographical origin of cultivars with an unknown background. The assignment procedure proved to work for cultivars from the higher differentiated regions, as for example from Austria and Portugal. Received: 10 April 1999 / Accepted: 25 May 1999     

A molecular genetic map of the long arm of chromosome 6R of rye incorporating the cereal cyst nematode resistance gene, CreR

 A genetic map of the long arm of chromosome 6R of rye was constructed using eight homoeologous group-6 RFLP clones and five PCR markers derived from the rye-specific dispersed repetitive DNA family, R173. The map was developed using a novel test-cross F₁ (TC-F₁) population segregating for resistance to the cereal cyst nematode. Comparisons were made between the map generated with other rye and wheat group-6 chromosome maps by the inclusion of RFLP clones previously mapped in those species. Co-linearity was observed for common loci. This comparison confirmed a dramatic reduction in recombination for chromosome 6R in the TC-F₁ population. The CreR locus was included in the linkage map via progeny testing of informative TC-F₁ individuals. CreR mapped 3.7 cM distal from the RFLP locus, XksuF37. Comparative mapping should allow the identification of additional RFLP markers more closely linked to the CreR locus. Received: 14 April 1998 / Accepted: 29 April 1998     

Intraspecific genetic variability analysis of Neovossia indica causing Karnal bunt of wheat using repetitive elements

Neovossia indica (Tilletia indica), causing Karnal bunt of wheat, affects major wheat growing regions all over the world. Karnal bunt ranks as one of the major diseases of wheat causing quality losses and monetary losses due to international quarantine regulations. The present work is the first report of a genetic diversity analysis of Indian isolates of N. indica. A library of N. indica isolate Ni7 was constructed in a λZAPII system, and three repetitive elements were identified for molecular analysis. These repetitive elements generated complex hybridization profiles producing fingerprint patterns of all seven isolates. Copy-number estimation of these three elements, pNiR9, pNiR12 and pNiR16, indicated the presence of 32, 61 and 64 copies, respectively. Cluster analysis based on hybridization patterns grouped together moderately virulent isolates Ni1, Ni7 and Ni8, thus suggesting a positive correlation between virulence typing and cluster analysis based on molecular data. Variability analysis of N. indica isolates will aid in checking new resistant sources in host germplasm. Received: 20 April 1999 / Accepted: 29 July 1999     

Single strand conformation polymorphism of genomic and EST-SSRs marker and its utility in genetic evaluation of sugarcane

Sugarcane is an important crop producing around 75 % of sugar in world and used as first generation biofuel. In present study, the genomic and gene based microsatellite markers were analyzed by low cost Single Strand Confirmation Polymorphism technique for genetic evaluation of 22 selected sugarcane genotypes. Total 16 genomic and 12 Expression Sequence Tag derived markers were able to amplify the selected sugarcane genotypes. Total 138 alleles were amplified of which 99 alleles (72 %) found polymorphic with an average of 4.9 alleles per locus. Microsatellite marker, VCSSR7 and VCSSR 12 showed monomorphic alleles with frequency 7.1 % over the average of 3.5 obtained for polymorphic locus. The level of Polymorphic Information Content (PIC) varied from 0.09 in VCSSR 6 to 0.88 in VCSSR 11 marker respectively with a mean of 0.49. Genomic SSRs showed more polymorphism than EST-SSRs markers on selected sugarcane genotypes whereas, the genetic similarity indices calculated by Jaccard’s similarity coefficient varied from 0.55 to 0.81 indicate a high level of genetic similarity among the genotypes that was mainly attributed to intra specific diversity. Hence, the SSR-SSCP technique helped to identify the genetically diverse clones which could be used in crossing program for introgression of sugar and stress related traits in hybrid sugarcane.