Molecular investigation of the genetic base of sugarcane cultivars (original) (raw)
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AGRIVITA Journal of Agricultural Science
This experiment was conducted to reveal genetic diversity among 38 genotypes of sugarcane (Saccharum officinarum L.) using RAPD markers. The population consisted of 8 genotypes from Australia, 7 from Africa, 10 from America, and 13 from Asia. Genetic similarity was ranging from 17% to 97% , with the average of 57%. UPGMA dendrograms divided the population into three major groups i.e. group 1, 2, and 3 which consisted of 23, 10, and 5 genotypes, respectively. Each major group comprised genotypes of different geographical origins. The dendrogram divided each group into some subgroups. There were 8 subgroups i.e. 4 subgroups in group 1, 2 subgroups in group 2, and 2 subgroups in group 3. Some genotypes of same geographical origin were clustered into in at least 3 different subgroups, meaning that they were genetically dissimilar. On the other hand, some other genotypes of different geographical origin were clustered into the same subgroup, meaning that they were genetically similar. This data would help sugarcane breeders to select parents for hybridization in order to maximize heterosis. This could be conducted by selecting parents of dissimilar genotypes.
Genetics and Molecular Research, 2016
We analyzed 80 plants of the sugarcane (Saccharum spp) variety 'RB867515' in order to investigate its diversity and genetic structure at the molecular level. Four simple sequence repeat (SSR) loci (UGSM51, SMC1237, SEGMS1069, and UGSM38) and five expressed sequence tag (EST)-SSR loci (ESTA68, ESTB92, ESTB145, ESTC66, and ESTC84) were used as molecular markers. The polymorphic loci rate was 66.6%. A total of 17 alleles and an average of 1.88 alleles/locus were detected. The number of alleles in the EST-SSR loci was lower than the number of alleles in the SSRs of non-expressed loci. The mean observed heterozygosity among the nine SSR loci was 0.3291. Genetic structure analysis showed that 'RB867515' contains alleles from three ancestral groups (K = 3), but there is little admixing of alleles in the same plant (from 0.8 to 17.3%); only 1.88% of the plants shared alleles from two or three groups. ESTB92, ESTC84, and UGSM38 were monomorphic, but there was evidence of polymorphism in ESTA68, ESTB145, ESTC66, UGSM51, SMC1237, and SEGMS1069, indicating that 'RB867515' has variability at the molecular level and the potential to be used as a parent in breeding programs. The molecular variability observed in 'RB867515' indicates that the clone terminology that is used to identify this cultivar is inconsistent with the original meaning of "clone", which is defined as a sample of genetically identical plants.
Euphytica, 2002
Genetic diversity in 28 prominent Indian sugarcane varieties cultivated under a wide range of agroclimatic conditions, was studied using 25 RAPD markers. The mean genetic distance among the 28 varieties was only 29.31%, implying that a large part of the genome is similar among the varieties. This probably arises from the lack of parental diversity, with few clones which are themselves related, contributing to the parentage of these varieties. The parentage of the varieties did not contribute significantly to the clustering pattern. Varieties belonging to the same parentage were grouped under different clusters while varieties from different parentages were grouped under the same cluster. The tropical and subtropical identities of the varieties also did not contribute to the clustering pattern as individual clusters included varieties from both tropics and subtropics. This shows that genetically similar varieties are present in both the regions. Among the varieties, Co 7717 was found to be totally distinct and divergent from rest of the varieties. The study reveals the limited genetic base of the current Indian commercial varieties and the need to diversify the genetic base by using new sources from the germplasm.
OnLine Journal of Biological Sciences, 2011
Problem statement: Increasing sugar productivity is the main concern of sugarcane (Saccharum officinarum L.) breeding programs. The complexity and size of the sugarcane genome is a major limitation in its genetic improvement. Characterization of sugarcane provides essential information of genetic diversity for breeders utilize for crop improvement. Approach and Results: The objective of this study was to evaluate the microsatellite markers (SSR) with 17 sugarcane accessions to access the genetic diversity and inter relationships in sugarcane. Genetic distances for SSR data (polymorphic fragments) were determined and relationships between samples were portrayed graphically in the form of a dendrogram and similarities are ranging from 36% to 100% were observed. The lowest genetic similarity of 36% was seen between sample 9 and 11 with other samples. These two genotypes differed from each other with only 68% similarity. Conclusion: Results illustrate that SSR markers could be useful for structuring the genetic diversity of collections according to geographical origin and ploidy level, assessment or formation of a core collection and especially construction of a genetic map.
The present study was performed to study genetic relationships and population differentiation of 90 introduced sugarcane accessions in Ethiopia by means of 22 SSR molecular markers. The 22 SSR markers amplified a total of 260 alleles, of which 230 were polymorphic with a mean of 10.45 alleles per SSR locus. The range in allele number was 4–22. A high level of polymorphism with a mean of 60.51% polymorphic loci within the genotypes was detected. The polymorphic information content (PIC) ranged from 0.231 to 0.375 with an average of 0.303. Measures of effective number of alleles and genetic diversity on average were 1.55 and 0.317, respectively, across all the 22 markers evaluated. The SSR genetic profiles obtained using the 22 markers enabled complete discrimination among all the 90 introduced sugarcane cultivars. The neighbor-joining unweighted pair group method with arithmetic mean (UPGMA) cluster analysis based on the simple matching dissimilarity indices unambiguously distinguished all sugarcane genotypes with three major clusters and 11 groups. The same clustering pattern was also found in the PCoA analysis. In all the geographical populations, genotypes from the same country were often in different clusters and likewise accessions from different countries often clustered together indicating the possibility of exchange of materials between countries. Population genetic differentiation showed Fst values among pairs of populations ranging from 0.0024 to 0.5134 with an overall average of 0.0590. The average gene flow (Nm) among populations was 1.7213. Nei’s unbiased genetic distance ranged from 0.018 to 0.279 with an overall average of 0.053. Genetic identity values were in the range of 0.756 to 0.992 with overall average of 0.950. The genetic relationship information of the cultivars will help sugarcane breeders to select the appropriate parents in their breeding programs to maximize yield as well as to maintain genetic diversity. Key words: Sugarcane, Ethiopia, simple sequence repeats (SSR), genetic diversity, population genetic differentiation.
Genetic diversity in sugarcane cultivars assessed by DNA markers and morphological traits
Revista Industrial y Agrícola de Tucumán, 2013
Fil: Perera, Maria Francisca. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Tucuman. Instituto de Tecnologia Agroindustrial del Noroeste Argentino; Argentina. Gobierno de Tucuman. Ministerio de Desarrollo Productivo. Estacion Experimental Agroindustrial Obispo Colombres; Argentina
Life Science Journal
Nine genotypes of sugarcane (Saccharum spp) namely G.T.54-9, G.84-47, POJ.28-78, Co.997, F.161, F.153, N.Co.310, G.74–96 and Phil.8013; which available at Sugar Crops Research Institute (SCRI) screened to detect the genetic polymorphism using RAPD and ISSR techniques. Based on RAPD data, the percentage of polymorphic amplified products ranged from 37.5-72.7%, the total number of the amplified RAPD produced by each primer varied from 8-11 amplified products. Unique DNA bands with different sizes were detected in particular genotypes, primer OP-A01produced two DNA bands displayed in the genotype G.T. 54-9 (258 bp and 700 bp). While primer OP-O10 produced two DNA bands, one band displayed in the genotype G.84-47 (924 bp) and one in G.T. 54-9 (1104 bp). Some of the primers produced polymorphic bands specific to a set of genotypes. These bands could be considered as genotype-specific bands. Based on ISSR data, the percentage of polymorphic amplified products ranged from 9.09 to 80%. The ...
Pakistan Journal of Botany, 2019
Large genome size and deficiency of adequate informative molecular markers bottlenecked genetic improvement in sugarcane. DNA fingerprinting and diversity analysis of sugarcane genotypes provide essential genetic evidences that breeders could utilize in crop improvement program. To investigate the genetic diversity based on 46 microsatellite markers, 16 promising exotic sugarcane genotypes were utilized. Twenty (20) out of 46 microsatellite markers were examined at Germplasm Evaluation Lab of BCI, National Agricultural Research Centre, Islamabad, whereas the remaining 26 were tested at the genomics lab of SIU-Carbondale, USA. The genotypes portrayed substantial level of genetic polymorphism. Ratio of monomorphic loci was 28.66% out of 164, whereas polymorphic loci were 71.34% with an average 3.57 alleles/locus. Out of 46 microsatellite markers, 10 (21.74%) produced monomorphic, 13 (28.26%) produced polymorphic bands and 23 (50%) produced both monomorphic and polymorphic bands. SSR markers SCM16 and UGSM574 produced maximum number of bands (10), whereas markers SMC7CUQ, SMC1604SA, MCSA053C10, SOMS118, UGSM154, UGSM312, mSSCIR3, SMC851MS, SOMS156, SMC336BS and SMC1751CLproduced the least number of band i.e., 1. In all 16 sugarcane genotypes, the PIC value of the polymorphic loci ranged between 0.009 and 0.947 with the mean value of 0.490/locus. Mean number of alleles/polymorphic locus was 3.30, whereas mean number of alleles/locus was calculated as 3.57. Through similarity matrix extent of genetic relatedness among the sugarcane genotypes was determined. Genetic similarity as pair-wise ranged between 71 to 93%. Minimum genetic similarity was noted 71% between genotypes CP89831 and MS94CP15, while the maximum between genotypes S97CP288 and MS99HO391. The phenogram categorized the 16 cultivars into main four (4) clusters/groups. Cluster-1/group-1 consisted two (2) genotypes only, 2 nd cluster consisted of five (5) genotypes, whereas 3 rd cluster consisted only one genotype (MS92CP979) which was branched solitary. The 4 th cluster was comparatively a large one and consisted of eight genotypes. This was suggested that the genotypes showed maximum level of genetic polymorphism might be further utilized in sugarcane varietal development and breeding plans.
Asian Journal of Research in Agriculture and Forestry
Simple sequence repeat (SSR) fingerprinting was chosen because of its high polymorphism, which enables precise analysis of genetic diversity, for the assessment of genetic variety among several sugarcane varieties. This method focuses on certain areas of the sugarcane genome and offers important insights into the distinctive genetic patterns and relationships between the many sugarcane types under study. To increase sugarcane production and resilience, crop development plans, breeding programmes, and conservation activities must be guided by the data obtained by SSR fingerprinting. This study aimed to assess the genetic diversity and fingerprinting of eight sugarcane varieties (Isd 16, Isd 20, Isd 21, Isd 24, Isd 28, Isd 29, Isd 30, and Isd 31) using four SSR primers. A simple and efficient method for DNA isolation was employed, and the primers successfully amplified a total of 59 bands from the eight varieties. The results showed that the marker SMC687CS exhibited the highest numbe...
Acta agriculturae Slovenica
Genetic diversity information among a population is important in exploiting heterozygosity for the improvement of crop species through breeding programmes. This study was therefore, conducted to assess genetic diversity and establish molecular relationships among 20 selected exotic sugarcane accessions from the Unilorin Sugar Research Institute germplasm using Inter Simple Sequence Repeat (ISSR) molecular markers. Genomic DNA was extracted from the sugarcane leaf. Fragments amplification was then performed by polymerase chain reaction (PCR) with ISSR markers and the data obtained were analyzed using MEGA 4 software. Analysis of the electropherogram showed a total of 39 loci consisting of 369 bands, out of which 95.8% were polymorphic. The biplot analysis showed all the markers contributed to the observed diversity with the least achieved with ISSR6. The principal co-ordinate analysis grouped the accessions into four clusters, comprising mixtures of all the six collection sites. The ...