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Genetic variability among cassava accessions based on SSR markers
Ribeiro, Márcia de Nazaré Oliveira;Carvalho, Samuel Pereira de;Santos, Jo?o Bosco dos;Antonio, Rafaela Priscila;
Crop Breeding and Applied Biotechnology , 2011, DOI: 10.1590/S1984-70332011000300009
Abstract: the aim of this study was to characterize and estimate the genetic similarity among 93 cassava accessions. the dna amplification was performed with 14 microsatellite primers. the amplification products were separated by a polyacrylamide gel electrophoresis, showing a polymorphism formation, through which the accessions were discriminated against. the genetic similarity among accessions of cassava was estimated by the dice coefficient. cluster analysis was carried out using the upgma method. the polymorphic primers amplified a total of 26 alleles with 2-4 alleles per loci. the genetic similarity ranged from 0.16 to 0.96. the average values for observed and expected heterozygosity were 0.18 and 0.46, respectively. twenty genetic similarity clusters were determined, demonstrating diversity among accessions, suggesting the possibility of heterotic hybrid generation.
Genetic Diversity among 18 Accessions of African Rice (Oryza glaberrima Steud.) Using Simple Sequence Repeat (SSR) Markers
H.A. Doku,E.Y. Danquah,A.N. Amoah,K. Nyalemegbe,H.M. Amoatey
Agricultural Journal , 2013, DOI: 10.3923/aj.2013.106.112
Abstract: Studies were carried out on 18 accessions of African rice (Oryza glaberrima Steud.) collected from four geographical regions of Ghana to assess genetic diversity and potential of these accessions, towards a thorough exploitation of the species, in a region-wide breeding programme to obtain new rice varieties better adapted to the harsh growing conditions of West and Central Africa (WCA). Simple Sequence Repeat (SSR) markers were used to estimate diversity among the accessions. Out of 24 SSR primers used, 23 (i.e., 95.83%) showed allelic polymorphism in the accessions studied. Overall genetic diversity was high (I = 1.178, He = 0.625 and Nei s He = 0.608) and the Fixation index statistics (Fst) revealed that 51.5% of the total variation exists among populations collected from the four geographical regions. All accessions were identified as separate entries with no duplications.
Comparison of Population Genetic Structures between Asian and American Mungbean Accessions Using SSR Markers  [cached]
Xiao-Qiang Wang,Soon-Wook Kwon,Yong-Jin Park
Journal of Agricultural Science , 2012, DOI: 10.5539/jas.v4n9p150
Abstract: The purpose of this study was to evaluate the genetic diversity and population structure of 65 mungbean accessions collected from East and Southeast Asia, the United States and Guatemala using 15 simple sequence repeat (SSR) markers. In total, 47 alleles were detected, the number of the alleles per locus range from two to six, with an average of 3.13. The mean major allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) of the 15 SSR loci were 0.76, 0.05, and 0.28, respectively. Of the 47 alleles, 17 (36.2%) were common, with a frequency of 0.05– 0.5; 16 (34.0%) were rare (frequency < 0.05) and 14 (29.8%) were abundant (frequency > 0.5). On the basis of the UPGMA dendrogram, most of the accessions were clustered into two main groups. The first group (Group I) included seven accessions and the second comprised 58 accessions, which were further divided into four subgroups. Four subpopulations were detected by model-based structure analysis. Fifty-five accessions (84.6%) showed a clear relation to each cluster based on their inferred ancestry value (>75%), while the remaining 10 accessions (15.4%) were categorized as admixtures. Mungbean accessions from US distributed to almost all clusters and 2 accessions shared genetic constituents showing it derived from mixed ancestry with Asean accessions. These results could be useful in identifying mungbean germplasms and facilitating their improvement programs.
NOTE-Polymorphic information content of SSR markers for Coffea spp.
Robson Fernando Missio,Eveline Teixera Caixeta,Eunize Maciel Zambolim,Laércio Zambolim
Crop Breeding and Applied Biotechnology , 2010,
Abstract: Thirty-three coffee SSR primers from enriched genomic library with (GT)15 and (AGG)10 repeats were analyzedin 24 coffee tree accessions. Twenty-two primers were polymorphic among accessions; the number of alleles ranged from 2 to13, with the mean number of 5.1 alleles per primer. PIC values ranged from 0.08 to 0.79. The highest mean PIC values werefound for C. canephora (0.46), and the lowest values for C. arabica (0.22) and triploids (0.22) accessions. The polymorphicSSR markers used in this study were useful for genetic fingerprinting in the coffee tree, especially in the C. canephora and theleaf rust resistant arabica cultivars.
Assessment of EST-SSR Markers for Evaluating Genetic Diversity in Watermelon Accessions from Zimbabwe  [PDF]
Claid Mujaju, Jasna Sehic, Hilde Nybom
American Journal of Plant Sciences (AJPS) , 2013, DOI: 10.4236/ajps.2013.47177
Abstract:

Fifteen expressed sequence tag (EST)-derived simple sequence repeats (EST-SSRs) were used to investigate genetic diversity in 139 plants obtained from seeds of 35 watermelon accessions collected from all the geographical provinces of Zimbabwe. In addition, 15 plants representing three commercial varieties developed in the United States (USA) were analyzed for comparison. A total of 65 alleles were detected among all the watermelon accessions. For the 13 polymorphic EST-SSR loci, number of alleles per locus varied from 2 to 13, with an average of 5 alleles per locus. Values for the polymorphic information content increased as the number of alleles increased, and varied from 0.15 to 0.77 with an average of 0.54 suggesting sufficient discriminatory power. Both cluster analysis and principal coordinate analysis (PCA) produced two major clusters; one with the 22 cow-melon accessions and the other with the 16 sweet watermelon accessions. Within the sweet watermelon group, two distinct sub-clusters formed, one of which contained only two of the commercial varieties from USA. Partitioning of genetic variation in the Zimbabwean material using analysis of molecular variation (AMOVA) revealed that 64% of the total variation resides between the two major forms, i.e. sweet watermelons and cow-melons, 28% between accessions within forms and 8% within accessions. The EST-SSR markers revealed a somewhat higher diversity in sweet watermelon accessions compared to that of cow-melons. This finding is contrary to previous reports using other markers (genomic SSR loci or RAPD) and/or a plant material that is likely to have experienced more stringent selection procedures compared to the landraces analyzed in our study.

SSR markers reveal genetic variation between improved cassava cultivars and landraces within a collection of Nigerian cassava germplasm
OK Moyib, OA Odunola, AGO Dixon
African Journal of Biotechnology , 2007,
Abstract: Thirty-one improved cultivars and five Nigerian landraces of cassava were assessed at genomic DNA level with 16 SSR primers for genetic diversity study. The minimum number of SSR primers that could readily be used for identification of the 36 cassava genotypes was also determined. For the genetic diversity study, the similarity coefficients generated between improved cultivars and Nigerian landraces ranged from 0.42 to 0.84, and 12 distinct DNA cluster groups were identified at 0.70 coefficients using Numerical Taxonomy and Multivariate Analysis System software package. For the genotype identification study, the 16 SSR primers were screened by their polymorphic information content (PIC) values. Five SSR primers that have PIC values between 0.50 and 0.67 were selected and further assessed using simple arithmetic progression combination method. The results obtained revealed a combination of these 5 primers from SSR primers collection at IITA that could readily distinguish the 36 cassava genotypes at 0.93 similarity coefficient. These five primers clustered the 36 cassavas into 16 groups at 0.70 similarity coefficient. Application of this few SSR primers would ultimately reduce the cost and time of research for genetic diversity and genotype identification studies for the genetic improvement program of cassava.
Development of cDNA-derived SSR markers and their efficiency in diversity assessment of Cymbidium accessions
Moe,Kyaw Thu; Hong,Woo-Ju; Kwon,Soon-Wook; Park,Yong-Jin;
Electronic Journal of Biotechnology , 2012,
Abstract: cymbidium spp. are popular ?owering plants. assessment of the genetic diversity in cultivated cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. thus, it is important to develop more efficient polymorphic dna markers. although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cdna library, a larger number of successful primers were obtained from the cdna library (59.9%) than from genomic dna library (51.1%). however, higher pic and gene diversity were identified in genomic ssrs. the average allele number per locus was also higher in genomic ssrs (7.3) than est-ssrs (5.2), among the 24 evaluated cymbidium accessions. at/ta was comparatively high in est-ssrs, while this motif was not as common in genomic ssrs. the ctt/aag/tct/aga/ttc/gaa and tgc/gca/gct/agc/ctg/cag motifs were the most abundant tri-nucleotide sequences in est-ssrs, while gtt/aac/tgt/aca/ttg/caa was the most frequent in genomic ssrs. the number of repeats ranged from 3 to 12 in est-ssrs. currently, 52 novel polymorphic ssr markers have been evaluated, which will be useful for germplasm assessments, core set construction, evaluation of genetic diversity, and marker assisted selection (mas) based cymbidium breeding.
Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L.
Mingfu Wen, Haiyan Wang, Zhiqiang Xia, Meiling Zou, Cheng Lu, Wenquan Wang
BMC Research Notes , 2010, DOI: 10.1186/1756-0500-3-42
Abstract: In total, 187 out of 419 expressed sequence tag (EST)-SSR and 54 out of 182 genomic (G)-SSR markers from cassava were polymorphic among the J. curcas accessions. The EST-SSR markers comprised 26.20% dinucleotide repeats, 57.75% trinucleotide repeats, 7.49% tetranucleotide repeats, and 8.56% pentanucleotide repeats, whereas the majority of the G-SSR markers were dinucleotide repeats (62.96%). The 187 EST-SSRs resided in genes that are involved mainly in biological and metabolic processes. Thirty-six EST-SSRs and 20 G-SSRs were chosen to analyze the genetic diversity among 45 J. curcas accessions. A total of 183 polymorphic alleles were detected. On the basis of the distribution of these polymorphic alleles, the 45 accessions were classified into six groups, in which the genotype showed a correlation with geographic origin. The estimated mean genetic diversity index was 0.5572, which suggests that our J. curcas germplasm collection has a high level of genetic diversity. This should facilitate subsequent studies on genetic mapping and molecular breeding.We identified 241 novel EST-SSR and G-SSR markers in J. curcas, which should be useful for genetic mapping and quantitative trait loci analysis of important agronomic traits. By using these markers, we found that the intergroup gene diversity of J. curcas was greater than the intragroup diversity, and that the domestication of the species probably occurred partly in America and partly in Hainan, China.Jatropha curcas L. is a perennial, monoecious shrub that belongs to the Euphorbiaceae family. The species is native to America but is distributed widely in the tropics [1,2]. Wild or semicultivated types of J. curcas can grow well under all unfavorable climatic and soil conditions [3]. The seeds of J. curcas contain 40-45% oil [4-6] with a high percentage of monounsaturated oleic and polyunsaturated linoleic acid. The seed oils can be classified as semi-drying [7]. In recent years, the economic importance of J. curcas for
Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on SSR markers
J Nasiri, A Haghnazari, J Saba
African Journal of Biotechnology , 2009,
Abstract: To assess the genetic relations inPisum genus and to examine putative duplicate accessions, 20 pea varieties (Pisum sativum L.) with 57 accessions from wild Pisum species fulvum, subspecies (subsp.) asiaticum, elatius, thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance (29%) is lower than the intragroups component of variance (71%). The lowest value of genetic differentiation ( Pisum genus and to examine putative duplicate accessions, 20 pea varieties (Pisum sativum L.) with 57 accessions from wild Pisum species fulvum, subspecies (subsp.) asiaticum, elatius, thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance (29%) is lower than the intragroups component of variance (71%). The lowest value of genetic differentiation (Pisum genus and to examine putative duplicate accessions, 20 pea varieties (Pisum sativum L.) with 57 accessions from wild Pisum species fulvum, subspecies (subsp.) asiaticum, elatius, thebaicum, abyssinicum, transcaucasicum and arvense were analyzed using 10 out of 20 microsatellite primer pairs. We genotyped all accessions. In total, 59 alleles were identified in whole collection. The maximum number of alleles (8 alleles) was obtained from the PEACPLHPP, AF004843, and AA43090 loci. The maximum number of private alleles (4) in the wild collection was detected in AF004843 locus but in the cultivar collection, it was detected in AA430902 and PSBLOX13.2 loci. Cluster analysis and principal coordinate analysis located accessions in 3 groups and cultivated varieties were obviously separated from the wild accessions. Analysis of molecular variance (AMOVA) revealed that the intergroups component of variance
Genetic diversity among farmer-preferred cassava landraces in Uganda
LF Turyagyenda, EB Kizito, ME Ferguson, Y Baguma, JW Harvey, P Gibson, BW Wanjala, DSO Osiru
African Crop Science Journal , 2012,
Abstract: Understanding of genetic diversity among a breeding population is an important requirement for crop improvement as it allows for the selection of diverse parental combinations and formation of heterotic pools for genetic gain. This study was carried out to determine genetic diversity within and among 51 farmer-preferred cassava (Manihot esculenta) landraces and 15 elite accessions grown in Uganda. Twenty six simple sequence repeat (SSR) markers used for genetic diversity assessment in this study revealed a total of 154 alleles, of which 24% were unique alleles present only in landraces. The genetic diversity and observed herozygosity in landraces were slightly higher than in elite accessions. Elite accessions clustered with some of the landraces indicating that there were some alleles in common. However, 58.8% of the landraces fell into 3 different clusters independent of the elite accessions. Including these landraces with unique alleles in cassava breeding schemes will increase the chances of producing farmer preferred adapted elite cultivars. The study also revealed genetic differentiation among accessions from different regions providing an opportunity for establishment of heterotic pools within a breeding programme.
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