Simple Sequence Repeat Data Research Articles

Comparison of relative efficiency of genomic SSR and EST-SSR markers in estimating genetic diversity in sugarcane.

Twenty-five primer pairs developed from genomic simple sequence repeats (SSR) were compared with 25 expressed sequence tags (EST) SSRs to evaluate the efficiency of these two sets of primers using 59 sugarcane genetic stocks. The mean polymorphism information content (PIC) of genomic SSR was higher (0.72) compared to the PIC value recorded by EST-SSR marker (0.62). The relatively low level of polymorphism in EST-SSR markers may be due to the location of these markers in more conserved and expressed sequences compared to genomic sequences which are spread throughout the genome. Dendrogram based on the genomic SSR and EST-SSR marker data showed differences in grouping of genotypes. A total of 59 sugarcane accessions were grouped into 6 and 4 clusters using genomic SSR and EST-SSR, respectively. The highly efficient genomic SSR could subcluster the genotypes of some of the clusters formed by EST-SSR markers. The difference in dendrogram observed was probably due to the variation in number of markers produced by genomic SSR and EST-SSR and different portion of genome amplified by both the markers. The combined dendrogram (genomic SSR and EST-SSR) more clearly showed the genetic relationship among the sugarcane genotypes by forming four clusters. The mean genetic similarity (GS) value obtained using EST-SSR among 59 sugarcane accessions was 0.70, whereas the mean GS obtained using genomic SSR was 0.63. Although relatively lower level of polymorphism was displayed by the EST-SSR markers, genetic diversity shown by the EST-SSR was found to be promising as they were functional marker. High level of PIC and low genetic similarity values of genomic SSR may be more useful in DNA fingerprinting, selection of true hybrids, identification of variety specific markers and genetic diversity analysis. Identification of diverse parents based on cluster analysis can be effectively done with EST-SSR as the genetic similarity estimates are based on functional attributes related to morphological/agronomical traits.

Molecular genetic diversity assessment of Citrus species grown in Iran revealed by SSR, ISSR and CAPS molecular markers

En este estudio, se analizó la diversidad genética en 19 cultivares de cítricos mediante la repetición de secuencia simple (SSR), la repetición de secuencia inter-simple (ISSR) y los marcadores de secuencia polimórfica amplificada segmentada (CAPS). Se utilizaron nueve cebadores para SSR, nueve cebadores ISSR y dos cebadores para CAPS para la puntuación del alelo. Se analizaron una región de ADN de cloroplasto (rbcL-ORF106) y una región de ADN mitocondrial (18S-5S) usando marcador de secuencia polimórfica amplificada escindida (CAPS) en 19 accesiones de cítricos cultivadas en Irán. En total, se detectaron 45 genes SSR y 131 ISSR polimórficos alelos y organelos del genoma del árbol. El análisis de conglomerados de los datos SSR y ISSR se realizó utilizando el método UPGMA y se basó en el coeficiente de Jaccard. El resultado de esta investigación mostró que los cebadores SSR e ISSR eran altamente informativos y eficientes para detectar la variabilidad genética y las relaciones de las accesiones de los cítricos. Y el análisis de marcadores de CAPS Los resultados mostraron que Bakraee y uno de tipo off cal mexicana tenían un patrón de bandas similar al Clementine Mandarin, mientras que Pummelo se consideraba como padre materno de otros genotipos estudiados Citron considerado como padre padre mostró un patrón de bandas definido entre 19 genotipos estudiados que confirmó Citoplasma herencia de orgánulos celulares de la madre.

ECUADORIAN POTATO LANDRACES: TRADITIONAL NAMES AND GENETIC IDENTITY

Ecuadorian potato landraces (Solanum tuberosum L.) are an important genetic resource, but they have been poorly described. Simple Sequence Repeats (SSR) markers were applied to 152 landraces to assess the genetic diversity of potatoes collected in three areas of high diversity: the Carchi, Chimborazo and Loja provinces. These SSR markers were previously used in the genotyping of more than 800 European potato varieties. The number of alleles and Polymorphism Information Content (PIC) of the markers found in this study were similar to those in European cultivars; however, the overlap in alleles was small. Based on SSR data, the relationship between local names of landraces and genetic identity showed several landraces with different names but identical molecular profiles. It also showed that landraces with identical names but obvious differences in tuber morphology were almost always genetically different. There was no clear grouping of material collected according to the regions under study that suggests extensive movement of seed potatoes all over Ecuador.

Comparative Analysis of SSR Markers Developed in Exon, Intron, and Intergenic Regions and Distributed in Regions Controlling Fruit Quality Traits in Prunus Species: Genetic Diversity and Association Studies

Simple sequence repeats (SSRs) are genome domains located in both coding and non-coding regions in eukaryotic genomes. Although SSRs are often characterized by low polymorphism, their DNA-flanking sequences could be a useful source of DNA markers, which could help in genetic studies and breeding because they are associated with genes that control traits of interest. In this study, 56 genotypes from different Prunus species were used, including peach, apricot, plum, and almond (already phenotyped for several agronomical traits, including self-compatibility, flowering and ripening time, fruit type, skin and flesh color, and shell hardness). These Prunus genotypes were molecularly characterized using 28 SSR markers developed in exons, introns, and intergenic regions. All these genes were located in specific regions where quantitative trait loci (QTLs) for certain fruit quality traits were also located, including flowering and ripening times and fruit flesh and skin color. A sum of 309 SSR alleles were identified in the whole panel of analyzed cultivars, with expected heterozygosity values of 0.61 (upstream SSRs), 0.17 (exonic SSRs), 0.65 (intronic SSRs), and 0.58 (downstream SSRs). These values prove the low level of polymorphism of the exonic (gene-coding regions) markers. Cluster and structural analysis based on SSR data clearly differentiated the genotypes according to either specie (for the four species) and pedigree (apricot) or geographic origin (Japanese plum). In addition, some SSR markers mainly developed in intergenic regions could be associated with genes that control traits of interest in breeding and could therefore help in marker-assisted breeding. These findings highlight the importance of using molecular markers able to discriminate between the functional roles of the gene allelic variants.

Genetic relationships and evolution of old Chinese garden roses based on SSRs and chromosome diversity

Old Chinese garden roses are the foundation of the modern rose, which is one of the best-selling ornamental plants. However, the horticultural grouping and evolution of old Chinese garden roses are unclear. Simple sequence repeat (SSR) markers were employed to survey genetic diversity in old Chinese garden roses and genetic differentiation was estimated among different rose groups. Fluorescence in situ hybridization was used to study the physical localization of 5 S rDNA genes and a karyotype analysis was performed. The SSR data suggest that old Chinese garden roses could be divided into Old Blush group, Odorata group and Ancient hybrid China group. The Old Blush group had the most primitive karyotype. The Ancient hybrid China group and modern rose had the most evolved karyotypes and the highest genetic diversity. During the evolution of rose cultivars, 5 S rDNA increased in number, partially weakened in signal intensity and exhibited variation in distance from the centromere. In conclusion, rose cultivars evolved from the Old Blush Group to the Odorata group, the Ancient Hybrid China group and the modern rose. This work provides a basis for the collection, identification, conservation and innovation of rose germplasm resources.

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase.

The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.

Morphological and molecular characterization of Solanum melongena and related species

India is considered as the domestication center for eggplant and its diverse germplasm is notable. In present study, 84 germplasm lines including 79 breeding lines of cultivated eggplant along with five wild species were differentiated on the basis of 21 morphological trait descriptors and 40 simple sequence repeat (SSR) markers. According to principle component analysis (PCA) of morphological traits, 70.33% of the total variation was explained with first 8 PCs. Out of 40 SSR markers, only 19 (50-100%) revealed polymorphism among various cultivated and wild genotypes with a range of 2 and 10 alleles and a mean of 4.9 alleles per marker. Onthe basis of PIC values and number of amplified alleles per marker, EEMS28 was the highest polymorphic marker, which was followed by CSM31 and CSM27. Jaccard’s similarity coefficient among genotypes varied from 0.38 -0.98 being the highest between cultivated genotypes and S. torvum. The morphological and SSR data were analyzed individually as well as combined using UPGMA cluster analysis. Morphogenetic divergence within the cultivated eggplant highlighted the possibility of their use in future breedingprogrammes. Wild species diverged into separate group on the basis of SSRs data, but merged into small round group of cultivated eggplant morphologically as well as morphogenetically.S. laciniatum and S. aethiopicum were more close to the cultivated eggplant and can be used in introgression breeding.

MSDB: A Comprehensive Database of Simple Sequence Repeats.

Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb.

New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh

Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

In order to identify the variation and estimate the genetic diversity among the fig (Ficus carica L.) genotypes collected from Algeria and Turkey, the genetic relationships between 86 genotypes were investigated using 23 inter primer binding sites (iPBS)-retrotransposon and 16 simple sequence repeat (SSR) primers. A total of 63 polymorphic bands for the iPBS-retrotransposon markers and 25 alleles for the SSR markers were identified with an average of 2.7 and 1.6 per primer, respectively. The average value of polymorphism information content (PIC) for the iPBS markers (0.73) was higher than that for the SSR markers (0.69). Applying the neighbor-joining method to the combined iPBS-retrotransposon and SSR data, the fig genotypes were clustered into two groups. The STRUCTURE software was used to determine the population structure. Among the genotypes studied, two populations (K = 2) were identified indicating a low diversity between the Algerian and Turkish varieties. Both types of markers were able to differentiate all the fig genotypes and were efficient in discriminating the closely related genotypes. Our data also showed that as a universal marker, iPBS-retrotransposon is a useful tool for the molecular characterization of fig genotypes.

Genetic relationships in a germplasm collection of Camellia japonica and Camellia oleifera using SSR analysis.

Camellia japonica produces different color and bigger flowers, widely being used for gardening green in southern China. However, cultivars were introduced from different regions, but their origin and pedigree information is either not available poorly documented, causing problems in authentication. Many low-yield trees in Camellia oleifera forests have been used as stocks for grafting C. japonica. However, the survival rate of grafts between these two species is related to genetic relationship between stock of C. oleifera and scion of C. japonica. We used simple sequence repeat (SSR) markers to genotype 41 C. japonica cultivars from different regions, as well as nine genotypes of C. oleifera in China. Twenty-one SSR markers generated 438 alleles, with an average of 20.85 alleles per locus. All alleles were used to generate Dice coefficients between two genotypes of all genotypes of these two species. Cluster analysis based on SSR data clustered genotypes showed clustering of genotypes into groups that agreed well with their taxonomic classification and geographic origin. Cultivar 'Damaonao' was a large tree with flowers of composite color, and showed the most genetic distance from other C. japonica cultivars and C. oleifera genotypes in the cluster analysis. The cultivars of C. japonica are distinct from genotypes of C. oleifera. The results for cultivars of C. japonica also revealed the presence of different cultivars with the same name, and identical cultivars but with a different name. SSR profiles can improve C. japonica germplasm management, and provide potential determine correlations between genetic relationship and graft compatibility among scions of C. japonica and genotypes of C. oleifera.

M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm.

Simple Sequence Repeat (SSR) markers are one of the most frequently used molecular markers in studies of crop diversity and population structure. This is due to their uniform distribution in the genome, the high polymorphism, reproducibility, and codominant character. Additional advantages are the possibility of automatic analysis and simple interpretation of the results. The M13 tagged PCR reaction significantly reduces the costs of analysis by the automatic genetic analyzers. Here, we also disclose a short protocol of SSR data analysis.

Diallel analysis and genetic diversity of some yellow maize inbred lines (Zea mays L.) using RAPD and SSR markers

Information about combining ability and genetic diversity among maize inbred lines is fundamental in designing breeding strategies for improving grain yield. Twenty one F1 hybrids were generated by crossing seven yellow maize inbred lines in a half diallel mating scheme in 2013 season. The 21 F1 hybrids plus the two check hybrids (SC166 and SC173) were evaluated in a randomized complete block design with three replications during 2014 season, to estimate combining ability effects and identify type of gene action governing the inheritance of grain yield and other important agronomic traits. Results showed that both general (GCA) and specific (SCA) combining ability mean squares were highly significant for all the studied characters. The GCA/SCA ratio was more than unity for all the studied traits, except days to 50% silking, plant height and grain yield, indicating the preponderance of the additive gene effects in the inheritance of these traits. The inbred line P1 appeared to be the best general combiner for earliness, grain yield and its components. The crosses P1×P2, P3×P7, P4×P7, and P5×P6 had the best SCA effects for grain yield and most of its component traits. The cross P1×P2 significantly out-yielded the two check hybrids (SC166 and SC173). The genetic diversity among the seven yellow parental inbred lines was assessed using two types of molecular markers; Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR). Seven random primers were used in the RAPD reactions, resulting in the amplification of 82 bands with 95.12% polymorphism. While, eight pairs of SSR primers were used and resulted in 49 fragments with 100% polymorphism. Genetic similarity among all possible pairs of inbred lines varied from 0.12 to 0.69, with an average of 0.34, for RAPD markers, and from 0.01 to 0.56, with an average of 0.24, for SSR markers. The similarity matrices for RAPD and SSR data were not significantly correlated (r=0.34, p >0.05). Genetic distances based on RAPD and SSR markers were insignificantly correlated with F1 hybrids grain yield, the correlation values being (r =0.02 and 0.429 P>0.05), respectively. Therefore, the parental genetic distance could not be used to predict the grain yield of the F1 hybrids in this study.

Development of novel simple sequence repeat markers from ramie (Boehmeria nivea L. Gaudich) and analysis of genetic diversity in its genetic resources

Boehmeria nivea (ramie), a subshrub of the Urticaceae family and an important fiber crop, has been grown in Asian countries, including Korea, for many centuries. Traditionally, in some regions of Korea, ramie leaves are also used as a major ingredient in ‘Songpyeon’ rice cakes. Despite its economic importance, the molecular genetics of ramie have not yet been studied in detail. Researchers from Yeong-Gwang Agricultural Technology Center collected genetic resources of ramie from a variety of local sites in Korea. Nuclear internal transcribed spacer sequences amplified from 90 genetic resources showed no variation in size or sequence between them or B. nivea reference samples, indicating that all the genetic resources could be taxonomically classified as B. nivea. To systematically and efficiently manage these genetic resources, we developed simple sequence repeat (SSR) markers for ramie using the magnetic bead hybridization selection method. Finally, we selected 17 SSR markers that showed possible polymorphism among the genetic resources and analyzed the genetic diversity of ramie collection. These 17 markers detected a total of 140 alleles, ranging from 3 to 17 alleles per accession. The average genetic diversity value was 0.61, ranging from 0.37 to 0.84. Average polymorphism information content was 0.56, ranging from 0.34 to 0.82. Genetic cluster analysis based on SSR data revealed that the genetic collection of ramie plants could be classified into four distinct clusters. A purity test on several of the genetic resources using polymorphic SSR markers revealed that some resources were impure. These newly developed SSR markers might be useful for diverse genetic analysis including the management of genetic collections, establishment of core collections, and cultivar identification.

A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database.

The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by <100 nt). Some 73% of the SSRs were composed of dinucleotide motifs. The SSRs were categorized for the numbers of repeats present, their overall length and were allocated to their linkage group. A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. A putative function has been assigned, using the gene ontology approach, to the set of genes harboring at least one SSR. The same search parameters were applied to reveal the SSR content of 14 other plant species for which genome sequence is available. Certain species-specific SSR motifs were identified, along with a hexa-nucleotide motif shared only with the other two Compositae species (sunflower (Helianthus annuus) and horseweed (Conyza canadensis)) included in the study. Finally, a database, called “Cynara cardunculus MicroSatellite DataBase” (CyMSatDB) was developed to provide a searchable interface to the SSR data. CyMSatDB facilitates the retrieval of SSR markers, as well as suggested forward and reverse primers, on the basis of genomic location, genomic vs genic context, perfect vs imperfect repeat, motif type, motif sequence and repeat number. The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates.

Comparative analysis of traditional and modern apricot breeding programs: A case of study with Spanish and Tunisian apricot breeding germplasm

Traditional plant breeding is based on the observation of variation and the selection of the best phenotypes, whereas modern breeding is characterised by the use of controlled mating and the selection of descendants using molecular markers. In this work, a comparative analysis of genetic diversity in a traditional (Tunisian) and a modern (Spanish) apricot breeding programme was performed at the phenotypic and molecular level using simple sequence repeat (SSR) markers. Seven phenotypic traits were evaluated in 42 Tunisian apricot accessions and 30 genotypes from the Spanish apricot programme. In addition, 20 SSR markers previously described as linked to specific phenotypic traits were assayed. Results showed that modern breeding using controlled crosses increases the size of the fruit. The fruit weight average observed in the Tunisian cultivars was of 20.15 g. In the case of traditional Spanish cultivars the average weight was 47.12 g, whereas the average weight of the other progenitors from France, USA and South Africa was 72.85 g. Finally, in the new releases from the CEBAS-CSIC breeding programme, the average weight was 72.82 g. In addition, modern bred cultivars incorporate desirable traits such as self-compatibility and firmness. Cluster and structural analysis based on SSR data clearly differentiates the genotypes according to their geographic origin and pedigree. Finally, results showed an association between some alleles of PaCITA7 and UDP96003 SSR markers with apricot fruit weight, one allele of UDAp407 marker with fruit firmness and one allele of UDP98406 marker with fruit ripening.

Genetic Structure of Modern Durum Wheat Cultivars and Mediterranean Landraces Matches with Their Agronomic Performance.

A collection of 172 durum wheat landraces from 21 Mediterranean countries and 20 modern cultivars were phenotyped in 6 environments for 14 traits including phenology, biomass, yield and yield components. The genetic structure of the collection was ascertained with 44 simple sequence repeat markers that identified 448 alleles, 226 of them with a frequency lower than 5%, and 10 alleles per locus on average. In the modern cultivars all the alleles were fixed in 59% of the markers. Total genetic diversity was HT = 0.7080 and the genetic differentiation value was GST = 0.1730. STRUCTURE software allocated 90.1% of the accessions in five subpopulations, one including all modern cultivars, and the four containing landrace related to their geographic origin: eastern Mediterranean, eastern Balkans and Turkey, western Balkans and Egypt, and western Mediterranean. Mean yield of subpopulations ranged from 2.6 t ha-1 for the western Balkan and Egyptian landraces to 4.0 t ha-1 for modern cultivars, with the remaining three subpopulations showing similar values of 3.1 t ha-1. Modern cultivars had the highest number of grains m-2 and harvest index, and the shortest cycle length. The diversity was lowest in modern cultivars (HT = 0.4835) and highest in landraces from the western Balkans and Egypt (HT = 0.6979). Genetic diversity and AMOVA indicated that variability between subpopulations was much lower (17%) than variability within them (83%), though all subpopulations had similar biomass values in all growth stages. A dendrogram based on simple sequence repeat data matched with the clusters obtained by STRUCTURE, improving this classification for some accessions that have a large admixture. landraces included in the subpopulation from the eastern Balkans and Turkey were separated into two branches in the dendrogram drawn with phenotypic data, suggesting a different origin for the landraces collected in Serbia and Macedonia. The current study shows a reliable relationship between genetic and phenotypic population structures, and the connection of both with the geographic origin of the landraces.

Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea.

Genetic Diversity of Namibian Pennisetum glaucum (L.) R. BR. (Pearl Millet) Landraces Analyzed by SSR and Morphological Markers.

Current Pennisetum glaucum (L.) R. BR. cultivars in Namibia have overall poor performance posing a threat to the nation's food security because this crop is staple for over 70% of the Namibian population. The crop suffers from undesirable production traits such as susceptibility to diseases, low yield, and prolonged reproductive cycle. This study aimed to understand the genetic diversity of the crop in Namibia by simple sequence repeats (SSRs) and morphology analysis. A total of 1441 genotypes were collected from the National Gene Bank representing all the Namibian landraces. A sample of 96 genotypes was further analyzed by SSR using Shannon-Wiener diversity index and revealed a value of 0.45 indicating low genetic diversity. Ordination using Principal Coordinate Analysis (PCoA) on SSR data confirmed clusters generated by UPGMA for the 96 P. glaucum accessions. UPGMA phenograms of 29 morphological characterized genotypes were generated for SSR and morphology data and the two trees revealed 78% resemblance. Lodging susceptibility, tillering attitude, spike density, fodder yield potential, early vigour, and spike shape were the phenotypic characters upon which some clusters were based in both datasets. It is recommended that efforts should be made to widen the current gene pool in Namibia.

Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.

Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.