SSR Techniques Research Articles

A Study on the Morphology and Molecular Biology of Tropical Strawberries

The studies on the morpho-molecular characteristics of different strawberry genotypes were conducted at Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh. BARI Strawberry 1, BARI Strawberry 2, BARI Strawberry 3, FA 005, and Festival were used for this experiment. This study was undertaken to assess five tropical strawberry genotypes at morphological and molecular level. BARI Strawberry 2 was recognised as the preeminent genotype among five strawberry cultivars based on fruit production per plant (594.73 grammes), yield per hectare (19.39 tonnes), and fruit count per plant (32.42). The SSR technique was utilised to assess genetic variation and connections among five strawberry cultivars. Initially, ten primers were evaluated, and finally, three primers—EMFv104, ARSFL-10, and ARSFL-15—were selected for analysis. ARSFL-10 produced the fewest polymorphic alleles (3), while the markers EMFv104 and ARSFL-15 generated the most polymorphism alleles (4). The allele frequency for each location ranged from 0.4 (EMFv104) to 0.6 (ARSFL-10). The PIC values ranged from 0.672 on EMFv104 to 0.4992 on ARSFL-10. EMFv104 and ARSFL-15 demonstrated gene diversity scores of 0.72, whereas ARSFL-10 achieved a value of 0.56. The genotypes demonstrating the minimal genetic dissimilarity were BARI Strawberry 1 and Festival, with a value of 0.16667. Primer EMFv104 and ARSFL-15 are regarded as the most efficacious SSR markers for strawberry genotypes.

Characterization of Genetic Variability of Common and Tartary Buckwheat Genotypes Using Microsatellite Markers.

Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. By analyzing 21 SSR markers, an average of 11.6 alleles per locus were amplified and an average PIC value of 0.711 was determined. We determined the heterozygous status of the individuals and variability in the set using the SSR analysis on the basis of expected heterozygosity (He, 0.477), observed heterozygosity (Ho, 0.675), Shannon's index (I, 0.820), and fixation indices (FST, FIS, FIT). Based on the SSR analyses, the lower level of expected heterozygosity in the analyzed set of Tartary buckwheat genotypes was observed compared to common buckwheat. With the help of a hierarchical cluster analysis using the UPGMA algorithm, Structure analysis, and PCoA analysis for the SSR markers, we divided the buckwheat varieties in the dendrogram into two main clusters according to the species. The AMOVA analysis showed that genetic variability between the individuals prevails in the analyzed set. The SSR technique proved to be a suitable tool for the determination of intra- and inter-varietal genetic variability and for analysis of diversity.

REZULTATE PRIVIND CONCENTRAŢIA, PURITATEA, INTEGRITATEA ADN-ULUI ȘI OPTIMIZAREA REACȚIILOR MULTIPLEX SCAR-SSR PENTRU UNELE SOIURI ROMÂNEȘTI DE MĂR

The study was performed to optimize the method of DNA extraction with CTAB, considering reducing working time (non-repeatability of the extraction stage) by obtaining an optimal quantitative concentration to make dilutions and avoid contamination, which would adversely affect the correct and clearly visible amplifications of areas of interest. On the other hand, the multiplexing of SCAR and SSR techniques aimed at reducing reagents consumption and working time. The 48 samples were represented by young (from the top of annual branches) and mature apple leaves harvested in different periods (June and July) from the same year. The leaves come from the apple collections located in two Romanian research units (Research Institute for Fruit Growing Pitesti, Argeș and Research Station for Fruit Growing Voinești, Dâmbovița). DNA was quantified for 48 samples and extracted from young leaves harvested in June and mature leaves, harvested in July. The readings made with the help of the Nanodrop 2000 spectrophotometer showed high concentration values for young leaves and lower concentrations for leaves harvested in July. Evaluation of the DNA concentration for the 48 samples allowed the quantitative/qualitative evaluation and a correlation of the amount of DNA with the stage of development of the leaf. Optimization of SCAR-SSR multiplex reactions for the same DNA concentration (50 ng / μl), led to optimal amplifications for the fragments associated with genes of interest in the SCAR technique, as well as for those amplified by the SSR technique.

Genetic structure of the collection of ryegrass (Lolium) cultivars: a study based on SSR and SCoT markers

Background. Current molecular and genetic approaches make it possible to accelerate ryegrass breeding, simplify source material evaluation, and increase its accuracy. The efficiency of PCR-based SSR and SCoT marker techniques was studied in the context of evaluating the genetic structure of annual and perennial ryegrass accessions and defining DNA-identifying markers.Materials and methods. Genomic DNA was isolated from the aggregate sample of 30 seedlings from each of the 15 analyzed cultivars according to the modified SDS DNA extraction protocol. In total, 20 SSR and 22 SCoT markers were used to assess genetic polymorphism. Basic parameters of the markers’ informative efficiency were identified. Genetic relationships among the studied cultivars were analyzed on the basis of the Neighbor-Joining dendrogram and Bayesian model.Results. To assess the genetic polymorphism of ryegrass species and varieties, 7 SSR loci were selected, for which 110 allelic variants were identified (34 alleles were unique for individual cultivars), and 9 SCoT loci, for which 78 polymorphic amplification fragments were identified, with 28 being cultivar-specific. The dendrogram of genetic similarity and modeling in the Structure v2.3.4 program according to the results of SSR and SCoT analyses distributed the cultivars by their traits according to their species, ploidy level, origin, and similarity. Based on PCoA, carried out using summarized data of SSR and SCoT analyses, a multidimensional diagram of genetic relationships among ryegrass cultivars was constructed.Conclusions. The systems of SSR and SCoT markers appeared to be an efficient tool to reveal genetic polymorphism and identify differences among ryegrass species and cultivars. We found unique DNA profiles that can be used for genetic identification. The results of the study have practical significance in cultivar-specific identification and selection of cultivars for various purposes.

Effect of Inclined Tension Crack on Rock Slope Stability by SSR Technique

The tension cracks and joints in rock or soil slopes affect their failure stability. Prediction of rock or soil slope failure is one of the most challenging tasks in the earth sciences. The actual slopes consist of inhomogeneous materials, complex morphology, and erratic joints. Most studies concerning the failure of rock slopes primarily focused on determining Factor of Safety (FoS) and Critical Slip Surface (CSS). In this article, the effect of inclined tension crack on a rock slope failure is studied numerically with Shear Strength Reduction Factor (SRF) method. An inclined Tension Crack (TC) influences the magnitude and location of the rock slope’s Critical Shear Strength Reduction Factor (CSRF). Certainly, inclined cracks are more prone to cause the failure of the slope than the vertical TC. Yet, all tension cracks do not lead to failure of the slope mass. The effect of the crest distance of the tension crack is also investigated. The numerical results do not show any significant change in the magnitude of CSRF unless the tip of the TC is very near to the crest of the slope. A TC is also replaced with a joint, and the results differ from the corresponding TC. These results are discussed regarding shear stress and Critical Slip Surface (CSS).

Mutagenesis of the odorant receptor co-receptor (Orco) reveals severe olfactory defects in the crop pest moth Helicoverpa armigera

BackgroundOdorant receptors (ORs) as odorant-gated ion channels play a crucial role in insect olfaction. They are formed by a heteromultimeric complex of the odorant receptor co-receptor (Orco) and a ligand-selective Or. Other types of olfactory receptor proteins, such as ionotropic receptors (IRs) and some gustatory receptors (GRs), are also involved in the olfactory system of insects. Orco as an obligatory subunit of ORs is highly conserved, providing an opportunity to systematically evaluate OR-dependent olfactory responses.ResultsHerein, we successfully established a homozygous mutant (Orco−/−) of Helicoverpa armigera, a notorious crop pest, using the CRISPR/Cas9 gene editing technique. We then compared the olfactory response characteristics of wild type (WT) and Orco−/− adults and larvae. Orco−/− males were infertile, while Orco−/− females were fertile. The lifespan of Orco−/− females was longer than that of WT females. The expressions of most Ors, Irs, and other olfaction-related genes in adult antennae of Orco−/− moths were not obviously affected, but some of them were up- or down-regulated. In addition, there was no change in the neuroanatomical phenotype of Orco−/− moths at the level of the antennal lobe (including the macroglomerular complex region of the male). Using EAG and SSR techniques, we discovered that electrophysiological responses of Orco−/− moths to sex pheromone components and many host plant odorants were absent. The upwind flight behaviors toward sex pheromones of Orco−/− males were severely reduced in a wind tunnel experiment. The oviposition selectivity of Orco−/− females to the host plant (green pepper) has completely disappeared, and the chemotaxis toward green pepper was also lost in Orco−/− larvae.ConclusionsOur study indicates that OR-mediated olfaction is essential for pheromone communication, oviposition selection, and larval chemotaxis of H. armigera, suggesting a strategy in which mate searching and host-seeking behaviors of moth pests could be disrupted by inhibiting or silencing Orco expression.

GENETIC RELATIONSHIP BETWEEN SOME BARLEY GENOTYPES (HORDEUM VULGARE L.) USING SSR TECHNIQUE (MICROSATELLITE)

The study was carried out in order to determine the degree of genetic kinship among fifteen barley genotypes using SSR technique with 14 pairs of primers. The study showed that, all the primers gave amplification products and showed polymorphism between the studied genotypes. The total number of alleles was 19, with an average of 1.35, and the number of polymorphic alleles was 19, the percentage of polymorphism was 100%. The number of total and polymorphic alleles ranged between one allele as the lowest value for primers (Bmac0209, Bmac0067, Bmag0225, Bmag012, Bmag0394, Bmag0353, Bmag0206, Bmac0031, GBM1362, EBmac0603) and three alleles as the highest value for the primer Bmag0006. The polymorphism information content (PIC) for each primer ranged from 0.32 (Bmac0209, Bmag0225) as the lowest value, to 0.721 (Bmag0385) as the highest value, and average PIC value was 0.446. The highest value of the percent agreement values (PAV) matrix was about 0.909, between Furat 7 and Mohsen White cultivars, which indicate the present of a high degree of genetic kinship, followed by the Furat 5 and Asowad Arabic (0.863), while the lowest value was 0.318 between H10 and Furat 4, indicating a great genetic variation between them. The previous results were in agreement with the genetic kinship analysis and cluster analysis which showed a high degree of genetic similarity between Furat 7 and Mohsen White, followed by Furat 5 and Asowad Arabic.

GAMMA-RAYS AND MICROWAVE IRRADIATION INFLUENCE ON GUAR (CYAMOPSIS TETRAGONOLOBA): I - MARKERS ASSISTED SELECTION FOR RESPONDING TO MUTAGENIC AGENTS

The recent investigation was carried out to determine the effect of different gamma-ray doses and 900 W (2450 MHz) microwave radiation with various exposure times, separately or in combinations, on the yield, yield components, and chemical properties of guar (Cyamopsis tetragonoloba), as well as, to detect variation induction. The cDNA-SCoT technique was used to obtain molecular markers related to some traits. SSR technique was used to sequence the target fragment related to plant height. Gamma-ray doses of 150 and 250 Gy alone, and in combination with 900 W microwaves irradiation applied with different duration or time span (1, 2, 3, and 4 min) influenced the plant height significantly, as well as, number of tillers plant-1 and fresh and dry forage yield, and fresh and dry leaf stem-1 ratio. In the second sample, seed yield at harvest time, e.g., pods plant-1, weight of pods plant-1, whole plant dry weight, number of seeds pod-1, length of pod, 100-seed weight, and seeds yield were affected by irradiation with different and varied responses. In the M1 generation, the 18 SCoT primers produced 327 bands ranging between 151–2895 bp in size, out of which 282 were polymorphic (86.24%). In the M2, the 18 SCoT primers produced 328 bands ranging between 212–2661 bp in size, out of which 299 were polymorphic (91.16%). The M1 and M2 generations exhibited 89 positive and 39 negative bands, which could be used as marker assisted-selection in response to treated guar plants with different gamma ray doses, separately or in combinations with microwave treatments.

Molecular Characterization of Different Varieties of rice (Oryza sativa L.) using SSR Markers

The present study was performed to analyze molecular diversity among different varieties of rice using SSR markers, which are effective and reliable tools for this type of analysis. A total of 34 different alleles were generated using 17 SSR primers. Out of these 33 alleles were found to be polymorphic and only one was monomorphic. On average, 2 alleles per primer and 1.94 polymorphic alleles per primer was calculated. In the cluster analysis three varieties KATKIRICE, SONUMRICE and 1010 were found to be diverse from other varieties of rice. These varieties may be used as diverse parents for the future breeding programs for rice improvement. According to Jaccard’s similarity coefficient, the highest genetic diversity was observed between KATKIRICE and CHANDRAHASNI. Both varieties were grouped distantly. Out of 17 primers, the best 10 primers were selected based on polymorphic banding patterns for genetic diversity analysis. These selected 10 primers are sufficient to discriminate the group of rice varieties. These findings not only highlight the capacity of the SSR technique but also help in the selection of diverse rice varieties for conservation and crop improvement.

Biodiversity of some fig cultivars in Southern Syria

This research has been conducted in the Biotechnology Laboratory in Damascus University_ Damascus, Syria where the genetic diversity of fourteen cultivars of figs (Ficus carica L.) growing in Swaida governorate which located in the south region of Syria were investigated using (Simple Sequence Repeats) SSRs technique, where 4 cultivars of them were genotypes scattered in the local fields without any scientific taxonomy and farmers did not classify them properly. Eight pairs of SSRs markers were used depend on their ability to separate between fig cultivars as mentioned in previous studies, six pairs of them gave amplified products in the polymerase chain reaction (PCR), while MFC3 and MFC6 primers did not give any amplification products. A total of 17 alleles were detected at six SSRs loci. The alleles number per locus ranged from 2 to 4 with an average of 2.83 alleles/locus. The observed heterozygosity (Ho) was 0.33, while the expected heterozygosity (He) was 0.17. The mean value of genetic similarity was 0.69 where fig cultivars has separated into two clusters in Cluster Analysis, which confirms a significant genetic similarity between most of the cultivars. MFC1 and MFC2 loci gave about 0.67 and 0.61 PIC (Polymorphism Information Content) values respectively, which confirms their ability to study the genetic diversity of fig cultivars more than other loci. F1 and F2 cultivars greatly affect the quality of the fruits as paternity traits as Caprifigs. Tammozi cultivar has low values of its genetic similarity with the rest of the cultivars which reflect great difference between it and other cultivars. Generally, the challenges in this study were in characterizing unrecognized fig cultivars in southern Syria to distinguish between them as they were not certified in agriculture ministry in Syria because the lack in studies related to the same topic as these cultivars were not studied before, thus, we managed to make a significant contribution in certifying fig cultivars in Syria using SSR technique.

Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers

BackgroundReleasing the draft genome of sweet orange provides useful information on genetic structure and molecular marker association with heritable breeding traits in citrus species and their structures. Last decades, microsatellite and retrotransposons are well known as a significant diverse component of the structural evolution. They represented the most potent elements for assessing sustainable utilization of the complicated classification in citrus breeding. Our study was performed to verify the structure analysis and the parentage genetic diversity among the Egyptian citrus rootstocks and the related species. ResultsHere, the performance of 26 SSR and 14 LTR-IRAP in addition to 20 LTR-REMAP markers have been used to conduct the discriminating power and the status of the genetic structure analysis among twenty specimens of citrus genotypes. As a result, the three markers approach exhibited a remarkable variation among the tested genotypes. Overall, the three markers have different discrimination power; the co-dominant SSR markers can differentiate within the group level only in addition to the species level of sour orange, while the dominant markers LTR-IRAP had the ability to discriminate among the group level in addition to species level and the origin of acids. Similarly, LTR-REMAP is suitable for classifying the group level and species level for mandarins as well the origin of Egyptian acids; probably due to it is integration of SSR and LTR-IRAP techniques. Structure and PCoA results of LTR-REMAP marker in strong support for the group structure of citrus species have been divided into four sets: acids, grapefruit/pummelo, mandarin/orange, and sour orange. ConclusionOur findings of the genetic structure analysis support the monophyletic nature of the citrus species; are able to provide unambiguous identification and disposition of true species and related hybrids like lemon, lime, citron, sour orange, grapefruit, mandarin, sweet orange, pummelo, and fortunella; and resulted in their placement in individual or overlap groups. The outcomes of these results will offer helpful and potential information for breeding programs and conservation approaches as a key stage toward identifying the interspecific admixture and the inferred structure origins of Egyptian citrus rootstock and acid cultivars.

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf.

Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.

Assessment of Genetic Diversity for Some Egyptian Wheat Varieties based on Morphological Characters and SSR Markers

The genetic diversity estimates can be useful in important genotypes selection for plant breeders. Eight durum and three bread wheat cultivars were used to study and compare morphological traits with molecular study using SSR technique based genetic diversity estimates. Significant and highly significant differences among wheat genotypes were observed for all traits except flag leaf attitude and outer glume pubescence. Highly significant differences were obtained between durum and bread wheat genotypes for most studied traits. Moderate to low broad-sense heritability estimates were obtained for morphological studied traits. Positive and high significant correlation was found for ear density with foliage color (r= 0.51), waxiness of flag leaf sheath (r= 0.57), waxiness of peduncle (r= 0.60) and peduncle length (r= 0.53), whereas a negative correlation was found between ear density and plant height (r= -0.52, P

Applicability of ISAP, ISSR and SSR markers in tomato breeding programs

Domesticated crops are characterized by narrow genetic base reflecting one or more bottlenecks during millennia-long selection. As a result, current breeding programs are limited in available germplasm and are forced to deal with incremental improvements of yield, resistance, nutritional value, etc. Since the establishment of modern genetics and biotechnology, several new approaches have emerged to extend the genetic base and germplasm improvement. Among these methods, induced mutagenesis appeared as most useful conventional breeding tool. Although, its successful application currently requires good knowledge of modern molecular tools. In this paper we will make an attempt to overview SSR, ISSR and ISAP techniques as well as to offer examples of their application in tomato breeding programs.

Reunion overseas: introduced wild boars and cultivated orange trees interact in the Brazilian Atlantic Forest

Abstract: Reunion in the overseas: introduced wild boars and cultivated orange trees interact in the Mata Atlântica (Brazil). Novel interactions are attracting a lot of interest, especially those occurring between wild animal species and agricultural crops as a consequence of human activities. Novel interactions usually concern to species that interact only because human activity but that otherwise would not even coexist. Typically novel interactions arise from biological invasions as well as from interactions between native and crop species. Less studied are novel interactions between species that originally interact in their native range but, as consequence of human activity (domestication, game introductions, etc.), are now interacting out of their original distribution under new ecological conditionsIn this article, we study the interaction between orange and wild boar, both species sharing Asian origin but being introduced in America and then subjected to new ecological conditions. Dispersers of sweet orange seeds are unknown. As wild boar consumes fruits frequently in citrus orchards, here we assessed whether i) it consumes orange seeds, ii) they are viable after passing through boar’s digestive tract and iii) orange seedlings may naturalise in the Mata Atlântica of Brazil, in a citrus farm surrounded by a large natural area called Mata da Virgínia. We used camera surveys in the orange orchards and in the jungle to identify orange fruit consumers in two periods in 2014 and 2015. The jungle was additionally surveyed looking for citrus seedlings finding more than 50 seedlings in which it was confirmed that they belong to sweet orange trees by SSR techniques. As the wild boar was identified as the main orange consumer, 19 fresh boar feces were collected and citrus seeds removed and sown to assess their viability. Citrus seeds were also planted in the jungle and their germination and seedling survival were studied. Three years after sowing, just 5% of the seedlings remained alive with an average height of less than 10 cm.

Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing.

BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries and de novo transcriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Although de novo transcriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

Lai tạo và tuyển chọn các dòng lúa chịu mặn từ tổ hợp lai hồi giao OM238/Pokkali

The hybridization and selection of salt tolerant and good quality rice varieties are the criteria for the current situation of climate change such as the present. Therefore, this study have transferred salinity tolerant genes of Pokkali to a good quality rice OM238 to determine the rice lines having both salinity tolerance and good quality. This study was caried out to: (1) to evaluate salinity tolerance phenotype by screening in artificial saline medium, (2) to test salinity tolerance gene by SSR technique, (3) to evaluate agronomic characteristics and grain quality based on International Rice Research Institute (IRRI) method. Breeding and selection to BC3F3 generation, then planted to tested at salty fields in BC3F4 and BC3F5 generations. The result revealed that two rice lines in the BC3F6 generation with both the salinity tolerant genes of Pokkali by RM1287 and high iron content in rice, amylose content £ 20%, gel consistency at group 1 (soft rice), low chalikiness of endosperm £ 8%, the long and slender rice grain to develop salinity tolerance and good quality rices.

GENETIC DIVERSITY AMONG SOME SPECIES OF THE GENUS ALLIUM L. USING SSR AND ISSR MARKERS

Genus Allium includes some economically important species like common onion, garlic, chives, and leek under worldwide cultivation. In this study, genetic diversity of some cultivars belonging to three species (Allium sativum L., Allium cepa L. and Allium currat L.) of this genus was investigated using sixteen SSR and three ISSR primers. All primers generated a total of 100 fragments, distributed as, 39% monomorphic, 33% polymorphic and 28% unique. The percentage of polymorphism identified by SSR and ISSR primers varied between 25 and 92.9%. With the highest variability detected for SSR and ISSR regions, the results of similarity demonstrated the presence of a concealable relationship amongst Allium species with a significant degree of similarity among clones belonging to the same species of this genus. DNA sequence of the monomorphic band generated from the five clones and cultivars used in the present work by one of the SSR primers (Asa20) were aligned together and with the earlier obtained sequences belonging to different genera and species. Although all of these sequences were obtained from one monomorphic band using the same primer, the pairwise alignment of the two onion clones showed only 75.49% of homology and nearly the same percentage of homology (73.76%) was obtained between the sequences generated from the two garlic clones. The dendrogram based on genetic similarities between cultivars showed three major clusters. Cluster 1 included only the Egyptian Leek cultivar; cluster 2 comprised the two garlic clones and cluster 3 composed of the two onion cultivars. Generally, the present results corroborate the idea that SSR and ISSR techniques seems to be a convenient tool for genetic diversity of the genus Allium.

Genetic diversity and population structure of 288 potato (Solanum tuberosum L.) germplasms revealed by SSR and AFLP markers

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. China has led world potato production in recent years. To understand the genetic diversity of potato germplasms and to enrich the current gene pool for potato improvement, we made a global collection consisted of 288 potato germplasms from eight countries and the International Potato Center (CIP). Using SSR and AFLP techniques, we evaluated the genetic diversity and population structure of these 288 potato accessions. A total of 190 alleles on 20 SSR loci were detected and all of the SSR alleles were polymorphic among these potato germplasms with an average of 9.5 alleles per SSR locus ranging from 2 to 23. The effective number of alleles per locus (Ne*), Nei's genetic diversity (H*), and Shannon's information index (I*) was from (0.1709±0.3698) to (1.6166±0.3414), (0.076±0.1388) to (0.3812±0.1886), and (0.1324±0.1970) to (0.5347±0.1440), respectively, and the mean polymorphic information content (PIC) value was 0.7312. A total of 988 AFLP alleles were detected by 10 AFLP primer combinations with 983 polymorphic alleles, and 99.49% alleles was polymorphic with an average of 98.3 polymorphic alleles per primer combination ranging from 91 to 116. The values of Ne*, H* and I* were from (1.5162±0.311) to (1.6423±0.3278), (0.3114±0.145) to (0.3675±0.1121), and (0.4761±0.1792) to (0.547±0.1322), respectively, and the average PIC value was 0.9871. Bayesian analysis discriminated the accessions into seven subgroup and an admix group. The majority of accessions from CIP and China were assigned into SG1, SG5, SG6, SG7 and admix group. Accessions in SG3 were mainly from CIP and two small groups SG2 and SG4 were mainly from northeastern China. In general, the results obtained from Bayesian statistical analysis, cluster analysis and principal coordinate analysis consistently revealed the lack of geographical differentiation among country-wide collections, indicating germplasm introduction was common for the countries out of potato origin center. The polymorphic markers and the differentiate genetic lineages found in this study provide useful information for potato improvement and conservation programs.

Smart search space reduction for approximate computing: A low energy HEVC encoder case study

Abstract The approximate computing paradigm provides methods to optimize algorithms while considering both application quality of service and computational complexity. Approximate computing can be applied at different levels of abstraction, from algorithm level to application level. Approximate computing at algorithm level reduces the computational complexity by approximating or skipping computational blocks. A number of applications in the signal and image processing domain integrate algorithms based on discrete optimization techniques. These techniques minimize a cost function by exploring an application parameter search space. In this paper, a new methodology is proposed that exploits the computation-skipping approximate computing concept. The methodology, named Smart Search Space Reduction(S ssr ), explores at design time the Pareto relationship between computational complexity and application quality. At run time, an approximation manager can then early select a good candidate configuration. S ssr reduces the run time search space and, in turn, reduces computational complexity. An efficient S ssr technique adjusts at design time the configuration selectivity while selecting at run time the most suitable functions to skip. The real time High Efficiency Video Coding Hevc encoder in All Intra(AI) profile is used as a case study to illustrate the benefits of S ssr . In this application, two discrete optimizations are performed. They explore different coding parameters and select the values leading to the minimal cost in terms of a tradeoff between bitrate, quality and computational energy by acting on both the Hevc coding-tree partitioning and the intra-modes. Combining two S ssr s iterations on this use case, the energy consumption is reduced by up to 77%. Moreover, the combination of the two S ssr s iterations in comparison to using only one reduces the BD-BR bitrate/quality metric by 4% for the same energy consumption.