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The fresh fruits of ‘Grande Naine’ (Cavendish AAA—Musa spp.) dominate the world market, especially in countries with a population in a situation of social vulnerability. However, Fusarium wilt, caused by the fungus Fusarium oxysporum f.sp. cubense race 4 Subtropical (Foc ST4), emerges as a serious threat to banana production, requiring the development of resistant cultivars based on biotechnological strategies, such as the induction of mutation in tissue culture. This study aimed to identify and characterize genetic variation in somaclones resistant to Fusarium oxysporum f.sp. cubense subtropical race 4 (Foc ST4), derived from ‘Grand Naine’ bananas, by molecular markers based on retrotransposons IRAP (Inter-retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Nine combinations of IRAP and six combinations of REMAP primers were used. The low number of polymorphic bands did not allow for genetic diversity studies; however, ten polymorphic bands between the somaclones and control were sequenced. Of these, three presented good base calling and were aligned, namely, 1AF, 2AF, and 3AF bands. Only the 1AF band presented function related to stress response with homology to a calcium-binding protein. These proteins act early in plant infection as secondary messengers activated by pathogen-associated molecular patterns (PAMPs), initiating the cascade of plant defense signals. The fact that this band is present in all somaclones reinforces previous assessments of their resistance to Foc ST4. The use of markers IRAP and REMAP produced polymorphic bands that can, through future primer design and field validations, accelerate the identification of resistant banana genotypes for use in banana genetic breeding programs.

Overdoses of pesticides lead to a decrease in the yield and quality of plants, such as beans. The unconscious use of deltamethrin, one of the synthetic insecticides, increases the amount of reactive oxygen species (ROS) by causing oxidative stress in plants. In this case, plants tolerate stress by activating the antioxidant defense mechanism and many genes. 5-Aminolevulinic acid (ALA) improves tolerance to stress by acting exogenously in low doses. There are many gene families that are effective in the regulation of this mechanism. In addition, one of the response mechanisms at the molecular level against environmental stressors in plants is retrotransposon movement. In this study, the expression levels of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), and stress-associated protein (SAP) genes were determined by Q-PCR in deltamethrin (0.5 ppm) and various doses (20, 40, and 80 mg/l) of ALA-treated bean seedlings. In addition, one of the response mechanisms at the molecular level against environmental stressors in plants is retrotransposon movement. It was determined that deltamethrin increased the expression of SOD (1.8-fold), GPX (1.4-fold), CAT (2.7-fold), and SAP (2.5-fold) genes, while 20 and 40 mg/l ALA gradually increased the expression of these genes at levels close to control, but 80 mg/l ALA increased the expression of these genes almost to the same level as deltamethrin (2.1-fold, 1.4-fold, 2.6-fold, and 2.6-fold in SOD, GPX, CAT, and SAP genes, respectively). In addition, retrotransposon-microsatellite amplified polymorphism (REMAP) was performed to determine the polymorphism caused by retrotransposon movements. While deltamethrin treatment has caused a decrease in genomic template stability (GTS) (27%), ALA treatments have prevented this decline. At doses of 20, 40, and 80 mg/L of ALA treatments, the GTS ratios were determined to be 96.8%, 74.6%, and 58.7%, respectively. Collectively, these findings demonstrated that ALA has the utility of alleviating pesticide stress effects on beans. [ABSTRACT FROM AUTHOR]

AbstractThis study investigated the effects of retrotransposon movements on the regeneration of 15- and 30-day-old leaves and roots of four different rice varieties grown in tissue culture medium at different salt concentrations (0, 50, 100, and 200 mmol/L) by Inter Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) polymerase chain reaction (PCR)-based marker methods. The study used Hopi, Houba, Osr30, Tos17 primers for IRAP analysis. The (GA)9C ISSR primer was used with four IRAP primers in REMAP analyses. There were different band profiles and polymorphism results between different salts concentrations of the same variety and various rice varieties. We observed that the polymorphism ratios for Houba ranged from 0 to 98% in IRAP and REMAP analyzes in the calculation made with the Jaccard similarity index in mutant samples. We report that mutant varieties give more valuable IRAP and REMAP results than non-mutant varieties. The results reported in this study contribute to understanding the effect of salinity stress on rice in terms of retrotransposon-based molecular markers. These results suggest that all tested retrotransposons are still active, causing genomic polymorphism among rice plantlets.

Jujube is both consumed as a food source and medicinal plant in local markets. It is expected that different geographical populations of Ziziphus jujuba , differ in their genetic content as they grow in different ecological conditions. It is important to have detailed information on population genetic structure and the available genetic variability to make a proper germplasm collection of jujube. We have no data on jujube populations of Iran based on SCoT and REMAP molecular markers, and therefore we planned a population genetic study of these trees in 10 geographical areas. We used SCoT and REMAP molecular markers for our genetic investigation. We found the loci with a high value of Gst (1.00) in SCoT and REMAP markers that can be used in fingerprinting of jujube. [ABSTRACT FROM AUTHOR]

Abstract Background Aegilops tauschii Coss. as a donor of wheat D genome has an important role in wheat breeding programs. Genetic and phylogeographic diversity of 79 Ae. tauschii accessions collected from north and northwest of Iran were analyzed based on retroelement insertional polymorphisms using inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers. Results In total, 306 and 151 polymorphic bands were amplified in IRAP and REMAP analyses, respectively. As a result, a high level of polymorphism was observed among the studied accessions as revealed by an average of 25.5 bands per primer/primer combination and mean PIC value of 0.47 in IRAP and an average of 25.16 bands per primer combination and mean PIC value of 0.47 in REMAP. Genetic relationships of the accessions were analyzed using distance- and model-based cluster analyses. Conclusion The result showed that genetic distance did not seem to be related to geographic distribution, and the accessions could be divided into three groups, which was further supported by principal coordinate analysis. These results on genetic diversity and population structure of Ae. tauschii in Iran should provide important knowledge on genetic resources and their applications in wheat breeding programs.

During 120 years of Polish breeding of oats (Avena sativa L.), dozens of new varieties have been developed. This study was undertaken to investigate the diversity and population structure of 72 Polish oat cultivars released since 1893. The analysis was based on pedigree data as well as ISSR and REMAP marker polymorphisms. The ancestry of common oat cultivars was traced back to 124 cultivars, breeding lines, and landraces. The five most common progenitors were 'Markische Landsorte', 'selection from Ligowo oat', 'Fransk Svarthavre', 'Blanche de Siberie', and 'selection from Schleswig-Holstein landrace'. We found that at least one of them was present in 78% of analysed objects. The studied cultivars were assigned to four groups according to the period of their breeding (before 1945, 1945–1969, 1970–2000, and after 2000) and six groups according to the breeding company (Strzelce Plant Breeding Company, DANKO Plant Breeding, Station of Plant Breeding in Rogaczewo, Małopolska Plant Breeding Company, Station of Plant Breeding in Borów, and other). A decrease in observed heterozygosity within the groups was observed only in the postwar period (1945–1969). As a result of breeders' efforts and extensive crosses with foreign materials initiated in 1970 and 1980, new alleles were provided to the oat gene pool. The highest number of new varieties came from the Strzelce and DANKO breeding companies. There were no significant differences between modern cultivars derived from different breeding companies. However, very early breeding centres functioning before 1945 had significantly different materials from the modern ones. The population genetic structure of the studied group of cultivars appeared to be quite simple. It was shown that their genetic makeup consisted of two or three distinct gene pools, depending on the method of polymorphism assessment. The performed research proved that Polish oat breeding using traditional breeding methods—such as selection or intraspecific and interspecific crosses—although focused on improving yield and tolerance to biotic and abiotic stress, did not significantly narrow the oat gene pool and has been releasing cultivars that are competitive in the European market. [ABSTRACT FROM AUTHOR]

The fresh fruits of 'Grande Naine' (Cavendish AAA- Musa spp.) dominate the world market, especially in countries with a population in a situation of social vulnerability. However, Fusarium wilt, caused by the fungus Fusarium oxysporum f.sp. cubense race 4 Subtropical (Foc ST4), emerges as a serious threat to banana production, requiring the development of resistant cultivars based on biotechnological strategies, such as the induction of mutation in tissue culture. This study aimed to identify and characterize genetic variation in somaclones resistant to Fusarium oxysporum f.sp. cubense subtropical race 4 (Foc ST4), derived from 'Grand Naine' bananas, by molecular markers based on retrotransposons IRAP (Inter-retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Nine combinations of IRAP and six combinations of REMAP primers were used. The low number of polymorphic bands did not allow for genetic diversity studies; however, ten polymorphic bands between the somaclones and control were sequenced. Of these, three presented good base calling and were aligned, namely, 1AF, 2AF, and 3AF bands. Only the 1AF band presented function related to stress response with homology to a calcium-binding protein. These proteins act early in plant infection as secondary messengers activated by pathogen-associated molecular patterns (PAMPs), initiating the cascade of plant defense signals. The fact that this band is present in all somaclones reinforces previous assessments of their resistance to Foc ST4. The use of markers IRAP and REMAP produced polymorphic bands that can, through future primer design and field validations, accelerate the identification of resistant banana genotypes for use in banana genetic breeding programs.

The date palm (Phoenix dactylifera L.) is the most important fruit-bearing crop in arid regions of the Middle East and North Africa. About 3,000 date varieties or cultivars are known worldwide that differ in flowering time, several agronomic traits, and fruit-related traits including moisture and sugar content. Phoenix dactylifera is the second most important horticultural crop of Iran that is cultivated mainly in the southern part of the country. It has about 400 known cultivars in Iran and therefore comprises an important part of the whole world date palm genetic resources. We have no detailed information on its population genetic structure. The present study was an attempt to provide the population genetic data on 14 date palm cultivars for the first time. The present study tried to identify genetic diversity of a few cultivars and provide data on their genetic structure with REMAP molecular marker. The results revealed a moderate level of genetic diversity both among and within the studied cultivars. We obtained mean genetic polymorphism of 20.8%. [ABSTRACT FROM AUTHOR]

The Persian walnut, also known Juglans regia of the genus Juglans is cultivated throughout the temperate regions of the world for its high-quality wood and edible nuts. Genetic diversity, structure and differentiation of cultivated walnut are important for effective conservation, management, and utilisation of germplasm. Recent study on genetic diversity and genotype differentiation in Persian walnut of Iran, revealed that these genotypes can be differentiated by ITS and ISSR, however, these markers show a low degree of genetic variability. ITS sequences revealed a lower degree of genetic difference of the studied Persian walnut genotypes compared to that of ISSR molecular markers. Therefore, it is important to investigate these genotypes by the other molecular markers to find out which one can produce more data on genetic structure and variability in these important genotypes. For the same reason, we continued this study by using cp-DNA (psbA-trnhG) gene, IRAP, and REMAP. To provide barcode for Iranian genotypes of Juglans regia is an other objective of this study. For IRAP and REMAP analyses studies, we randomly selected 60 plants from 6 populations including 3 wild and 3 cultivated populations. For cp- DNA analysis we used 21 plants of Juglans regia randomly selected from 6 studied populations. The present study revealed a high level of genetic variability in Juglans regia genotypes in those sequences investigated by IRAP and REMAP molecular markers. We reported that IRAP and REMAP molecular markers cannot be efficiently used in walnut germplasm genetic screening. [ABSTRACT FROM AUTHOR]

The internal copy (IC) is a simple, yet powerful in-storage processing function, which changes the locations of data blocks without invoking any data transfer between the host and storage. Owing to the out-of-place update constraint of flash memory, solid-state disks (SSDs) employ a flash translation layer (FTL) to manage the logical-to-physical address translation. By leveraging the address indirection feature of SSDs, the IC can be processed only by remapping flash pages to new logical addresses without flash read/write operations. In the existing studies on remap-based IC, SSDs were assumed to have only a single FTL instance. However, recent large-capacity SSDs adopt an arrayed architecture including multiple FTL controllers, where each controller runs an FTL instance to manage its own partitioned address space. For the arrayed SSDs, inter-partition copy requests cannot be handled by address remapping because each partition is managed by a different FTL instance. In this study, we propose an inter-partition remap technique for IC-enabled arrayed SSDs. Additionally, we present the block allocation technique to minimize the number of inter-partition copy requests. Our proposed IC techniques were implemented on an actual arrayed SSD, and showed significant performance improvements compared to the previous remap techniques in several use cases. [ABSTRACT FROM AUTHOR]

Background: Aegilops tauschii Coss. as a donor of wheat D genome has an important role in wheat breeding programs. Genetic and phylogeographic diversity of 79 Ae. tauschii accessions collected from north and northwest of Iran were analyzed based on retroelement insertional polymorphisms using inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers. Results: In total, 306 and 151 polymorphic bands were amplified in IRAP and REMAP analyses, respectively. As a result, a high level of polymorphism was observed among the studied accessions as revealed by an average of 25.5 bands per primer/primer combination and mean PIC value of 0.47 in IRAP and an average of 25.16 bands per primer combination and mean PIC value of 0.47 in REMAP. Genetic relationships of the accessions were analyzed using distance- and model-based cluster analyses. Conclusion: The result showed that genetic distance did not seem to be related to geographic distribution, and the accessions could be divided into three groups, which was further supported by principal coordinate analysis. These results on genetic diversity and population structure of Ae. tauschii in Iran should provide important knowledge on genetic resources and their applications in wheat breeding programs. [ABSTRACT FROM AUTHOR]

Aegilops is known as the ancestor species of wheat and has a major role in the evolution of wheat. Considering the importance of this species and the fact that Iran is the center of the distribution, fifteen IRAP and REMAP markers were used to evaluate the genetic diversity of Ae. tauschii accessions from different regions of Iran and its relationship with Triticum durum and Triticum aestivum. A high level of polymorphism (99%) was observed for both retrotransposon markers. Polymorphism information content, the effective number of alleles (Ne), Nei's genetic diversity (H), and Shannon's information index (I) for IRAP markers were more than REMAP markers. The most genetic diversity was detected in Ae. tauschii accessions. The cluster analysis separated the accessions into three distinct groups. Ae. tauschii accessions from Golestan province grouped in the same cluster with T. aestivum genotypes, indicating that these accessions are probably more like to the progenitor of the bread wheat D genome. Our results revealed that retrotransposon-based molecular markers could be used as the appropriate and reliable marker system to evaluate genetic diversity and relationship in Triticum and Aegilops accessions. [ABSTRACT FROM AUTHOR]

This study investigated the effects of retrotransposon movements on the regeneration of 15- and 30-day-old leaves and roots of four different rice varieties grown in tissue culture medium at different salt concentrations (0, 50, 100, and 200 mmol/L) by Inter Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) polymerase chain reaction (PCR)-based marker methods. The study used Hopi, Houba, Osr30, Tos17 primers for IRAP analysis. The (GA)9C ISSR primer was used with four IRAP primers in REMAP analyses. There were different band profiles and polymorphism results between different salts concentrations of the same variety and various rice varieties. We observed that the polymorphism ratios for Houba ranged from 0 to 98% in IRAP and REMAP analyzes in the calculation made with the Jaccard similarity index in mutant samples. We report that mutant varieties give more valuable IRAP and REMAP results than non-mutant varieties. The results reported in this study contribute to understanding the effect of salinity stress on rice in terms of retrotransposon-based molecular markers. These results suggest that all tested retrotransposons are still active, causing genomic polymorphism among rice plantlets. [ABSTRACT FROM AUTHOR]

Background: Catharanthus roseus (L.) G. Donis a medicinal plant species belonging to the Apocynaceae family, which produces vinblastine and vincristine along with 100 other monoterpenoid indole alkaloids. The process of biosynthesis of C. roseus alkaloids is complex, in which many genes, enzymes, and regulators are involved. Induced mutations may be considered as a potential source for producing a higher amount of vinblastine and vincristine in this plant species. Therefore, the objective of the present study was to examine the effects of different treatments utilized on the induced genetic changes in C. roseus plants and enzyme activities. Methods and results: Spermine, jasmonic acid, methyjasmonate, putrescine, and cold plasma treatments were used for seed treatments. Different molecular markers, namely inter simple sequence repeat, inter retrotransposon amplified polymorphism, and retrotransposon microsatellite amplified polymorphism were employed to reveal the induced genetic changes. Antioxidant enzyme activities were also studied. The treated plants showed genetic variability and a significant increase in antioxidant enzyme activity compared to the control plants. The putrescine treatment resulted in the highest level of activity in superoxidase. A significant positive correlation occurred between the molecular markers data and antioxidant enzyme activities in treated plants. Conclusion: Our data revealed that the different phytohormones and cold plasma treatments could induce both genetic and chemical content changes in C. roseus plants. [ABSTRACT FROM AUTHOR]

During 120 years of Polish breeding of oats (Avena sativa L.), dozens of new varieties have been developed. This study was undertaken to investigate the diversity and population structure of 72 Polish oat cultivars released since 1893. The analysis was based on pedigree data as well as ISSR and REMAP marker polymorphisms. The ancestry of common oat cultivars was traced back to 124 cultivars, breeding lines, and landraces. The five most common progenitors were ‘Markische Landsorte’, ‘selection from Ligowo oat’, ‘Fransk Svarthavre’, ‘Blanche de Siberie’, and ‘selection from Schleswig-Holstein landrace’. We found that at least one of them was present in 78% of analysed objects. The studied cultivars were assigned to four groups according to the period of their breeding (before 1945, 1945–1969, 1970–2000, and after 2000) and six groups according to the breeding company (Strzelce Plant Breeding Company, DANKO Plant Breeding, Station of Plant Breeding in Rogaczewo, Małopolska Plant Breeding Company, Station of Plant Breeding in Borów, and other). A decrease in observed heterozygosity within the groups was observed only in the postwar period (1945–1969). As a result of breeders’ efforts and extensive crosses with foreign materials initiated in 1970 and 1980, new alleles were provided to the oat gene pool. The highest number of new varieties came from the Strzelce and DANKO breeding companies. There were no significant differences between modern cultivars derived from different breeding companies. However, very early breeding centres functioning before 1945 had significantly different materials from the modern ones. The population genetic structure of the studied group of cultivars appeared to be quite simple. It was shown that their genetic makeup consisted of two or three distinct gene pools, depending on the method of polymorphism assessment. The performed research proved that Polish oat breeding using traditional breeding methods—such as selection or intraspecific and interspecific crosses—although focused on improving yield and tolerance to biotic and abiotic stress, did not significantly narrow the oat gene pool and has been releasing cultivars that are competitive in the European market.

Portage is a scalable and extensible remap library for numerical simulations. It supports state-of-the-art remap schemes for meshes and particles in 2D and 3D up to a second-order accuracy. Portage ensures critical properties such as local/global conservation and bounds preservation for mesh remap. It enables multi-material field remap through a dedicated plugin, and leverages the hybrid parallelism exposed by advanced architectures using multi-processing and multi-threading.

Volcanic activity is a major natural disturbance that can catastrophically change an ecosystem over a short time scale. The eruption of Mt. Agung strato-volcano in 1963-1964 was considered among the most important volcanic event of the 20th century due to its effect on global climate. Studies on vegetation and landscape of Mt. Agung post-1970-1980 has been scarce. The current eruption of Mount Agung in June-July 2018, brought awareness of the importance urge to document the past and current landscape along with vegetation on Mt. Agung. Our study aimed to utilize remote sensing technique to explore the pattern of current (2017) land cover and vegetation density on Mt. Agung and estimate of vegetated areas and whether it has changed from the past. LANDSAT 8 images (www.earthexplorer.usgs.gov/) were used in this study. Supervised classification in ENVI was employed to obtain land use or land cover of the Mt. Agung area. Normalized Difference Vegetation Index (NDVI) was also calculated using the feature in the ARC GIS. Online web-based application, REMAP was used to obtain information on past and present condition of the crater of Mt. Agung to see whether there have been changes in vegetated areas around the crater using REMAP (www.remap-app.org). Results showed there are basically five main landcover that can be recognized namely forest (20758.23 ha), settlement (4058.37 ha), water area (41606.64 ha), open area (15335.64 ha) and farming (34554.78 ha). Our NDVI analysis also resulted in areas with have high density (78836.04 ha), medium density (15490.26 ha) and also no vegetation (31008.24 ha). Using web-based GIS application REMAP, we found that there has been an increase (approximately 1 km2) in vegetation cover from the 1980s to 2016. The changes in vegetation near the crater of Mt. Agung is relatively slow when compared to another volcano such as Mt. Merapi. Remote sensing application has enabled us to obtain information on vegetation change relatively easily compared to conduct an extensive on-ground survey where more time and funding is needed.

Wheat is one of the most significant food crops among cereals worldwide in terms of cultivation area and consumption. The reduction in wheat yield due to stress conditions has a major impact on the economy. Long Terminal Repeat (LTR) retrotransposons are considered to be one of the most important mobile elements, which are moved by the environmental alterations in the plant genome and are remarkable in the rearrangement of the genome. The research has been structured to elucidate the impact of selenium on DNA damage and LTR retro-transposition polymorphism in wheat subjected to drought stress. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) procedures were used to describe the DNA damage stages and retro-transposition polymorphism. The outcomes revealed that drought stress induced by polyethylene glycol (-4, -6, and -8 bar PEG 8000) led to a rise in retro-transposition polymorphism, and also a reduction in genomic template stability (GTS). However, DNA damage and retro-transposition polymorphism decreased by treatment with disodium selenite (6, 8, and 10 µM of Na2O4Se) co-treated with similar dosages of PEG 8000. These results suggest that droughtinduced destructive impacts on wheat could be alleviated by exogenously applied disodium selenite. [ABSTRACT FROM AUTHOR]

Genetic diversity analysis is an important tool in crop improvement. Species with high genetic diversity are a valuable source of variation used in breeding programs. The aim of this study was to assess the genetic diversity of four species belonging to the genus Aegilops, which are often used to expand the genetic variability of wheat and triticale. Forty-five genotypes belonging to the genus Aegilops were investigated. Within- and among-species genetic diversity was calculated based on REMAP (retrotransposon–microsatellite amplified polymorphism) molecular markers. Obtained results showed that REMAP markers are a powerful method for genetic diversity analysis, which produces a high number of polymorphic bands (96.09% of total bands were polymorphic). Among tested genotypes, Ae. crassa and Ae. vavilovii showed the highest genetic diversity and should be chosen as a valuable source of genetic variation. [ABSTRACT FROM AUTHOR]

Portage is a scalable and extensible remap library for numerical simulations. It supports state-of-the-art remap schemes for meshes and particles in 2D and 3D up to a second-order accuracy. Portage ensures critical properties such as local/global conservation and bounds preservation for mesh remap. It enables multi-material field remap through a dedicated plugin, and leverages the hybrid parallelism exposed by advanced architectures using multi-processing and multi-threading. [ABSTRACT FROM AUTHOR]

Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice's coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs. [ABSTRACT FROM AUTHOR]

Copyright of Fire Ecology is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary: CMT‐nek is a new scientific application for performing high fidelity predictive simulations of particle‐laden, explosively dispersed turbulent flows. CMT‐nek is compute‐intensive and targeted for deployment on exascale platforms. The moving particles are the primary source of load imbalance when the application is executed on parallel processors. In a demonstration problem, all the particles are initially in a closed container until a detonation occurs and the particles move apart. If all processors get an equal share of the fluid domain, then only some of the processors get sections of the domain that are initially laden with particles, leading to disparate loads on the processors. To eliminate load imbalance in different processors and to speed up the makespan, we present different load‐balancing algorithms for CMT‐nek on large‐scale multicore platforms. The load on a processor is determined using different techniques. The performance of the different load‐balancing algorithms is compared, and the associated overheads are analyzed. Evaluations of the application with and without load‐balancing are conducted, and these show that with load‐balancing, simulation time becomes faster by a factor of up to 9.97. The performance was further improved by a factor of up to 1.42 using machine‐learning–based algorithms. [ABSTRACT FROM AUTHOR]

Copyright of Mediterranean Agricultural Sciences is the property of Akdeniz Universitesi Ziraat Fakultesi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sifnioti, D.E.; Dolphin, T.J., and Vincent, C.E., 2020. Performance of hindcast wave model data used in UK coastal waters. In: Malvárez, G. and Navas, F. (eds.), Global Coastal Issues of 2020. Journal of Coastal Research, Special Issue No. 95, pp. 1284–1290. Coconut Creek (Florida), ISSN 0749-0208. Long-term wave data are a necessity for various marine applications, but wave observations can be temporally and spatially sparse, are often absent in the required locations and can be costly and often cannot be obtained in a short notice. The models used are the UK's Met Office's European 38-year wave hindcast "ReMap", which has spatial resolution of 8 km and temporal step of 3 hours, and ECMWF's (European Centre for Medium-Range Weather Forecasts) "ERA5" reanalysis dataset from 1979 to present with a spatial resolution of 31 km and a temporal step of 1 hour. Both datasets include wave and wind parameters, thus providing valuable long-term data that can be used in coastal regions where wave observations are unavailable. In this paper we assess the errors in performance of the ReMap and ERA5 data by comparing these with wave observations made at two coastal sites in the southern North Sea. ReMap and ERA5 showed a strong correlation with measured waves for significant wave height (Hs) (r = 0.84 - 0.9), fair correlation for peak wave period (Tp) (r = 0.58 - 0.68) and good correlation for mean zero up-crossing wave period (Tz) (r = 0.73 – 0.79), with different error statistics per location and per dataset. Analysis of the 90th percentile shows that the ReMap and ERA5 overestimated Hs by approximately 0.5 m, and by up to 1.2 s for Tp and 0.6s for Tz. Monthly and annual means are also presented and discussed. Overall the performances of ReMap and ERA5 against the measured waves were similar. It is concluded that the ReMap and ERA5 data can be used with reasonable confidence in coastal regions where no direct measurements are available for 'average' conditions, but caution needs to be taken for extreme conditions as an over prediction for extremes is likely. [ABSTRACT FROM AUTHOR]

Transposable element-based molecular markers can be utilized to investigate genetic diversity and to create genetic linkage maps. In this study, Class I and class II transposons were employed to obtain a comparative account of genetic diversity between wild and cultivated barley genotypes. Three types of PCR-based techniques were used: IMP (Inter MITE Polymorphism), IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Specific primer pairs for IMP, IRAP, and REMAP detected a total of 200 bands with an average of 20 bands per marker. The mean polymorphic information content (PIC) and discrimination power (D) values in all 47 genotypes from these three types of transposon-based polymorphisms were 0.910 and 0.935, respectively. Unweighted Pair Group Method with Arithmetic mean (UPGMA)-based cluster analysis classified all 47 genotypes, both wild and cultivated, into separate groups consistent with their geographical origins. Sequencing followed by chromosome location of polymorphic bands enables precise gene introgression from wild gene pool to cultivated barley. The highly polymorphic nature of these marker systems makes them suitable for use in varietal identification and MAS-based breeding programs in barley and other cereals.

Moniliophthora perniciosa is the causal agent of the witches' broom disease (WBD) in cacao but the morphological and molecular diversity of M. perniciosa in Ecuador—the top fine flavor cacao producer worldwide—are poorly understood and the pathogen's sensitivity to compost teas is unknown. A total of 90 isolates of M. perniciosa were obtained from symptomatic samples of cocoa branches and pods collected from four cocoa-producing regions of Ecuador. Growth of each isolate was assed and fitted to a Gompertz model, and the molecular variability was evaluated by sequencing the ITS1, 5.8s, and ITS2 rDNA regions as well as by inter-retrotransposon amplified polymorphism (IRAP), retrotransposon microsatellite amplified polymorphism (REMAP), and simple sequence repeats (SSR) analyses. Sensitivity of M. perniciosa to a compost tea was evaluated at concentrations of 0.5, 1, 1.5, 2, 2.75, and 3.5% in PDA. Results showed morphological and growth rate homogeneity across isolates. Mycelial growth fitted to Gompertz model gave similar parameter estimates for isolates from the different sampling sites. No molecular variability was observed based on ITS and SSR analysis but IRAP and REMAP tests showed high polymorphism. The total genetic diversity based on IRAP and REMAP tests was 0.28 and the genetic diversity within population was 0.24, with Nei's diversity, Shannon's Information, and percent polymorphism values of 0.315, 0.48, and 95.24, respectively for the whole sampled population; isolates from Los Rios province being the most polymorphic. Compost tea sensitivity analysis performed on 85 of the isolates showed a significant inhibitory effect at concentrations of 2.75% or above but concentrations below 1.5% significantly enhanced the growth of most isolates of the pathogen. Results confirmed the high genetic diversity of M. perniciosa and provided insights into growth rate and compost tea sensitivity of the pathogen in Ecuador. [ABSTRACT FROM AUTHOR]

Lagrangian shock hydrodynamics simulations will fail to proceed past a certain time if the mesh is approaching tangling. A common solution is an Arbitrary Lagrangian Eulerian (ALE) form, in which the mesh is improved (remeshing) and the solution is remapped onto the improved mesh. The simplest remeshing techniques involve moving only the nodes of the mesh. More advanced remeshing techniques involve altering the mesh connectivity in portions of the domain in order to prevent tangling. Work has been done using Voronoi-based polygonal mesh generators and 2D quad/triangle mesh adaptation. This paper presents the use of tetrahedral mesh adaptation methods as the remeshing step in an otherwise Lagrangian finite element shock hydrodynamics code called Alexa. [ABSTRACT FROM AUTHOR]

Atmospheric tracer transport is a computationally demanding component of the atmospheric dynamical core of weather and climate simulations. Simulations typically have tens to hundreds of tracers. A tracer field is required to preserve several properties, including mass, shape, and tracer consistency. To improve computational efficiency, it is common to apply different spatial and temporal discretizations to the tracer transport equations than to the dynamical equations. Using different discretizations increases the difficulty of preserving properties. This paper provides a unified framework to analyze the property preservation problem and classes of algorithms to solve it. We examine the primary problem and a safety problem; describe three classes of algorithms to solve these; introduce new algorithms in two of these classes; make connections among the algorithms; analyze each algorithm in terms of correctness, bound on its solution magnitude, and its communication efficiency; and study numerical results. A new algorithm, QLT, has the smallest communication volume, and in an important case it redistributes mass approximately locally. These algorithms are only very loosely coupled to the underlying discretizations of the dynamical and tracer transport equations and thus are broadly and efficiently applicable. In addition, they may be applied to remap problems in applications other than tracer transport. [ABSTRACT FROM AUTHOR]

The process of assembling a species’ reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment’s continuity is disrupted in the target assembly. Such a conversion may lead to a relevant degree of data loss in some circumstances such as copy number variation (CNV) analysis, where the quantitative representation of a genomic region takes precedence over base-specific accuracy. segment_liftover aims at continuity-preserving remapping of genome segments between assemblies and provides features such as approximate locus conversion, automated batch processing and comprehensive logging to facilitate processing of datasets containing large numbers of structural genome variation data.

The process of assembling a species’ reference genome may be performed in a number of iterations, with subsequent genome assemblies differing in the coordinates of mapped elements. The conversion of genome coordinates between different assemblies is required for many integrative and comparative studies. While currently a number of bioinformatics tools are available to accomplish this task, most of them are tailored towards the conversion of single genome coordinates. When converting the boundary positions of segments spanning larger genome regions, segments may be mapped into smaller sub-segments if the original segment’s continuity is disrupted in the target assembly. Such a conversion may lead to a relevant degree of data loss in some circumstances such as copy number variation (CNV) analysis, where the quantitative representation of a genomic region takes precedence over base-specific accuracy. segment_liftover aims at continuity-preserving remapping of genome segments between assemblies and provides features such as approximate locus conversion, automated batch processing and comprehensive logging to facilitate processing of datasets containing large numbers of structural genome variation data.

Einkorn wheat is known as the donor of ‘A’ genome to cultivated wheat and source of many important genes. Therefore, genetic erosion in cultivated wheat provides a good reason to investigate genetic diversity in these species. In the present study, genetic diversity of 14 populations of Triticum urartu and Triticum boeoticum collected from west and north-west of Iran was examined by IRAP and REMAP markers. In total, 26 out of 36 IRAP and 41 out of 88 REMAP combinations amplified polymorphic and scorable banding patterns. IRAP and REMAP combinations produced 6.53 and 5.21 polymorphic bands per assay, respectively. Mean of polymorphism information content for IRAPs and REMAPs were 0.38 and 0.40 and marker index values for them were 2.60 and 2.09, respectively. Analysis of molecular variance based on IRAP and REMAP data revealed significant within and among population variances, although within population variance was higher than that of among population. Primer combinations based on Sukkula and Nikita retrotransposons produced the highest number of markers in the whole population. Cluster and principal coordinate analyses using REMAP data grouped the populations based on the species and geographical origin, but grouping based on IRAP could not separate the two species. However, based on both marker systems considerable diversity was observed among and within the studied populations. [ABSTRACT FROM AUTHOR]

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the wild ancestor of all cultivated tetraploid and hexaploid wheats and harbors a large amount of genetic diversity. This diversity is expected to display eco-geographical patterns of variation, conflating gene flow, and local adaptation. As self-replicating entities comprising the bulk of genomic DNA in wheat, retrotransposons are expected to create predominantly neutral variation via their propagation. Here, we have examined the genetic diversity of 1 Turkish and 14 Israeli populations of wild emmer wheat, based on the retrotransposon marker methods IRAP and REMAP. The level of genetic diversity we detected was in agreement with previous studies that were performed with a variety of marker systems assaying genes and other genomic components. The genetic distances failed to correlate with the geographical distances, suggesting local selection on geographically widespread haplotypes ('weak selection'). However, the proportion of polymorphic loci correlated with the population latitude, which may reflect the temperature and water availability cline. Genetic diversity correlated with longitude, the east being more montane. Principal component analyses on the marker data separated most of the populations. [ABSTRACT FROM AUTHOR]

Flax (Linum usitatissimum L., 2n = 30), is an annual self-pollinated crop. It is used in oil and fiber industries, and also valued for pharmaceutical and nutraceutical applications. Characterization of flax gene pool and evaluation of genetic diversity are crucial for germplasm conservation and breeding. In present study, eighteen retrotransposon microsatellite amplified polymorphism markers were used to evaluate the genetic diversity of cultivated flax within and among populations. Thirty samples of flax plants from three different climates and geographic regions in Iran were used for present investigation. Analysis of molecular variance test showed significant genetic difference (PhiPT = 0.595, P = 0.001) among the studied populations in L. usitatissimum. 41% of total genetic variability was due to within population diversity, whereas 59% was due to among population genetic differentiation. The PCoA plot and cluster analysis grouped plants of Saveh population in a cluster entirely separated from the other two populations and showed high genetic affinity between the two Shiraz and Orumieh populations. STRUCTURE plot identified two distinct gene pools for flax, so that the population of Saveh is different from other populations, but some degree of shared alleles occurred between them. [ABSTRACT FROM AUTHOR]

From the very origins of numerical hydrodynamics in the Lagrangian work of von Neumann and Richtmyer [83] , the issue of total energy conservation as well as entropy production has been problematic. Because of well known problems with mesh deformation, Lagrangian schemes have evolved into Arbitrary Lagrangian–Eulerian (ALE) methods [39] that combine the best properties of Lagrangian and Eulerian methods. Energy issues have persisted for this class of methods. We believe that fundamental issues of energy conservation and entropy production in ALE require further examination. The context of the paper is an ALE scheme that is extended in the sense that it permits cyclic or periodic remap of data between grids of the same or differing connectivity. The principal design goals for a remap method then consist of total energy conservation, bounded internal energy, and compatibility of kinetic energy and momentum. We also have secondary objectives of limiting velocity and stress in a non-directional manner, keeping primitive variables monotone, and providing a higher than second order reconstruction of remapped variables. In particular, the new contributions fall into three categories associated with: energy conservation and entropy production, reconstruction and bounds preservation of scalar and tensor fields, and conservative remap of nonlinear fields. The paper presents a derivation of the methods, details of implementation, and numerical results for a number of test problems. The methods requires volume integration of polynomial functions in polytopal cells with planar facets, and the requisite expressions are derived for arbitrary order. [ABSTRACT FROM AUTHOR]

Mutation breeding is an alternative method for developing agriculturally important crops. A large set of Sagittario bread wheat seeds ( Triticum aestivum L. cv.) were exposed to gamma ray irradiation (200 Gy) to obtain drought-tolerant mutant lines. To study drought tolerance, polyethylene glycol (PEG) 6000 was applied to the M and M individuals under in vitro conditions. Except in well-watered (100%) control plants, drought stress was triggered by a 50% decrease in the irrigation water applied to M and M plants in a greenhouse. Afterwards, 11 candidate drought-tolerant lines were obtained at the M stage and subjected to molecular analysis. The highest percentage of polymorphisms (72.4%) was detected with Retrotransposons Microsatellite Amplified Polymorphism (REMAP) markers followed by Inter-Simple Sequence Repeat (ISSR; 62.07%) and Inter-Retrotransposon Amplified Polymorphism (IRAP) markers (52.94%). A dendrogram tree and a principal coordinate analysis (PCoA) plot classified the experimental samples into three distinctive groups. Additionally, the activities of several antioxidant enzymes were evaluated in both vegetative and flowering stages, and mutant lines showing the highest biochemical performance under stress were detected in the same group through phylogenetic analysis. Gamma ray irradiation was used to improve drought-tolerant wheat lines for forward/reverse genomic studies and marker-assisted selection in crops. [ABSTRACT FROM AUTHOR]

Eggplant is a widely cultivated vegetable crop of great economic importance. Its long lasting history of domestication, selection and breeding has led to the development of numerous cultivars with variable traits. In the present study, we assessed the diversity levels within and among eleven Greek and foreign cultivars, using 22 morphological descriptors and two different classes of molecular markers (retrotransposon microsatellite amplified polymorphism-REMAP markers and nuclear microsatellites). Our results, in accordance with other studies in the field showed: a) the limited levels of genetic polymorphism within the cultivars; b) the high morphological and genetic divergence existing among them as indicated by the genetic distance values calculated, which could be attributed to selection, inbreeding and bottleneck effects; and c) the lack of concordance among morphological descriptors and molecular markers. Despite these, our analysis showed that the utilization of combinations of markers is an effective method for the characterization of plant material providing also useful diagnostic tools for the identification and authentication of the selected Greek cultivars.

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the wild ancestor of all cultivated tetraploid and hexaploid wheats and harbors a large amount of genetic diversity. This diversity is expected to display eco-geographical patterns of variation, conflating gene flow, and local adaptation. As self-replicating entities comprising the bulk of genomic DNA in wheat, retrotransposons are expected to create predominantly neutral variation via their propagation. Here, we have examined the genetic diversity of 1 Turkish and 14 Israeli populations of wild emmer wheat, based on the retrotransposon marker methods IRAP and REMAP. The level of genetic diversity we detected was in agreement with previous studies that were performed with a variety of marker systems assaying genes and other genomic components. The genetic distances failed to correlate with the geographical distances, suggesting local selection on geographically widespread haplotypes (‘weak selection’). However, the proportion of polymorphic loci correlated with the population latitude, which may reflect the temperature and water availability cline. Genetic diversity correlated with longitude, the east being more montane. Principal component analyses on the marker data separated most of the populations.