genetic relationships
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BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Zhiyong Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  

Abstract Background Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. Results We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264–364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. Conclusions As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.


Author(s):  
J. G. Bazarova ◽  
A. V. Logvinova ◽  
B. G. Bazarov

A fundamental problem in materials science consists in establishing a relationship between the chemical composition, structure, and properties of materials. This issue can be solved through the study of multicomponent systems and the directed synthesis of promising compounds. Of practical interest here are active dielectrics that are based on complex oxide compounds, specifically molybdates. Among complex molybdates and tungstates, ternary caged molybdates of the following structural types are of greatest importance: nasicon, perovskite, langbeinite, etc. Due to their widely varying elemental and quantitative compositions, such molybdates are convenient models for structural and chemical design, as well as the establishment of “composition–structure– properties” genetic relationships. Bismuth-containing complex molybdate systems exhibit the formation of phases having ferro-piezoelectric, ionic, and other properties. In this work, the Rb2MoO4–Bi2(MoO4)3–Zr(MoO4)2 ter nary salt system was studied for the first time using the method of intersecting sections in the subsolidus region (450–650 ℃). To this end, quasibinary sections were identified; triangulation was performed. Ternary molybdates Rb5BiZr(MoO4)6 and Rb2BiZr2(MoO4)6,5 were formed in the system using a ceramic technology. These compounds are isostructural to the previously obtained REE molybdates (M5LnZr(MoO4)6) but contain trivalent bismuth instead of rare earth elements. The structure of Rb5BiZr(MoO4)6 was adjusted via the Rietveld refinement technique using the TOPAS 4.2 software package. The ternary molybdate crystallizes in a trigonal system, with the following unit cell parameters of the R`3c space group: a = 10.7756(2) and c = 39.0464(7) Å. According to the studies of thermal properties exhibited by M5BiZr(MoO4)6, these ternary molybdates undergo the first-order phase transition in the temperature range of 450–600 ºC. The IR and Raman spectra of M5BiZr(MoO4)6 reveal the crystallization of ternary molybdates in the R`3c space group. The conducted comparative characterization of M2MoO4–Bi2(MoO4)3–Zr(MoO4)2 phase diagrams suggests that the phase equilibria of these systems depend on the nature of molybdates of monovalent elements.


2022 ◽  
Vol 12 (1) ◽  
pp. 450
Author(s):  
Anthoula Gleridou ◽  
Ioannis Tokatlidis ◽  
Alexios Polidoros

Genetic differentiation between 40 lentil genotypes was tested using molecular markers. The genotypes were produced from a Greek landrace of commercial interest via the honeycomb breeding methodology, i.e., single-plant selection in the absence of competition, across three successive pedigree generations. The selected genotypes from each generation were examined for genetic relationships using 15 SSR molecular markers with HRM analysis. As expected, low variation among consecutive generations at the level of 2.5–7.7% was detected. Analysis of molecular variance (AMOVA) revealed that partitioning of this variation was at higher percentage within each generation’s population than between them. Population structure analysis indicated that ongoing selection could effectively shift the allelic composition in each generation. The applied honeycomb breeding methodology that effectively improved progeny yield and seed quality increased the percentage of favorable alleles altering allelic composition but not eliminating genetic variation of the breeding population.


2022 ◽  
Vol 81 (1) ◽  
Author(s):  
Iskender Tiryaki ◽  
Nuray Isidogru

The objectives of the present study were to determine salt tolerance levels of 12 different common vetch (Vicia sativa L.) cultivars at germination stage in the presence of 250 mM NaCl and to reveal genetic relationships based on gene targeted functional markers (GTFMs) associated with salt tolerance. The results revealed the presence of a significant genetic variation among the cultivars although s alt stress significantly reduced all germination parameters tested. The cultivar Ozveren was the most salt tolerant with 20.1% reduction in final germination percentage compared to control seeds while cultivars Alınoglu, Ayaz and Bakir did not germinate. The maximum delays in germination rate (G50 = 3.78 days) and synchrony (G10-90 = 3.45 days) were obtained from the cultivars Urkmez and Ozveren, respectively. The GTFMs provided a total of 53.1% polymorphism. The primers of MtSOS2 gene gave the highest numbers of alleles per primer pair while the highest polymorphism rate (77.8%) was obtained from the MtP5CS gene. The first three components of principal component analysis explained 57.63% of total variation. This study concluded that the cultivars determined to be salt tolerant and sensitive at germination stage distributed into three main clades determined by UPGMA analysis while the GTFMs associated with salt tolerance successfully determined the genetic relationships of common vetch cultivars.


2022 ◽  
Vol 12 ◽  
Author(s):  
Lin Zhang ◽  
Zhendong Zhu ◽  
Weian Du ◽  
Shengbin Li ◽  
Changhui Liu

Insertion/deletion (InDel) polymorphisms, as ideal forensic markers, show useful characteristics of both SNPs and STRs, such as low mutation rate, short amplicon size and general applicability of genotyping platform, and have been used in human identification, population genetics and biogeographic research in recent years. X-chromosome genetic markers are significant in population genetic studies and indispensable complements in some complex forensic cases. However, the population genetic studies of X-chromosome InDel polymorphisms (X-InDels) still need to be explored. In this study, the forensic utility of a novel panel including 38 X-InDel markers was evaluated in a sample of Han population from Henan province in China. It is observed that the heterozygosities ranged from 0.0054 to 0.6133, and the combined discrimination power was 1–9.18 × 10−17 for males and 1–7.22 × 10−12 for females respectively. The mean exclusion chance in trios and duos were 0.999999319 and 0.999802969 respectively. Multiple biostatistics methods, such as principal component analysis, genetic distances analysis, phylogenetic reconstruction, and structure analysis was used to reveal the genetic relationships among the studied Henan Han group and other 26 reference groups from 1,000 Genomes Project. As expected, the Henan Han population was clustered with East Asian populations, and the most intimate genetic relationships existed in three Han Chinese populations from Henan, Beijing and South China, and showed significant differences compared with other continental groups. These results confirmed the suitability of the 38 X-InDel markers both in individual identification and parentage testing in Han Chinese population, and simultaneously showed the potential application in population genetics.


2022 ◽  
Vol 9 ◽  
Author(s):  
Wei-Hua Cui ◽  
Xin-Yu Du ◽  
Mi-Cai Zhong ◽  
Wei Fang ◽  
Zhi-Quan Suo ◽  
...  

Abstract While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa ‘Plena’ was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. ‘Fenghua’. Only R. ‘Jinbian’ and R. ‘Crimson Glory’ featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.


Author(s):  
И.А. Богуш ◽  
Г.В. Рябов ◽  
В.И. Черкашин ◽  
Н.А. Исаева

Ультрабазиты Северного Кавказа являются древнейшими магматическими породами, возраст которых определяется как нижнепалеозойский (ордовик-силур). Эти породы играют ключевую роль в металлогении благородных металлов Кавказа. С ультрабазитами связаны гигантские запасы металлов в региональной углеродсодержащей девонской черносланцевой толще Северного Кавказа. Практическое значение имеют пермскские пропилиты (Чучкурское месторождение) и металлоносные юрские коры выветривания ультрабазитовых массивов. До настоящего времени не оценены благородные металлы лиственитов Северного Кавказа, сопровождающих ультрабазиты. Цель работы. Показать, что ультраосновные породы являются донорами благородных металлов (Au, Pt, Pd) для Северного Кавказа на протяжении всего фанерозоя. Подтвердить пространственно-временную связь ультрабазитов с благороднометалльным оруденением в черных сланцах Кавказа. Доказать на примере Беденского массива ультрабазитов наличие рудоносной коры выветривания, залегающей на размытой поверхности серпентинитов. Методы исследований. Сделан краткий исторический обзор исследований ультрабазитов с ориентацией на генетические связи благородных металлов (Au, Pt, Pd) с ультрабазитовой магмой. Проведен анализ геологических материалов по наиболее крупным на Северном Кавказе Беденскому и Малкинскому ультрабазитовым массивам - их составу, геохимическим особенностям и потенциальной рудоносности. Результаты работы. По химическому составу ультрабазиты Северного Кавказа отнесены к альпинотипному формационному типу. Установлена рудообразующая роль альпинотипных ультрабазитов для благородных металлов в осадочных и метаморфических толщах фанерозоя региона. Благородные металлы активно проявляются в металлогении фанерозойских геотектонических эпох: каледонской, герцинской, киммерийской и альпийской, имея единый первичный ультрабазитовый источник. Свежие, неизмененные серпентиниты в настоящее время не обнаруживают аномальные содержания благородных металлов, представляющих промышленный интерес. Насыщение серпентинитов благородными металлами проявляется при их экзогенной переработке в обогащенных продуктах их разрушения. Потенциально промышленными осадочными комплексами, состоящими из обогащенных продуктов разрушения серпентинитов, являются коры выветривания серпентинитов и осадочные черносланцевые толщи Северного Кавказа. Ультрабазитовая магма на Северном Кавказе послужила первичным глубинным источником благородных металлов в осадочных и метаморфогенных фанерозойских толщах Кавказа The ultrabasites of the North Caucasus are the oldest igneous rocks, whose age is defined as the Lower Paleozoic (Ordovician-Silurian). These rocks play a key role in the metallogeny of the noble metals of the Caucasus. Huge reserves of metals in the regional carbonaceous Devonian black shale stratum of the North Caucasus are associated with ultrabasites. Permian propylites (Chuchkurskoye deposit) and metal-bearing Jurassic crusts of weathering of ultrabasic massifs are of practical importance. To date, the noble metals of the listvenites of the North Caucasus accompanying ultrabasites have not been evaluated. Aim. Show that ultrabasic rocks are donors of noble metals (Au, Pt, Pd) for the North Caucasus throughout the entire Phanerozoic. Confirm the spatio-temporal relationship of ultrabasic rocks with noble metal mineralization in the black shales of the Caucasus. Prove the presence of an ore-bearing weathering crust on the eroded surface of serpentinites using the example of the Bedensky ultrabasic massif. Methods. A brief historical review of ultrabasite studies with a focus on the genetic relationships of noble metals (Au, Pt, Pd) with ultrabasite magma is made. The analysis of geological materials on the Bedene and Malkin ultrabasite massifs, the largest in the North Caucasus, is carried out - their composition, geochemical features and potential ore content. Results. According to the chemical composition, the ultrabasites of the North Caucasus are attributed to the alpinotype formation type. The ore-forming role of alpinotype ultrabasites for noble metals in sedimentary and metamorphic strata of the Phanerozoic region has been established. Noble metals are actively manifested in the metallogeny of the Phanerozoic Geotectonic epochs: Caledonian, Hercynian, Cimmerian and Alpine, having a single primary ultrabasic source. Fresh, unaltered serpentinites do not currently show anomalous contents of noble metals of industrial interest. The saturation of serpentinite with noble metals is manifested during their exogenous processing in the enriched products of their destruction. Potentially industrial sedimentary complexes consisting of enriched products of destruction of serpentinites are the weathering crusts of serpentinites and sedimentary black-shale strata of the North Caucasus. Ultrabasic magma in the North Caucasus served as the primary deep-seated source of precious metals in sedimentary and metamorphogenic Phanerozoic strata of the Caucasus


Author(s):  
Olga Kozhar ◽  
Mee-Sook Kim ◽  
Jorge Ibarra Caballero ◽  
Ned Klopfenstein ◽  
Phil Cannon ◽  
...  

Emerging plant pathogens have been increasing exponentially over the last century. To address this issue, it is critical to determine whether these pathogens are native to ecosystems or have been recently introduced. Understanding the ecological and evolutionary processes fostering emergence can help to manage their spread and predict epidemics/epiphytotics. Using restriction site-associated DNA sequencing data, we studied genetic relationships, pathways of spread, and evolutionary history of Phellinus noxius, an emerging root-rotting fungus of unknown origin, in eastern Asia, Australia, and the Pacific Islands. We analyzed patterns of genetic variation using Bayesian inference, maximum likelihood phylogeny, populations splits and mixtures measuring correlations in allele frequencies and genetic drift, and finally applied coalescent based theory using Approximate Bayesian computation (ABC) with supervised machine learning. Population structure analyses revealed five genetic groups with signatures of complex recent and ancient migration histories. The most probable scenario of ancient pathogen spread is movement from ghost population to Malaysia and the Pacific Islands, with subsequent spread to Taiwan and Australia. Furthermore, ABC analyses indicate that P. noxius spread occurred thousands of generations ago, contradicting previous assumptions that this pathogen was recently introduced to multiple geographic regions. Our results suggest that recent emergence of P. noxius in eastern Asia, Australia, and the Pacific Islands is likely driven by anthropogenic and natural disturbances, such as deforestation, land-use change, severe weather events, and/or introduction of exotic plants. This study provides a novel example of applying genome-wide allele frequency data to unravel dynamics of pathogen emergence under changing ecosystem conditions.


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