Genetic Diversity and Structure of Core Collection of Huangqi (Astragalus) Developed by Genomic Simple Sequence Repeat Markers

Huangqi (Astragalus) is a versatile herb that possesses several therapeutic effects against a variety of diseases, especially lung diseases. The aim of this study was to establish a core collection of Astragalus germplasm resources based on molecular 10 SSR markers. Based on 380 samples of Astragalus collected from different areas, five different methods were utilized to construct the core collection of Astragalus, including PowerCore-based M strategy, CoreFinder-based M strategy, Core Hunter-based stepwise sampling, PowerMarker-based simulated annealing algorithm based on allele maximization, and PowerMarker-based simulated annealing algorithm based on maximizing genetic diversity. Of the constructed Astragalus core collections, the CoreFinder-based M strategy was found to be the most suitable approach as it reserved all the alleles and most of the genetic diversity parameters were higher than those of the initial collection. Additional analyses demonstrated that the genetic diversity of the core collection matched the properties of the initial collection. Further, the phylogenetic trees indicated that the population structure of the core collection was similar to that of the initial collection. In addition, our results showed that the optimal grouping value of K was 2. The construction of a core collection is beneficial for the understanding, management, and utilization of Astragalus. Moreover, this study will act as a valuable reference for constructing core collections for other plants or fungi.

Construction of the Core Collection of Catalpa fargesii f. duclouxii (Huangxinzimu) Based on Molecular Markers and Phenotypic Traits

To promote the conservation and utilization of Catalpa fargesii f. duclouxii (Huangxinzimu) germplasm resources, a total of 252 accessions were used to construct a preliminary core collection according to phenotypic traits and single nucleotide polymorphism (SNP) markers. In this study, 24 phenotypic traits, namely, 9 quantitative traits and 15 qualitative traits, were investigated. The core collection of C. fargesii f. duclouxii (Huangxinzimu) was constructed to remove redundant samples from the collected materials. First, the phenotypic core collection, with a sample proportion of 30, consisting of 24 clones, was constructed according to two genetic distances (Euclidean distance and Mahalanobis), four system clustering methods (the unweighted pair-group average method, Ward’s method, the complete linkage method, and the single linkage method), and three sampling methods (random sampling, deviation sampling, and preferred sampling). The best construction strategies were selected for further comparison. Three core collections (D2C3S3-30, D2C3S3-50, and D2C3S3-70) were constructed according to the optimal construction strategy at three sampling proportions. The core collection D2C3S3-30 with the best parameters was evaluated by using six parameters: the mean difference percentage (MD), variance difference percentage (VD), periodic rate of range (CR), changeable rate of the coefficient of variation (VR), minimum rate of change (CRMIN), and maximum rate of change (CRMAX). Three core collections (M-30, M-50, and M-70) were constructed by molecular markers, and the optimal core collection M-30 was selected by using five parameters, namely, Ho, He, PIC, MAF, and loci. The combination of D2C3S3-30 and M-30 was used to construct the final core collection DM-45, 45 samples representing the complete range of phenotypic and genetic variability. In this study, phenotypic traits combined with molecular markers were used to construct core collections to effectively capture the entire range of trait variation, effectively representing the original germplasm and providing a basis for the conservation and utilization of C. fargesii f. duclouxii (Huangxinzimu).

Visualized Analysis of Heavy Ion Radiotherapy: Development, Barriers and Future Directions

BackgroundHeavy ion radiotherapy (HIRT) has great advantages as tumor radiotherapy.MethodsBased on 1,558 literatures from core collections of Web of Science from 1980 to 2020, this study visually analyzes the evolution of HIRT research, and sorts out the hotspots and trends of HIRT research using CiteSpace software.ResultsResearch on HIRT has received more extensive attention over the last 40 years. The development of HIRT is not only closely related to radiation and oncology, but also closely related to the development of human society. In terms of citation frequency, “International Journal of Radiation Oncology*Biology*Physics” was the top journal. In terms of influence, “Radiotherapy and Oncology” was the top journal. “Radiation therapy” and “carbon ion radiotherapy” were the two most frequently used keywords in this field.ConclusionThe evolution of the HIRT research has occurred in approximately three stages, including technological exploration, safety and effectiveness research and technological breakthroughs. Finally, some suggestions for future research are put forward.

Estudio de la internacionalización de la Universidad Nacional de Mar del Plata desde la perspectiva de la producción científica. Análisis de la colaboración y liderazgo científico

En este trabajo se exponen los resultados obtenidos del análisis y caracterización de la internacionalización de la actividad científica de la Universidad Nacional de Mar del Plata (UNMDP) a partir del estudio de la producción publicada desde su creación. La investigación abarca el período 1978-2019 y está centrada en los artículos publicados durante dicho lapso. Las fuentes secundarias utilizadas fueron Web of Science Core Collections (Clarivate) y Scopus (Elsevier) de las que se recuperaron los registros que conforman el objeto de estudio. Para el análisis de esta dimensión fueron aplicados los indicadores de colaboración autoral (instituciones y países), colaboración por grandes áreas temáticas, liderazgo científico e idioma de publicación. Además de los resultados y las respectivas representaciones de los indicadores propuestos se desarrollan algunas reflexiones sobre la medición de la internacionalización en instituciones de educación superior y los desafíos que presenta para una institución universitaria.

Genome-Wide Association Study Reveals the QTLs for Seed Storability in World Rice Core Collections

Seed storability is a main agronomically important trait to assure storage safety of grain and seeds in rice. Although many quantitative trait loci (QTLs) and associated genes for rice seed storability have been identified, the detailed genetic mechanisms of seed storability remain unclear in rice. In this study, a genome-wide association study (GWAS) was performed in 456 diverse rice core collections from the 3K rice genome. We discovered the new nine QTLs designated as qSS1-1, qSS1-2, qSS2-1, qSS3-1, qSS5-1, qSS5-2, qSS7-1, qSS8-1, and qSS11-1. According to the analysis of the new nine QTLs, our results could well explain the reason why seed storability of indica subspecies was superior to japonica subspecies in rice. Among them, qSS1-2 and qSS8-1 were potentially co-localized with a known associated qSS1/OsGH3-2 and OsPIMT1, respectively. Our results also suggest that pyramiding breeding of superior alleles of these associated genes will lead to new varieties with improved seed storability in the future.

Genotype × Environment Interaction for Resistance to Early Leaf Spot of Groundnut Mini Core Collections in the Savannas of Nigeria

Background: The genetic yield potential of groundnut (Arachis hypogaea L.) has been continuously challenged by several diseases including early leaf spot (ELS).Methods: In the current study, we evaluated groundnut mini core collections under artificial and natural disease epiphytotics in six environments to identify stable elite sources for ELS resistance and pod yield. Mixed model analysis was done to adequately capture the variance component as a result of genotype (G), environment (E) and G × E interaction (GEI).Result: Highly significant (p less than 0.001) effects for G and GEI on ELS and pod weight were observed. The parametric and non-parametric stability models ranked the genotype differently for their stability to ELS. The GGE biplot identified ICG 1519 as a stable genotype for the ELS resistance. For pod weight, ICG 8896 and ICG 7897 were consistently stable from all the stability models including the GGE biplot. ICG 9449 and ICG 4540 were identified as stable genotypes for both ELS and pod weight. These elite sources of ELS resistance identified in the current study will be useful in the development and deployment of groundnut varieties with resistance to ELS and high pod yielding potentials.

Composite core set construction and diversity analysis of Iranian walnut germplasm using molecular markers and phenotypic traits

Iran is a center of origin and diversity for walnuts (Juglans regia L.) with very good potential for breeding purposes. The rich germplasm available, creates an opportunity for study and selection of the diverse walnut genotypes. In this study, the population structure of 104 Persian walnut accessions was assessed using AFLP markers in combination with phenotypic variability of 17 and 18 qualitative and quantitative traits respetively. The primers E-TG/M-CAG, with high values of number of polymorphic bands, polymorphic information content, marker index and Shannon’s diversity index, were the most effective in detecting genetic variation within the walnut germplasm. Multivariate analysis of variance indicated 93.98% of the genetic variability was between individuals, while 6.32% of variation was among populations. A relatively new technique, an advanced maximization strategy with a heuristic approach, was deployed to develop the core collection. Initially, three independent core collections (CC1–CC3) were created using phenotypic data and molecular markers. The three core collections (CC1–CC3) were then merged to generate a composite core collection (CC4). The mean difference percentage, variance difference percentage, variable rate of coefficient of variance percentage, coincidence rate of range percentage, Shannon’s diversity index, and Nei’s gene diversity were employed for comparative analysis. The CC4 with 46 accessions represented the complete range of phenotypic and genetic variability. This study is the first report describing development of a core collection in walnut using molecular marker data in combination with phenotypic values. The construction of core collection could facilitate the work for identification of genetic determinants of trait variability and aid effective utilization of diversity caused by outcrossing, in walnut breeding programs.

Establishment of a core collection of Cynodon based on morphological data

In a field plot study conducted in Danzhou, Hainan province, China, a total of 537 wild Cynodon accessions from 22 countries and classified into 11 groups according to taxonomy and origin, were characterized in terms of 11 phenotypic traits in order to construct a core collection. For this, the optimal strategy was developed by screening within the following method levels: (i) 7 sampling proportions (5, 10, 15, 20, 25, 30 and 35%); (ii) 3 sampling methods (preferential sampling, deviation sampling and random sampling); (iii) 5 clustering methods [single linkage, completed linkage, median linkage, unweighted pair-group average (UPGMA) and Ward’s method]; (iv) 3 genetic distances (Euclidean distance, Mahalanobis distance and principal component distance); and (v) 3 sampling proportions within groups (simple, logarithmic and square root proportions). Mean difference percentage, variance difference percentage, coincidence rate of range and variation coefficient changing rate were the criteria adopted for evaluating how well the core collection represented the original collection. The correlation between the original and core collections was determined for comparison. The core collections were validated with the sample distribution diagram of the main components. Results showed that the optimal sampling method for constructing a Cynodon core collection was preferential sampling, the optimal sampling proportion being 20%. The optimal sampling proportion within groups was the square root proportion, the optimal genetic distance was Mahalanobis distance and the optimal clustering method was UPGMA. The proposed core collection of Cynodon is composed of 108 accessions; it was constructed following the optimal sampling strategy identified and retained the original collection´s phenotypic diversity, phenotypic trait correlations and phenotypic group structure. Thus, this collection could be considered a representative sample of the entire resource.

Comparison of structure analyses and core collections for the management of walnut genetic resources

The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.