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

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248623
Author(s):  
Razieh Mahmoodi ◽  
Mohammad Reza Dadpour ◽  
Darab Hassani ◽  
Mehrshad Zeinalabedini ◽  
Elisa Vendramin ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Core Collection ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Phenotypic Variability ◽  
Juglans Regia ◽  
Phenotypic Traits ◽  
Core Collections ◽  
Shannon’S Diversity Index

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.

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

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1518
Author(s):  
Huifen Xue ◽  
Xiaochi Yu ◽  
Pengyue Fu ◽  
Bingyang Liu ◽  
Shen Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Core Collection ◽  
Snp Markers ◽  
Rate Of Change ◽  
Phenotypic Traits ◽  
Clustering Methods ◽  
Single Linkage ◽  
Core Collections ◽  
The Core ◽  
Linkage Method

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).

Genetic diversity analysis of the Greek lentil (Lens culinaris) landrace ‘Eglouvis’ using morphological and molecular markers

2018 ◽  
Vol 16 (5) ◽  
pp. 469-477 ◽  
Author(s):  
Georgios F. Tsanakas ◽  
Photini V. Mylona ◽  
Katerina Koura ◽  
Anthoula Gleridou ◽  
Alexios N. Polidoros
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Variability ◽  
Morphological Analysis ◽  
Phenotypic Variability ◽  
Market Price ◽  
Genetic Distances ◽  
Reaction Products ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

AbstractThe Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Population genetic study in Juglans regia L. (Persian walnut) and its taxonomic status within the genus Juglans L.

Phytotaxa ◽  
2018 ◽  
Vol 376 (4) ◽  
pp. 154 ◽  
Author(s):  
MEGHDAD MAGHSOODI ◽  
MASOUD SHEIDAI ◽  
FAHIMEH KOOHDAR
Keyword(s):  
Molecular Markers ◽  
Genetic Structure ◽  
Genetic Variability ◽  
Genetic Study ◽  
Population Genetic ◽  
Juglans Regia ◽  
Its Sequences ◽  
Population Genetic Study ◽  
Nrdna Its ◽  
Persian Walnut

Juglans regia commonly known as Persian walnut of the genus Juglans (Juglandaceae) is cultivated throughout the temperate regions of the world for its high quality wood and edible nuts. Though Persian walnut grows on 70,000 ha in Iran, we have no detailed information on genetic structure of walnut cultivars in the country. A detailed knowledge of genetic diversity and spatial genetic structure is essential for conservation and management of tree species. The species like Persian walnut, which has wide range of geographical distribution, should harbor extensive genetic variability to adapt to environmental fluctuations they face. Therefore, detailed population genetic study of local populations become important for conservation and breeding studies. The main aim of the present study was to investigate the population genetic structure of seven Persian walnut populations including 3 wild and 4 cultivated populations by using ISSR and SRAP molecular markers. We also aimed to compare the genetic variability revealed by ISSR neutral multilocus marker and nrDNA ITS sequences. Finally, we tried to investigate the species relationship within the genus Juglans L. by using molecular phylogeny methods based on nrDNA ITS sequences. The results showed that both multilocus molecular markers and ITS sequences can differentiate Persian walnut populations. The studied populations differed genetically and showed isolation by distance (IBD).

Assessing genetic variation for heat stress tolerance in Indian bread wheat genotypes using morpho-physiological traits and molecular markers

2016 ◽  
Vol 15 (6) ◽  
pp. 539-547 ◽  
Author(s):  
P. Sharma ◽  
S. Sareen ◽  
M. Saini ◽  
Shefali
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Heat Stress ◽  
Molecular Markers ◽  
Heat Tolerance ◽  
Polymorphic Information Content ◽  
Physiological Traits ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Wheat Genotypes

AbstractHeat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.

scholarly journals Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE) using RAPD Markers

2010 ◽  
Vol 53 (2) ◽  
pp. 375-387 ◽  
Author(s):  
Luciana do Valle Rego Oliveira ◽  
Ricardo Tadeu de Faria ◽  
Claudete de Fátima Ruas ◽  
Paulo Maurício Ruas ◽  
Melissa de Oliveira Santos ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Variability ◽  
Genetic Analysis ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Core Collection ◽  
Rapd Markers ◽  
Dna Amplification ◽  
Breeding Programs

In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.

scholarly journals Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1121
Author(s):  
Hela Chikh-Rouhou ◽  
Najla Mezghani ◽  
Sameh Mnasri ◽  
Neila Mezghani ◽  
Ana Garcés-Claver
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Molecular Data ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

scholarly journals Establishment of a core collection of Cynodon based on morphological data

2020 ◽  
Vol 8 (3) ◽  
pp. 203-213
Author(s):  
C.Q. Huang ◽  
T. Long ◽  
C.J. Bai ◽  
W.Q. Wang ◽  
J. Tang ◽  
...  
Keyword(s):  
Mahalanobis Distance ◽  
Core Collection ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Optimal Sampling ◽  
Square Root ◽  
Sample Distribution ◽  
Core Collections ◽  
The Core ◽  
Preferential Sampling

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.

scholarly journals Phenotypic and molecular assessment of genetic structure and diversity in a panel of winged yam (Dioscorea alata) clones and cultivars

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Paterne Agre ◽  
Flora Asibe ◽  
Kwabena Darkwa ◽  
Alex Edemodu ◽  
Guillaume Bauchet ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Phenotypic Variability ◽  
Breeding Population ◽  
Snp Markers ◽  
Breeding Program ◽  
Joint Analysis ◽  
Phenotypic Traits ◽  
Dioscorea Alata ◽  
Phenotypic Data ◽  
Heterotic Groups

AbstractA better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.

scholarly journals Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1182 ◽  
Author(s):  
Meriem Miyassa Aci ◽  
Antonio Lupini ◽  
Giuseppe Badagliacca ◽  
Antonio Mauceri ◽  
Emilio Lo Presti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Protein Content ◽  
Structure Analysis ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content.

Sign in / Sign up

Export Citation Format

Share Document