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

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.

Download Full-text

Genetic variability of dairy cattle breeds in Lithuania

Biologija ◽

10.6001/biologija.v67i3.4513 ◽

2021 ◽

Vol 67 (3) ◽

Author(s):

Romualdas Lapickis ◽

Loreta Griciuvienė ◽

Asta Aleksandravičienė ◽

Indrė Lipatova ◽

Algimantas Paulauskas

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Dairy Cattle ◽

Genetic Material ◽

Genetic Distances ◽

Principal Coordinates Analysis ◽

Black And White ◽

Cattle Breeds ◽

Principal Coordinates ◽

High Degree

Large numbers of different scientific studies are conducted to preserve the breeds and improve the existing ones by introducing the variability of the plate genes, which best shows the phenotypic characteristics that can improve the health of dairy cattle and the quality of their production. The main purpose of this study was to perform an analysis of genetic variability of Lithuanian cattle breeds. Three subpopulation groups were studied: Lithuanian Black and White (95 individuals), Lithuanian Red (49), and Lithuanian White and Red (48). Bovine genetic material was genotyped using a total of 11 fluorescent microsatellite primers to estimate genetic variability. All loci presented a high degree of polymorphism and a total of 292 different alleles (Na) were detected. Thirty-two private alleles were detected in all evaluated subpopulations. After completing pairwise population assignment, which is based on the distribution of allelic frequencies, three populations showed the tendency to group into three separate clusters. However, the performed Principal Coordinates Analysis (PCoA), which is based on genetic distances, showed no anticipated clear grouping. Bayesian structure analysis revealed three genetic clusters. Analysis of FST (0.001–0.027) and Nei genetic distance (0.029–0.084) revealed that the genetic diversity of inter subpopulation in cattle groups was estimated to be lower than the genetic diversity of intra subpopulation.

Download Full-text

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

Agronomy ◽

10.3390/agronomy10081182 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1182 ◽

Cited By ~ 1

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.

Download Full-text

Microsatellite-Based Analysis of Genetic Diversity and Population Structure of Rainbow Trout (Oncorhynchus mykiss) Cultured in Ukraine

Genetics of Aquatic Organisms ◽

10.4194/2459-1831-v5_1_04 ◽

2020 ◽

Vol 5 (1) ◽

pp. 29-39

Author(s):

Оlena Bielikova ◽

Serhii Тarasjuk ◽

Antonina Mruk ◽

Olga Zaloilo ◽

Alexander Didenko

Keyword(s):

Genetic Diversity ◽

Rainbow Trout ◽

Allelic Diversity ◽

Genetic Distances ◽

Principal Coordinates Analysis ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Principal Coordinates ◽

High Level ◽

High Degree ◽

Simple Sequence

The genetic structure of rainbow trout farmed in Ukraine were characterized based on microsatellite loci. The selected set of SSR-markers (Simple-sequence repeatsmarkers) had a high degree of polymorphism that allowed determining the specificity of each local stock (average PIC value = 0.785 ± 0.034). The microsatellite analysis of rainbow trout from the studied stocks showed a high level of genetic diversity (uHe = 0.825 ± 0.030, PIC = 0.785 ± 0.034, I = 1.836 ± 0.127). The level of allelic diversity of the selected loci was high, where the average number of alleles per locus was 7.833, the effective number of alleles per locus was 5.687. The range of amplicon sizes of the studied loci and private alleles for each local group was determined. The cluster analysis showed the presence of three clusters. The range of genetic variability was presented in the graphical interpretation of the principal coordinates analysis (PCoA). Based on unbiased genetic distances, the Kharkiv and Transcarpathian local stocks were found to be the closest, while the Chernivtsi stock was the most distant from them.

Download Full-text

Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

Download Full-text

Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

Acta Botanica Croatica ◽

10.37427/botcro-2021-012 ◽

2021 ◽

Vol 80 (2) ◽

Author(s):

Mostafa Ebadi ◽

Rosa Eftekharian

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Morphological Characters ◽

Mantel Test ◽

Morphological Data ◽

Principal Coordinates Analysis ◽

Cauline Leaf ◽

Senecio Vulgaris ◽

Molecular Features ◽

Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

Download Full-text

Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽

10.3390/genes10020097 ◽

2019 ◽

Vol 10 (2) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Xiaofeng Chi ◽

Faqi Zhang ◽

Qingbo Gao ◽

Rui Xing ◽

Shilong Chen

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Gene Flow ◽

Tibetan Plateau ◽

Environmental Changes ◽

Restricted Gene Flow ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

Download Full-text

Development and characterization of microsatellite markers in Cynara cardunculus L.

Genome ◽

10.1139/g04-111 ◽

2005 ◽

Vol 48 (2) ◽

pp. 217-225 ◽

Cited By ~ 38

Author(s):

Alberto Acquadro ◽

Ezio Portis ◽

David Lee ◽

Paolo Donini ◽

Sergio Lanteri

Keyword(s):

Molecular Markers ◽

Fold Increase ◽

The United States ◽

Enriched Library ◽

Globe Artichoke ◽

Cynara Cardunculus ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Novel Approach ◽

Wild Cardoon

Cynara cardunculus L. is a species native to the Mediterranean basin that comprises 2 crops, globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC), as well as wild cardoon (var. sylvestris (Lamk) Fiori). Globe artichoke represents an important component of the South European agricultural economy but is also cultivated in North Africa, the Near East, South America, the United States, and China. Breeding activities and molecular marker studies have been, to date, extremely limited. Better knowledge of the genome of the species might be gained by developing a range of molecular markers. Here, we report on the development of 14 microsatellites (simple sequence repeats (SSRs)) through a novel approach that we have defined as the microsatellite amplified library (MAL). The approach represents a combination of amplified fragment length polymorphism and a primer extension based enriched library, is rapid, and requires no hybridization enrichment steps. The technique provided a ~40-fold increase in the efficiency of SSR identification compared with conventional library procedures. The developed SSRs were applied for genotyping 36 accessions of C. cardunculus, including a core of 27 varietal types of globe artichoke, 3 accessions of cultivated cardoon, and 6 Sicilian accessions of wild cardoon. Principal coordinates analysis made it possible to differentiate both cultivated and wild forms from each other.Key words: globe artichoke, wild and cultivated cardoon, molecular markers, AFLP, MAL (microsatellite amplified library).

Download Full-text

Temporal diversity changes among 198 Nordic bread wheat landraces and cultivars detected by retrotransposon-based S-SAP analysis

Plant Genetic Resources ◽

10.1017/s1479262108983544 ◽

2008 ◽

Vol 6 (02) ◽

pp. 113-125 ◽

Cited By ~ 11

Author(s):

Shu-Chin Hysing ◽

Torbjörn Säll ◽

Hilde Nybom ◽

Erland Liljeroth ◽

Arnulf Merker ◽

...

Keyword(s):

Genetic Diversity ◽

Bread Wheat ◽

Growth Habit ◽

Gene Diversity ◽

Pedigree Information ◽

Principal Coordinates Analysis ◽

Subsequent Increase ◽

Principal Coordinates ◽

Frequent Exchange ◽

Wheat Landraces

The sequence-specific amplified polymorphism (S-SAP) method was used to genotype 198 Nordic bread wheat landraces and cultivars from the 19th to the 21st centuries. It was shown that theSukkula-9900-LARD retrotransposon primer was highly suitable for resolving closely related wheat materials. Cluster analysis was generally consistent with pedigree information and revealed a clear separation for growth habit but not for countries. A principal coordinates analysis (PCoA) showed a separation into different time periods (before 1910, 1910–1969 and 1970–2003). These results are consistent with the breeding history and pedigree information, indicating that little hybridization has occurred between winter and spring wheat, in contrast to frequent exchange of germplasm between the Nordic countries. Estimates of gene diversity, the PCoA results, and changes in band frequencies across time indicate that plant breeding has led to substantial genetic shifts in Nordic wheat. Diversity was reduced through selections from landraces during the early 20th century, followed by a period of relatively lower genetic diversity, and a subsequent increase and net gains in diversity from the late 1960s onwards through the use of exotic germplasm. Thus, an anticipated loss of overall genetic diversity was found to be negligible, although allele losses have occurred at specific loci.

Download Full-text

High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily

Plants ◽

10.3390/plants8050116 ◽

2019 ◽

Vol 8 (5) ◽

pp. 116 ◽

Cited By ~ 2

Author(s):

Fiore ◽

Mercati ◽

Spina ◽

Blangiforti ◽

Venora ◽

...

Keyword(s):

Genetic Diversity ◽

Durum Wheat ◽

Extreme Environments ◽

Principal Component ◽

Detailed Knowledge ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Wide Range ◽

Wheat Landraces ◽

Durum Wheat Landraces

During the XX Century, the widespread use of modern wheat cultivars drastically reduced the cultivation of ancient landraces, which nowadays are confined to niche cultivation areas. Several durum wheat landraces adapted to the extreme environments of the Mediterranean region, are still being cultivated in Sicily, Italy. Detailed knowledge of the genetic diversity of this germplasm could lay the basis for their efficient management in breeding programs, for a wide-range range of traits. The aim of the present study was to characterize a collection of durum wheat landraces from Sicily, using single nucleotide polymorphisms (SNP) markers, together with agro-morphological, phenological and quality-related traits. Two modern cv. Simeto, Claudio, and the hexaploid landrace, Cuccitta, were used as outgroups. Cluster analysis and Principal Coordinates Analysis (PCoA) allowed us to identify four main clusters across the analyzed germplasm, among which a cluster included only historical and modern varieties. Likewise, structure analysis was able to distinguish the ancient varieties from the others, grouping the entries in seven cryptic genetic clusters. Furthermore, a Principal Component Analysis (PCA) was able to separate the modern testers from the ancient germplasm. This approach was useful to classify and evaluate Sicilian ancient wheat germplasm, supporting their safeguard and providing a genetic fingerprint that is necessary for avoiding commercial frauds to sustaining the economic profits of farmers resorting to landraces cultivation.

Download Full-text

Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

Canadian Journal of Plant Science ◽

10.4141/cjps10014 ◽

2010 ◽

Vol 90 (4) ◽

pp. 443-452 ◽

Cited By ~ 2

Author(s):

T. Karuppanapandian ◽

H W Wang ◽

T. Karuppudurai ◽

J. Rajendhran ◽

M. Kwon ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Vigna Mungo ◽

Polymorphic Band ◽

Black Gram ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Rapd And Issr

The DNA fingerprinting methodologies, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were used to estimate genetic diversity and relationships among 20 black gram (Vigna mungo L. Hepper) varieties. Thirty selected RAPD primers amplified 255 bands, 168 of which were polymorphic (66.5%). On average, these primers produced 8.5 bands, 5.6 of which were polymorphic. Polymorphic band number varied from 2 (A-05) to 10 (OPA-02), with sizes ranging from 100 to 2550 bp. Twenty-four selected ISSR primers produced 238 amplified products, 184 of which were polymorphic (77.8%). On average, these primers generated 9.8 bands, with 7.7 polymorphic bands ranging in number from 4 (ISSR-13) to 11 (ISSR-03), and size from 100-2650 bp. Genetic relationships were estimated using similarity coefficient (Jaccard’s) values between different accession pairs; these varied from 30.7 to 85.0 for RAPD, and from 37.2 to 88.4 with ISSR. UPGMA analysis indicated that the varieties ranged in similarity from 0.50 to 1.00 (mean of 0.75) for RAPD, and from 0.47 to 1.00 (mean of 0.76) with ISSR. Cluster analysis of RAPD and ISSR results identified three clusters with significant bootstrap values, which revealed greater homology between the varieties. Principal coordinates analysis also supported this conclusion. Among the black gram varieties, WBU-108 and RBU-38 were highly divergent, whereas LBG-648 and LBG-623 were genetically similar. The markers generated by RAPD and ISSR assays can provide practical information for the management of genetic resources and these results will also provide useful information for the molecular classification and breeding of new black gram varieties.Key words: Black gram, cluster analysis, genetic diversity, ISSR, molecular markers, RAPD

Download Full-text