Genetic Diversity and Structure of Walnut Populations in Central and Southwestern China Revealed by Microsatellite Markers

Molecular markers were used to study the genetic diversity, structure, and relationship of Juglans L. with nine populations (five from Juglans regia L. and four from Juglans sigillata Dode) in central and southwestern China. A moderate level of genetic diversity was observed at the population level with the number of effect alleles per locus (A E) ranging from 1.75 to 3.35 (average 2.39) and the proportion of polymorphic loci (P) equaling 100.0%. The expected heterozygosity (H E) within populations ranged from 0.389 to 0.687, and the average was 0.525. The proportion of genetic variation presented among populations accounted for 18.6% of the total genetic diversity. The overall gene flow (N m) among populations equaled 1.10. The unweighted pair-group method using arithmetic averages (UPGMA) clustering and the Mantel test showed that genetic distances among the nine populations are in a good agreement with their geographic distribution, supporting the viewpoint that J. regia and J. sigillata belong to one species. We suggest that the central area of the southwestern mountain regions of China could be considered as a priority for walnut genetic resource conservation.

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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.

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High level of genetic diversity among spelt germplasm revealed by microsatellite markers

Genome ◽

10.1139/g04-065 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1043-1052 ◽

Cited By ~ 14

Author(s):

P Bertin ◽

D Grégoire ◽

S Massart ◽

D de Froidmont

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum L ◽

Genetic Distances ◽

Group Method ◽

Germplasm Collections ◽

Pair Group ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Shared Alleles

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 – proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 ± 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.Key words: spelt, SSR, microsatellites, genetic diversity, germplasm.

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Genetic diversity in table grapes based on RAPD and microsatellite markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011000900010 ◽

2011 ◽

Vol 46 (9) ◽

pp. 1035-1044 ◽

Cited By ~ 9

Author(s):

Patrícia Coelho de Souza Leão ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Similarity Index ◽

Genetic Distances ◽

Table Grape ◽

Group Method ◽

Molecular Characteristics ◽

Table Grapes ◽

Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

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AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽

10.1139/g02-100 ◽

2003 ◽

Vol 46 (1) ◽

pp. 51-58 ◽

Cited By ~ 46

Author(s):

A Segovia-Lerma ◽

R G Cantrell ◽

J M Conway ◽

I M Ray

Keyword(s):

Genetic Diversity ◽

Medicago Sativa ◽

High Throughput ◽

Genetic Distances ◽

Group Method ◽

Aflp Analysis ◽

Dna Templates ◽

Arithmetic Average ◽

Pair Group ◽

Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

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Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽

10.3390/f10030278 ◽

2019 ◽

Vol 10 (3) ◽

pp. 278 ◽

Cited By ~ 2

Author(s):

Hong-Ying Guo ◽

Ze-Liang Wang ◽

Zhen Huang ◽

Zhi Chen ◽

Han-Bo Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Mantel Test ◽

Group Method ◽

Arithmetic Means ◽

Mountain Area ◽

Pair Group ◽

Hill Area ◽

Population Genetic Variation ◽

High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽

10.2298/gensr2101363y ◽

2021 ◽

Vol 53 (1) ◽

pp. 363-378

Author(s):

Juan Yin ◽

Majid Khayatnezhad ◽

Abdul Shakoor

Keyword(s):

Genetic Diversity ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Morphological Characters ◽

Mantel Test ◽

Group Method ◽

Plant Resources ◽

High Genetic Diversity ◽

Pair Group ◽

Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

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Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽

10.1139/g05-022 ◽

2005 ◽

Vol 48 (4) ◽

pp. 731-737 ◽

Cited By ~ 28

Author(s):

N A Barkley ◽

M L Newman ◽

M L Wang ◽

M W Hotchkiss ◽

G A Pederson

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Phylogenetic Relationships ◽

Expressed Sequence Tag ◽

Genetic Distances ◽

Group Method ◽

Arithmetic Means ◽

Pair Group ◽

Expressed Sequence ◽

Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

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Morpho-agronomic Characters Under Drought Stress and Genetic Diversity on the Local Landraces of Cowpea [Vigna unguiculata (L.) Walp] From East Nusa Tenggara Province, Indonesia

Journal of Agricultural Science ◽

10.5539/jas.v13n3p17 ◽

2021 ◽

Vol 13 (3) ◽

pp. 17

Author(s):

Dwi Setyo Rini ◽

Anni Nuraisyah

Keyword(s):

Genetic Diversity ◽

Vigna Unguiculata ◽

Polymorphic Information Content ◽

Similarity Index ◽

Mantel Test ◽

Group Method ◽

Agronomic Characters ◽

Pair Group ◽

Drought Tolerant ◽

Matter Production

This study was performed to reveal the morpho-agronomic characters under drought and genetic diversity using SRAP (Sequence-related amplified polymorphism) marker on local landraces of cowpea (Vigna unguiculata (L). Walp) collected from East Nusa Tenggara Province, Indonesia. Data on drought response indexes according to the dry matter production of cowpea plants classified Carolina and Pinu Pahar as drought-sensitive and drought-tolerant cowpea genotypes, respectively. The assessment of the genetic diversity of cowpea genotypes was performed by using 25 SRAP combination primers. A total of 250 bands were produced by which 245 bands (98%) were polymorphic. The value of PIC (Polymorphic Information Content) of SRAP primers in this study varied from the highest value (0.97) to the lowest value (0.71) generated by primer pairs Me4-Em1 and Me3-Em4, respectively, with an average of PIC 0.87. An unweighted pair group method based on arithmetic averages (UPGMA) in this study was performed according to Nei and Li’s similarity index. The analysis of UPGMA and PCoA successfully separated Carolina and Pinu Pahar genotypes into different clusters. The result of the Mantel test showed that there was no significant correlation between the independent morpho-agronomic analysis and SRAP molecular matrix data.

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Molecular Characterization of Persian Walnut Populations in Iran with Microsatellite Markers

HortScience ◽

10.21273/hortsci.45.9.1403 ◽

2010 ◽

Vol 45 (9) ◽

pp. 1403-1406 ◽

Cited By ~ 18

Author(s):

Rohollah Karimi ◽

Ahmad Ershadi ◽

Kourosh Vahdati ◽

Keith Woeste

Keyword(s):

Juglans Regia ◽

Natural Populations ◽

Genetic Distances ◽

Group Method ◽

Restricted Gene Flow ◽

Pair Group ◽

Hardy Weinberg Equilibrium ◽

High Level ◽

Genetic Structure And Diversity

The genetic structure and diversity of natural populations of Juglans regia L. in Iran were characterized using 11 microsatellite loci. A total of 105 individuals from seven populations were sampled. A high level of genetic diversity was observed within populations with the number of alleles per locus (A) ranging from three to 11 (average = 5.73), the proportion of polymorphic loci was 100%, and the expected heterozygosity ranged from 0.598 to 0.848 (average = 0.707). The proportion of genetic differentiation present among populations accounted for 12% of the total variation. Such considerable interpopulation differentiation detected in J. regia L. could have resulted from several factors, including restricted gene flow between populations. Significant departures from Hardy-Weinberg equilibrium were observed for WGA276, WGA32, and WGA321 loci. The deviations were primarily the result of the surplus of heterozygotes. The unweighted pair group method with arithmetic mean cluster analyses based on Nei's unbiased genetic distances separated the seven populations into two main groups.

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Genetic Analyses of Saprolegnia Strains Isolated from Salmonid Fish of Different Geographic Origin Document the Connection Between Pathogenicity and Molecular Diversity

Journal of Fungi ◽

10.3390/jof7090713 ◽

2021 ◽

Vol 7 (9) ◽

pp. 713

Author(s):

Abdelhameed Elameen ◽

Svein Stueland ◽

Ralf Kristensen ◽

Rosa F. Fristad ◽

Trude Vrålstad ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Data ◽

Genetic Relationships ◽

Geographic Origin ◽

Mantel Test ◽

Group Method ◽

Aflp Analysis ◽

Its Sequencing ◽

Sequencing Data ◽

Pair Group

Saprolegnia parasitica is recognized as one of the most important oomycetes pests of salmon and trout species. The amplified fragment length polymorphism (AFLP) and method sequence data of the internal transcribed spacer (ITS) were used to study the genetic diversity and relationships of Saprolegnia spp. collected from Canada, Chile, Japan, Norway and Scotland. AFLP analysis of 37 Saprolegnia spp. isolates using six primer combinations gave a total of 163 clear polymorphic bands. Bayesian cluster analysis using genetic similarity divided the isolates into three main groups, suggesting that there are genetic relationships among the isolates. The unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCO) confirmed the pattern of the cluster analyses. ITS analyses of 48 Saprolegnia sequences resulted in five well-defined clades. Analysis of molecular variance (AMOVA) revealed greater variation within countries (91.01%) than among countries (8.99%). We were able to distinguish the Saprolegnia isolates according to their species, ability to produce oogonia with and without long spines on the cysts and their ability to or not to cause mortality in salmonids. AFLP markers and ITS sequencing data obtained in the study, were found to be an efficient tool to characterize the genetic diversity and relationships of Saprolegnia spp. The comparison of AFLP analysis and ITS sequence data using the Mantel test showed a very high and significant correlation (r2 = 0.8317).

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