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

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1043-1052 ◽  
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.

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

2008 ◽  
Vol 133 (2) ◽  
pp. 197-203 ◽  
Author(s):  
Hua Wang ◽  
Dong Pei ◽  
Rui-sheng Gu ◽  
Bao-qing Wang
Keyword(s):  
Genetic Diversity ◽  
Juglans Regia ◽  
Central Area ◽  
Population Level ◽  
Genetic Distances ◽  
Mantel Test ◽  
Southwestern China ◽  
Group Method ◽  
Pair Group ◽  
Genetic Diversity And Structure

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.

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

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.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
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.

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

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
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.

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

scholarly journals Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

2019 ◽  
Vol 18 (4) ◽  
pp. 93-109
Author(s):  
Ilaria Marcotuli ◽  
Andrea Mazzeo ◽  
Domenica Nigro ◽  
Stefania Lucia Giove ◽  
Angelica Giancaspro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ficus Carica ◽  
Accurate Information ◽  
Main Crop ◽  
Polymorphic Pattern ◽  
Genetic Diversity And Structure ◽  
The Mean ◽  
High Level ◽  
Simple Sequence ◽  
Modern Technologies

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

scholarly journals Characterization and Identification of Pawpaw Cultivars and Advanced Selections by Simple Sequence Repeat Markers

2010 ◽  
Vol 135 (2) ◽  
pp. 143-149 ◽  
Author(s):  
Kirk W. Pomper ◽  
Jeremiah D. Lowe ◽  
Li Lu ◽  
Sheri B. Crabtree ◽  
Shandeep Dutta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Marker ◽  
Genetic Erosion ◽  
Null Alleles ◽  
Group Method ◽  
Genomic Libraries ◽  
Pair Group ◽  
Marker Loci ◽  
High Level ◽  
In The Beginning

Pawpaw [Asimina triloba (L.) Dunal.], a tree fruit native to eastern North America, is in the beginning stages of commercialization. Cultivars available in the early 20th century have been lost, and significant genetic erosion may have occurred. Polymorphic microsatellite marker loci were developed from enriched genomic libraries. Five marker loci were used to fingerprint 28 cultivars and 13 selections. For the 41 genotypes, 102 alleles were amplified and major allele frequency (0.16–0.94), number of genotypes (2–27), and allele size (144–343 bp) varied greatly by locus. Four loci were highly polymorphic, as indicated by values for expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content, but only two alleles were detected at locus Pp-C104. A high level of genetic diversity was observed in the studied genotypes. The Ho (0.68) and He (0.70) were similar and indicated few null alleles. In the 41 genotypes, 39 unique fingerprints were observed. These new microsatellite marker loci will be useful for cultivar fingerprinting, management of collections, and investigation of genetic diversity in collections and wild populations. Grouping of genotypes in an unweighted pair group method with arithmetic mean dendrogram was generally consistent with their origins.

Genetic variation within and among populations of Camelliajaponica (Theaceae) in Korea

1996 ◽  
Vol 26 (4) ◽  
pp. 537-542 ◽  
Author(s):  
Myong Gi Chung ◽  
Soon Suk Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Pollen Dispersal ◽  
Island Populations ◽  
Generation Times ◽  
Genetic Diversity And Structure ◽  
Stump Sprouting ◽  
Ability To Regenerate ◽  
The Mean ◽  
High Level

The genetic diversity and structure of 17 Korean populations of Camelliajaponica L., a broad-leaved evergreen tree, was examined. Although most populations are restricted to several islands near the southern and southwestern coast of the Korean Peninsula, they maintain higher levels of genetic variation within populations than do long-lived, woody angiosperms. For example, 13 of 16 loci examined were polymorphic in at least one population, the mean number of alleles per locus was 2.63, and mean expected heterozygosity was 0.265. These values were comparable with those for continuously distributed, mainland populations of C. japonica in Japan. However, a considerably high level of heterozygote deficiency was observed in Korean populations of C. japonica (mean FIS = 0.202). About 13% of the total genetic variation was found among populations (GST = 0.129). Indirect estimates of the number of migrants per generation (1.69, calculated from FST; 2.14, calculated from the mean frequency of eight private alleles) indicate that gene flow among island populations is moderate. Factors contributing to the high levels of genetic diversity found in the entire species of C. japonica include long generation times, ability to regenerate by stump sprouting, predominant outcrossing induced by animal vectors, and occasional pollen dispersal by birds.

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

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 278 ◽  
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.

scholarly journals Genetic Diversity in Populations of Phytophthora citricola Associated with Horticultural Crops in California

Plant Disease ◽  
2007 ◽  
Vol 91 (12) ◽  
pp. 1556-1563 ◽  
Author(s):  
R. G. Bhat ◽  
G. T. Browne
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Group Method ◽  
Aflp Data ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Horticultural Crops ◽  
Pair Group ◽  
Phytophthora Citricola ◽  
High Level

California populations of the plant pathogen Phytophthora citricola were examined for amplified fragment length polymorphism (AFLP), pathogenicity on almond, and sensitivity to mefenoxam. The characterizations of AFLP variation and mefenoxam sensitivity were based on 86 isolates (44 from almond, 11 from avocado, 3 from strawberry, 18 from walnut, and 10 from six other hosts). Cluster analysis of the AFLP data using the unweighted pair group method indicated a high level of genetic diversity among the isolates, and four main clusters were identified—one dominated by isolates from almond, another including all isolates from avocado, and two including isolates from several hosts other than avocado. Analysis of molecular variance revealed that 38.4 and 24.9% of the AFLP variation were associated with host and geographical factors, respectively. Of 24 isolates, including those from almond, avocado, strawberry, and walnut, 22 were aggressive on almond shoots; there was no evidence of host specificity. All but 1 of the 86 isolates grew at different rates on V8 juice medium amended with mefenoxam at 1 ppm, indicating partial tolerance to the fungicide. Isolates of P. citricola from California populations are genetically diverse, and much of the variation is associated with host and geography. These populations are all potentially pathogenic on almond and tolerant to mefenoxam.

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