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).

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.

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 in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
Author(s):  
Francisco Elias Ribeiro ◽  
Luc Baudouin ◽  
Patricia Lebrun ◽  
Lázaro José Chaves ◽  
Claudio Brondani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Cape Verde ◽  
Coconut Palm ◽  
Different Populations ◽  
The Mean ◽  
High Level ◽  
Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

Analysis of the polymorphism of expressed sequencetag-Simple sequence repeat in quail

2016 ◽  
Author(s):  
Jun Yan Bai ◽  
You Zhi Pang ◽  
Yan Xia Qi ◽  
Xiao Hui Zhang ◽  
Yin Xian Yun
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Improvement ◽  
Melanin Synthesis ◽  
Sequence Repeat ◽  
Average Heterozygosity ◽  
Information Contents ◽  
The Mean ◽  
Simple Sequence

Aiming at accelerating the application of molecular markers in the genetic improvement of quails, six EST-SSR markers were successfully developed using a bioinformatics method. Polymorphisms of three quail populations (Chinese yellow, China black and Korean quail) were detected. The results showed that there were 2-6 alleles in six EST-SSR markers. The mean polymorphism information contents of Chinese yellow , China blackand Korean quail were 0.5451, 0.4962 and 0.4937, respectively. The average heterozygosity values were 0.6134, 0.5759 and 0.5613. Among the six EST-SSR markers, three were highly polymorphicand the others were moderately polymorphic. The newly-developed six EST-SSR markers may be used to determine the genetic diversity of quails. The six EST-SSR markers identified were related to carbohydrate metabolism and melanin synthesis, but the specific mechanisms need to be further analyzed.

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

2016 ◽  
Vol 96 (5) ◽  
pp. 808-818 ◽  
Author(s):  
Neil Hobson ◽  
Habibur Rahman
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Low Cost ◽  
Pak Choi ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Genetic Pools ◽  
High Level ◽  
Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

Comparison of the genetic diversity in two species of cycads

2005 ◽  
Vol 53 (3) ◽  
pp. 219 ◽  
Author(s):  
Longqian Xiao ◽  
Xun Gong ◽  
Gang Hao ◽  
Xuejun Ge ◽  
Bo Tian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Mean Value ◽  
The Mean ◽  
The Difference ◽  
General Opinion ◽  
Simple Sequence ◽  
Striking Contrast

Inter-simple sequence repeat (ISSR) markers were used to examine the level and distribution of genetic diversity in two cycad species: Cycas parvula S.L.Yang and C. balansae Warburg. The former is found in only two adjacent populations and the latter in a relatively wider distribution. Although genetic diversity in C. balansae (He = 0.1301) is higher than that in C. parvula (He = 0.0538), both are still low in comparison with the mean value (He = 0.169) in gymnosperms. This confirms the general opinion that cycads are genetic relics. The genetic differentiation in both species, however, presents a striking contrast: Gst is 0.0978 in C. parvula, but 0.4003 in C. balansae, which may be ascribed to the difference in distances between their populations.

scholarly journals Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection of Plantgao species

2020 ◽  
Author(s):  
Bagheri Motahareh ◽  
Bahram Heidrai ◽  
Zolfaghar Shahriari ◽  
Ali Dadkhodaie ◽  
Zahra Heidari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Phylogenetic Network ◽  
Germplasm Conservation ◽  
Inter Simple Sequence Repeats ◽  
Geographical Regions ◽  
The Mean ◽  
Polymorphic Bands ◽  
Simple Sequence ◽  
Issr Primers

AbstractAnalysis of genetic diversity in medicinal plants assists germplasm conservation and selection for use in breeding schemes. The aims of the present study were to assess genetic diversity and differentiation of several Plantago species using Inter Simple Sequence Repeats (ISSR) markers and identify marker-trait associations (MTAs). Thirty-one Plantago accessions belonging to eight species with various mating system and chromosome number were collected from geographical regions of Iran environments. Polymorphism in the DNA of Plantago accessions were analyzed using polymerase chain reaction (PCR) of 25 ISSR primers. The data for number of polymorphic bands were analyzed on the basis of several genetic diversity parameters. The results of gel analysis indicated that the ISSR primers amplified 5 to 21 polymorphic bands with 100 to 3000 bp size. The mean polymorphism was 83.83% and five primers showed 100% polymorphism among Plantago accessions. The Polymorphism Information Content (PIC) for ISSR as a dominant marker ranged from 0.1103 to 0.3829 with the mean 0.2727 in the species tested. Accessions in P. amplexicaulis and P. pysillum species represented the highest Nei’s and Shannon’s genetic diversity whilst the lowest obtained for P. lagopus. Analysis of phylogenetic network generated by the Neighbor-Net Algorithm showed moderate split of the eight species tested and the network depicted moderate conflict. The principal coordinate analysis (PCoA) results showed lower conflict in separation of accessions of the eight species. Fifty-six significant MTAs were detected for the traits tested in Plantago accessions, of which six were shared between three seed and mucilage traits and 24 were common between two traits. The coefficient of determination (R2) for the identified MTAs varied between 32 and 73%. In conclusion, the results of genetic diversity analysis suggested that ISSR marker could efficiently differentiate Plantago species and the information of genetic diversity might assist Plantago improvement and conservation.

scholarly journals De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

2020 ◽  
Author(s):  
Duy Dinh Vu ◽  
Syed Noor Muhammad Shah ◽  
Mai Phuong Pham ◽  
Van Thang Bui ◽  
Minh Tam Nguyen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
De Novo ◽  
Average Length ◽  
Species Conservation ◽  
Illumina Hiseq ◽  
Bottleneck Analysis ◽  
Genetic Diversity And Structure ◽  
Geographical Distances ◽  
High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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