scholarly journals Intraspecific Diversity of Monilinia fructicola and M. laxa Populations from Blossoms and Fruit of Different Hosts in Greece

Plant Disease ◽  
2015 ◽  
Vol 99 (10) ◽  
pp. 1353-1359 ◽  
Author(s):  
A. Papavasileiou ◽  
G. S. Karaoglanidis ◽  
T. J. Michailides
Keyword(s):  
Genetic Diversity ◽  
Sweet Cherry ◽  
Gene Diversity ◽  
Diversity Indices ◽  
Intraspecific Diversity ◽  
Monilinia Fructicola ◽  
Sequence Repeat ◽  
Sexual Recombination ◽  
Derived Data ◽  
Of Greece

The genetic variation among 145 isolates of Monilinia fructicola and 156 isolates of M. laxa collected from two distinct regions of Greece (Imathia and Larissa) was analyzed using intersimple-sequence repeat markers. The Monilinia spp. isolates had been collected from infected fruit or blossoms of peach, apricot, sweet cherry, and plum. Calculation of Nei’s gene diversity and Shannon’s diversity indices showed that M. fructicola populations had higher genetic diversity compared with M. laxa populations in both regions sampled. The levels of genetic diversity were similar between populations obtained from diseased blossoms and fruit for each species and the main variances were all from within rather than between populations for the respective regions, hosts, and organ of origin. Genetic distance (Nei’s analysis) was lower between peach and apricot populations than between cherry and plum populations of M. fructicola. M. fructicola isolates from peach and apricot and from sweet cherry and plum were clustered together, while M. laxa isolates clustering based on the host of origin was not possible. The analysis of index of association showed the absence of sexual recombination for both species. The derived data support the hypothesis of a long presence of M. fructicola in Greece, and provide evidence of specialization of M. fructicola populations based on their host of origin.

scholarly journals ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

scholarly journals Systematic Conservation Planning for Intraspecific Genetic Diversity

2017 ◽  
Author(s):  
Ivan Paz-Vinas ◽  
Géraldine Loot ◽  
Virgilio Hermoso ◽  
Charlotte Veyssiere ◽  
Nicolas Poulet ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Planning ◽  
Allelic Richness ◽  
Single Species ◽  
Diversity Indices ◽  
Intraspecific Diversity ◽  
Systematic Conservation Planning ◽  
Conservation Areas ◽  
Conservation Units ◽  
Priority Areas

AbstractIntraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus, Phoxinus phoxinus, Barbatula barbatula, Gobio occitaniae, Leuciscus burdigalensis and Parachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne River basin, France) to determine hot- and cold-spots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness, classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.

scholarly journals Systematic conservation planning for intraspecific genetic diversity

2018 ◽  
Vol 285 (1877) ◽  
pp. 20172746 ◽  
Author(s):  
Ivan Paz-Vinas ◽  
Géraldine Loot ◽  
Virgilio Hermoso ◽  
Charlotte Veyssière ◽  
Nicolas Poulet ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Planning ◽  
Allelic Richness ◽  
Single Species ◽  
Diversity Indices ◽  
Intraspecific Diversity ◽  
Systematic Conservation Planning ◽  
Conservation Areas ◽  
Conservation Units ◽  
Priority Areas

Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus,Phoxinus phoxinus, Barbatula barbatula,Gobio occitaniae,Leuciscus burdigalensisandParachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

scholarly journals Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

2020 ◽  
Vol 50 (3) ◽  
pp. 204-212
Author(s):  
Stalin Juan Vasquez GUIZADO ◽  
Muhammad Azhar NADEEM ◽  
Fawad ALI ◽  
Muzaffer BARUT ◽  
Ephrem HABYARIMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Population Level ◽  
Diversity Indices ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Peruvian Amazon ◽  
Over Exploitation ◽  
Issr Primers

ABSTRACT Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

scholarly journals Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR)

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Mansyur M Mansyur ◽  
Panca Dewi MH Karti ◽  
Luki Abdullah ◽  
Ali Husni ◽  
Puji Lestari
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Mutation Breeding ◽  
Sequence Repeat ◽  
Average Value ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract. Mansyur, Karti PMH, Abdullah L, Husni A, Lestari P. 2019. Genetic diversity of mutant napiergrass using Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). Biodiversitas 20: 2403-2409. Napiergrass is one of the tropical grasses which has a very important role in developing ruminant livestock, its productivity is high and its nutritional content is quite good. Plant breeding to produce new varieties that have better productivity continues. One of them is through mutation breeding and in vitro culture. The purpose of this research was to look at the genetic diversity among napiergrasses using the Expressed Sequence Tag Simple Sequence Repeat (EST-SSR). This study used 14 SSR molecular markers. The results showed that mutant DNA of napiergrass can be clearly amplified by all the EST-SSR primers used. The average number of alleles was 4.57, the average frequency of the main allele was 42%, and the average value of gene diversity was 0.66. While the PIC average value was 0.60. There were five markers that were very informative and have PIC values ​​above 0.7, among others, namely ICMP3045, ICMP3018, PSMP2090, PSMP2209, and PSMP2019. Phylogenetic analysis shows that 37 numbers of napiergrass mutants split into two main clusters at a coefficient of 0.56. The first cluster consists of 26 lines while the second cluster consists of 11 mutants. The parent napiergrass is in the first cluster. There are two pairs of mutants that have the same diversity, namely R20-11 with R 20-20-3 and R100-1 with R100-3.

scholarly journals Assessment of genetic diversity in Fusarium wilt tolerant and susceptible oil palm (Elaeis guineensis Jacq) progenies in Nigeria using inter- simple sequence repeat (ISSR) molecular markers

2019 ◽  
Author(s):  
Nnamdi Ifechukwude Chidi ◽  
Adedotun Adeyinka Adekunle ◽  
Temitope Oluwaseun Samuel ◽  
Emmanuel Ifechukwude Eziashi ◽  
David Okeh Igwe
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Oil Palm ◽  
Simple Sequence Repeat ◽  
Elaeis Guineensis ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Mean Value ◽  
Sequence Repeat ◽  
Simple Sequence

Abstract Background Improving oil palm in Nigeria for food security and subsequent export requires a better understanding of the genetic diversity among oil palm progenies tolerant and susceptible to Fusarium wilt disease. In view of the limitations of the orthodox method used in screening this disease, and the advantages of molecular markers, fourteen (14) Inter-simple sequence repeat (ISSR) DNA markers were applied to evaluate the genetic diversity, population structure and cluster resolutions of alleles responsible for tolerance of 560 Elaeis guineensis Jacq palms representing 8 different progenies distributed across NigeriaResults The amplification product revealed a moderately high level of genetic diversity with a total of 46 alleles identified, resulting in an average of 4.9091 alleles per locus detected between the oil palm progenies. Polymorphic information content (PIC) values varied between 0.3706-0.7861, with a mean value of 0.6829. The genetic diversity values ranged from 0.4063-0.8125 with a mean of 0.7216, while the major allele frequency ranged from 0.2500- 0.7500 with a mean value of 0.3750. Shannon's information index (I), Nei's gene diversity (H), and the effective number of alleles (Ne) had values of 0.6931, 0.5000, and 2.000, respectively. The genetic diversity was highest in progeny 3023, and lowest in progeny 4189. Mean values of the total gene diversity (Ht), gene diversity within the population (Hs) of the progenies, coefficient of gene differentiation among the progenies (Gst) and level of gene flow (Nm) were 0.4899, 0.3520, 0.2815 and 1.2764, respectively. The dendrogram clustered the progenies into six major clusters, while Principal Component Analysis (PCA) grouped the progenies into five clusters. PCA further identified the coordinate positions of tolerant and susceptible alleles of oil palm progeniesConclusion This study confirmed the identification of the coordinate positions of tolerant alleles in the gene loci, which could be exploited by breeders to developing tolerant oil palm seedlings.

scholarly journals Evaluation of Genetic Diversity Among Kongpo Monkshood (Aconitum kongboense L.) Germplasm Accessions Revealed by Inter Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (7) ◽  
pp. 940-943 ◽  
Author(s):  
Fanjuan Meng ◽  
Ruoding Wang ◽  
Mu Peng ◽  
Chao Wang ◽  
Zhongkui Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Tibet Plateau ◽  
Polymorphism Analysis ◽  
Sequence Repeat ◽  
The Mean ◽  
Simple Sequence

Inter simple sequence repeat (ISSR) were used to evaluate the genetic diversity of Kongpo Monkshood (Aconitum kongboense L.) in Motuo, Tibet Plateau. From 70 accessions of three populations, 10 out of 100 informative ISSR primers were chosen for polymorphism analysis. Percentage of polymorphic bands was 50% to 66.67% with a mean of 58.42%. The effective number of alleles (Ne) was between 1.545 (population 3) and 1.586 (population 2), and the mean value was 1.564; the Nei’s gene diversity (h) ranged from 0.315 to 0.327 with the average value of 0.320; the value of Shannon’s information index (I) ranged from 0.459 to 0.478, with the mean of 0.469. Based on molecular data, cluster analysis classified the 70 cultivars into three groups. Most accessions were related to the geographical origin and their genetic backgrounds. Bayesian structure and PCoA analysis were consistent with the dendrogram result. Based on the analysis, it will provide a reference for Kongpo Monkshood breeding purposes and contribute to identification, rational exploitation, and conservation of germplasms.

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