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 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 Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers

2011 ◽  
Vol 62 (2) ◽  
pp. 177 ◽  
Author(s):  
Tadesse Sefera ◽  
Bekele Abebie ◽  
Pooran M. Gaur ◽  
Kebebew Assefa ◽  
Rajeev K. Varshney
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Dna Fingerprint ◽  
Pedigree Information ◽  
Sequence Repeat ◽  
Dissimilarity Matrix ◽  
Breeding Programs ◽  
Simple Sequence ◽  
Chickpea Cultivars

The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR diversity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic diversity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

scholarly journals Genetic Diversity Assessment of Selected Annona muricata L. Germplasm in Sri Lanka

2020 ◽  
pp. 1-13
Author(s):  
S. H. M. R. N. P. Samaradiwakara ◽  
W. L. G. Samarasinghe ◽  
P. G. S. Shantha ◽  
K. G. C. N. Jayarathna ◽  
P. Dehigaspitiya ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Polymorphic Band ◽  
Annona Muricata ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Simple Sequence

Annona muricata L. commonly known as soursop is an underutilized fruit crop species in Sri Lanka gaining much importance in the recent past due to its high nutritional and medicinal value. Soursop germplasm collections are available within the country and assessing the genetic diversity is needed to proceed with conservation, detecting promising lines and breeding programs. This study was conducted to assess the genetic diversity of 50 soursop individuals using Inter-Simple Sequence Repeat (ISSR) markers. The study was conducted at Plant Genetic Resources Centre of the Department of Agriculture in Gannoruwa during 2017 to 2019. DNA of the 50 soursop samples were extracted using CTAB method and Polymerase Chain Reaction (PCR) was carried using 13 Inter Simple Sequence Repeat (ISSR) Markers. PCR products were visualized using 1.5 percent Agarose gel electrophoresis under the Biorad Gel documentation system and analyzed using POPGENE 1.31. PCR amplified 139 bands from 13 ISSR markers among which 118 were found to be polymorphic. The polymorphic band percentage was 85 percent while as the average number of bands observed (Na) was 1.8489 and the effective allele number (Ne) was 1.5377. The Nei's gene diversity index (h) was 0.3079. The Shannon Information Index (I) found to be 0.4556. Dendrogram constructed based on the UPGMA method clustered the studied accessions into four major clusters at 80 percent similarity level. Results revealed considerable degree of genetic diversity existed within the studied soursop germplasms at Sri Lanka. Existing genetic diversity within soursop individuals will serve as germplasm bank to identify and utilize potential germplasm resources for conservation and future breeding programs to develop quality soursop varieties in Sri Lanka.

scholarly journals Genetic Diversity, Population Structure and Relationship of Ethiopian Barley (Hordeum vulgare L.) Landraces as reveled by Simple Sequence Repeat (SSR) Markers

2021 ◽  
Author(s):  
Allo Aman Dido ◽  
B.J.K. Singh ◽  
Ermias Assefa ◽  
M.S.R. Kr ◽  
Dawit Degefu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Diversity Index ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Sequence Repeat ◽  
Genetic Rescue ◽  
Hordeum Vulgare L ◽  
Barley Genotypes ◽  
Simple Sequence

Abstract Characterization of genetic resources maintained at genebanks has important implications for future utilization and collection activities. A total of 49 simple sequence repeat (SSR) or microsatellite markers were used to study genetic diversity and relationships among 376 barley landraces collected from different barley producing parts of Ethiopia and eight cultivars. Overall, 478 alleles with an average of 9.755 alleles per locus were obtained of which 97.07% of the loci were observed to be polymorphic. Nei’s genetic diversity index (h) was 0.654, and the Shannon diversity index (I) was 0.647, indicating that the genetic diversity in barley genotypes studies was moderately high. At the population level, the percentage of polymorphic loci (PPL) averaged 98.37%, h = averaged 0.388, and I = averaged 0.568. The highest level of genetic diversity was observed in the AR population (PPL =100%, h = 0.439, I = 0.624); the lowest was observed in the JM population (PPL = 75.51%, h = 0.291, I =0.430). AMOVA revealed significant genetic differentiation within and between populations (P < 0.001), with 84.21% of the variation occurring within populations and 15.79% occurring among populations. Genetic variation analysis showed a coefficient of gene differentiation of 0.053 and a gene flow value of 4.467 among populations. The 384 barley genotypes were divided into seven genetic clusters according to STRUCTURE, Neighbour joining tree and principal coordinate analysis, correlating significantly with geographic distribution. These results will assist with the formulation of conservation strategies, such as genetic rescue and on-farm in situ and ex situ conservation.

scholarly journals Grapevine Non-vinifera Genetic Diversity Assessed by Simple Sequence Repeat Markers as a Starting Point for New Rootstock Breeding Programs

2019 ◽  
Vol 70 (4) ◽  
pp. 390-397 ◽  
Author(s):  
Daniele Migliaro ◽  
Gabriella De Lorenzis ◽  
Giovambattista Simone Di Lorenzo ◽  
Barbara De Nardi ◽  
Massimo Gardiman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Simple Sequence Repeat Markers ◽  
Starting Point ◽  
Simple Sequence ◽  
Rootstock Breeding

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.

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