scholarly journals Assessment of Genetic Relationship among Male and Female Fig Genotypes Using Simple Sequence Repeat (SSR) Markers

2017 ◽  
Vol 45 (1) ◽  
pp. 172-178
Author(s):  
Sevin TEOMAN ◽  
Meryem IPEK ◽  
Umran ERTURK ◽  
Nesrin Aktepe TANGU ◽  
Erdem DURGUT ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genetic Relationship ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Aegean Sea ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Male Tree ◽  
Simple Sequence

Fig (Ficus carica L.) is a traditional crop in Turkey and widely cultivated around the Mediterranean areas. The gynodioecious fig species is present in two sexual forms, i.e. the domesticated fig (female tree) and the caprifig (male tree). Caprifigs are crucial for high quality fig production and breeding while, the studies on assessment of genetic relationship among caprifigs is limited. The aim of this study was to determine genetic diversity among 45 caprifigs and 2 female figs collected from four provinces in Marmara and Aegean Sea Regions of Turkey using simple sequence repeat (SSR) markers. In this work, 24 SSR markers were tested, one was monomorphic and the remaining markers amplified 82 alleles. The number of polymorphic alleles per SSR marker ranged from 2 to 7. The observed heterozygosity (Ho) differed from 0.18 to 0.76 and expected heterozygosity (He) ranged between 0.24 and 0.81. The polymorphism information content (PIC) varied from 0.42 to 0.98. A UPGMA analysis based on Dice similarity matrix clustered fig genotypes into two main groups and similarly, STRUCTURE analysis placed fig genotypes into two different gene pools (K=2). Fig genotypes collected from the same region were not clustered together in a group indicating that the fig genotypes did not cluster on the basis of their collection sites. Our results demonstrated that caprifigs and female figs are not genetically distinct and they clustered together in a group. All fig genotypes had distinct SSR marker profiles suggesting that there were no synonyms or homonyms. These results revealed a high genetic variation among fig genotypes and 23 SSR markers were enough to discriminate all fig genotypes analysed in this study demonstrating that SSR marker system is suitable for genetic analysis in figs.

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 Assessment of the Genetic Diversity of Joha Rice Germplasms by using Simple Sequence Repeat Markers

2021 ◽  
Author(s):  
P. Saikia ◽  
B. Neog ◽  
N. Gogoi ◽  
D. Baruah
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationship ◽  
Simple Sequence Repeat ◽  
Similarity Index ◽  
Morphological Characters ◽  
Aromatic Rice ◽  
Sequence Repeat ◽  
Rice Landraces ◽  
Simple Sequence

Background: Joha Rice are aromatic rice landraces, having small to medium grain size, indigenous to Assam, India. Due to the introduction of high yielding hybrid varieties, many endemic rice landraces including Joha Rice, are in a verge of extinction, as these can only be conserved and maintained by repetitive cultivation. As there is a conflict of local names for these landraces, many landraces with similar morphological characters have been reported from various parts. Simple sequence repeat (SSR) markers with longer perfect repeats have earlier proved successful and essential in studying the genetic diversity among rice cultivars. The present study is aimed to evaluate the genetic relationship among fifteen (15) aromatic Joha rice landraces endemic to Upper Brahmaputra Valley, Assam.Methods: In the present investigation, different landraces of Joha rice were surveyed during 2016-2019. 15 landraces were selected, based on their morphological characters and local data. The collected germplasm of Joha rice was grown in the experimental plots and DNA from young, healthy leaves were isolated which were further used for determination of genetic diversity using SSR markers. Thirty-eight SSR markers were used to evaluate the genetic relationship among the fifteen aromatic rice landraces.Result: A total of 110 polymorphic alleles were detected by 34 markers across all the landraces, with an average of 3.25 per locus. The Polymorphic Information Content (PIC) ranged from 0.24 to 0.83, with an average of 0.5 for each marker. The marker RM154, RM454 and RM489 produced maximum six alleles showing PIC value of 0.82, 0.82 and 0.83, indicating a high polymorphism. UPGMA cluster analysis using Jaccard’s similarity index produced a dendrogram clustering the rice landraces in three major groups and five subgroups. Group II, which consisted of five sub-groups and 12 landraces, showed diverse genotypes. These landraces showed significant genetic similarities. 

scholarly journals Genetic relationships between Chinese, Japanese, and Brazilian soybean gene pools revealed by simple sequence repeat (SSR) markers

2007 ◽  
Vol 30 (1) ◽  
pp. 85-88 ◽  
Author(s):  
Naoki Yamanaka ◽  
Hiroyuki Sato ◽  
Zhenyu Yang ◽  
Dong He Xu ◽  
Lizandra Lucy Catelli ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Gene Pools ◽  
Sequence Repeat ◽  
Soybean Gene ◽  
Simple Sequence

scholarly journals Typing European Chestnut (Castanea sativa Mill.) Cultivars Using Oak Simple Sequence Repeat Markers

HortScience ◽  
2004 ◽  
Vol 39 (6) ◽  
pp. 1212-1216 ◽  
Author(s):  
P. Boccacci ◽  
A. Akkak ◽  
D. Torello Marinoni ◽  
G. Bounous ◽  
R. Botta
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Castanea Sativa ◽  
Quercus Petraea ◽  
Sequence Repeat ◽  
European Chestnut ◽  
Expected Heterozygosity ◽  
Castanea Sativa Mill ◽  
Simple Sequence ◽  
The Ideal

Microsatellite or simple sequence repeat (SSR) markers show many characteristics of the ideal molecular marker, and recent studies have shown that loci developed in one species may allow analysis in taxonomically related species. In this study, 52 primer pairs developed in two oak species—Quercus robur L. and Quercus petraea (Matt.) Lieb.—were used to amplify DNA of 5 chestnut cultivars; 28 of them yielded amplicons and 12 polymorphic loci were selected and used to fingerprint 12 european chestnut (Castanea sativa Mill.) cultivars grown in the Piedmont region of northwestern Italy. The number of alleles per locus ranged from 3 to 8, mean expected heterozygosity was 0.592 (range: 0.288 to 0.868), and mean observed heterozygosity was 0.667 (range: 0.333 to 1.000). The results demonstrate the usefulness of some SSR markers isolated in Quercus for the fingerprinting and genetic mapping of Castanea cultivars.

scholarly journals PENGEMBANGAN MARKA SIMPLE SEQUENCE REPEAT UNTUK Jatropha spp.

2020 ◽  
Vol 17 (4) ◽  
pp. 140
Author(s):  
DARMAWAN SAPTADI ◽  
R.R. SRI HARTATI ◽  
ASEP SETIAWAN ◽  
BAMBANG HELIYANTO ◽  
SUDARSONO SUDARSONO
Keyword(s):  
Ssr Markers ◽  
Jatropha Curcas ◽  
Simple Sequence Repeat ◽  
Genomic Dna ◽  
Ssr Marker ◽  
Sequence Repeat ◽  
Physic Nut ◽  
Jatropha Curcas L ◽  
Dna Database ◽  
Simple Sequence

<p>ABSTRAK</p><p>Pemuliaan tanaman jarak pagar (Jatropha curcas L.) untukmenghasilkan varietas berdaya hasil dan berkadar minyak tinggi perludilakukan. Penggunaan marka molekuler dapat membantu mempercepattercapainya tujuan pemuliaan tanaman jarak pagar. Marka simple sequencerepeat (SSR) merupakan marka ko-dominan yang efektif untuk mendu-kung program pemuliaan tanaman, tetapi penerapannya pada jarak pagarmasih terbatas. Penelitian yang dilakukan bertujuan untuk : (i) merancangprimer spesifik SSR menggunakan aksesi DNA jarak pagar yang tersediadi GenBank DNA database dan (ii) mengevaluasi efektivitas pasanganprimer yang dirancang untuk menghasilkan marka SSR yang polimorfikuntuk jarak pagar dan J. multifida. Dua puluh delapan pasang primerspesifik SSR telah berhasil dirancang menggunakan aksesi DNA asal jarakpagar yang ada di GenBank DNA database. DNA genomik jarak pagar danJ. multifida yang diisolasi dapat digunakan sebagai templat untukamplifikasi PCR. Dari 28 pasang primer yang dikembangkan, semuanyamampu menghasilkan marka SSR dari genom jarak pagar dan hanya 19pasang primer yang menghasilkan marka SSR dari genom J. multifida.Dari 19 pasangan primer spesifik SSR yang dievaluasi mampu dihasilkan44 alel dengan ukuran produk amplifikasi berkisar antara 100-360 bp.Sebanyak 35 alel (79,5%) yang diamati merupakan alel yang polimorfik.Marka SSR yang didapatkan tidak polimorfik intra-aksesi jarak pagar atauintra-aksesi J. multifida tetapi polimorfik untuk inter-aksesi kedua spesies.Karena marka SSR yang dihasilkan bersifat polimorfik untuk aksesi jarakpagar dengan aksesi J. multifida maka dapat digunakan sebagai markauntuk mendeteksi hasil persilangan F 1 inter-spesies J. curcas x J. multifida.</p><p>Kata kunci : Jatropha curcas L., jarak pagar, J. multifida, DNA berulang,rancangan primer</p><p>ABSTRACT</p><p>Development of Simple Sequence Repeat Markers forJatropha spp.</p><p>Breeding of physic nut (Jatropha curcas L.) to obtain new varietiesthat are high in yield and oil content needs to be conducted. Molecularmarker could be used to assist breeding of physic nut (J. curcas). Simplesequence repeat (SSR) marker is a co-dominant marker and theoretically itcould be used to support physic nut breeding program. However, onlylimited information has been available regarding molecular analysis ofphysic nut. The objectives of this research were: (i) to design SSR specificprimer based on DNA sequences available in the GenBank DNA databaseand (ii) to evaluate effectiveness of the primer pairs to produce polymor-phic SSR markers for J. curcas and J. multifida. Twenty eight primer pairswere designed and developed using physic nut DNA available in theGenBank DNA database. Total genomic DNA isolated from J. curcas andJ. multifida could be used as DNA templates for PCR amplification. Of the28 primer pairs developed in this research yielded SSR marker using J.curcas genomic DNA, while only 19 out of 28 pairs yielded SSR markersusing J. multifida genomic DNA. As many as 44 alleles with the size ofamplified products ranged from 100-360 bp were identified. Thirty fivealleles (79.5%) out of 44 identified ones were polymorphic. Results ofanalysis indicated that identified SSR markers generated using thedesigned primers were not polymorphic intra accession of J. curcas norintra-accession of J. multifida either. However, the generated SSR markerswere polymorphic for inter-accession of the two Jatropha species. Sincethe generated markers were only polymorphic for J. curcas and J.multifida, they could be used as markers for identifying interspecific F 1hybrids derived from crossing between J. curcas and J. multifida.</p><p>Key words: Jatropha curcas L., physic nut, J. multifida, DNA repeatsequence, primer design</p>

A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽  
2006 ◽  
Vol 49 (4) ◽  
pp. 354-364 ◽  
Author(s):  
G P Gill ◽  
P L Wilcox ◽  
D J Whittaker ◽  
R A Winz ◽  
P Bickerstaff ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Marker Loci ◽  
Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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