scholarly journals Keragaman Genetik Inbrida Jagung QPM dan Provit-A Berdasarkan Marka SSRs (Simple Sequence Repeats)

2016 ◽  
Vol 35 (2) ◽  
pp. 133
Author(s):  
Nining Nurini Andayani ◽  
M. Yasin H.G ◽  
Marcia B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Genetic Distances ◽  
Large Variability ◽  
Maize Germplasm ◽  
High Level ◽  
Biology Laboratory ◽  
Simple Sequence

Information on genetic diversity of QPM and Provit-A maize germplasm is important to support breeding program, in order to form a high yielding maize hybrid. Simple sequence repeats (SSR) have been extensively utilized as genetic markers to study the genetic diversity, cultivar identification, and gene mapping. The objectives of this research were to investigate the genetic diversity and to obtain information the genetic relationship among 20 maize accessions using 29 SSRs. The research was carried out at the Moleculer Biology Laboratory of Indonesian Cereals Research Institute (ICERI) in Maros, South Sulawesi. Twenty nine polymorphic primers that covered the 10 maize chromosomes were used to fingerprint the genotype of the lines, detecting 83 allels, with an average allel number of 3 allels per locus, ranging from 2 to 6 alleles per locus. The results indicated that polymorphism information content (PIC) ranged from 0.10 (nc133 and phi072) to 0.74 (phi064) with the average of 0.45. Genetic distance based on genetic similarity estimate ranged from 0.39 to 0.92. The high level of PIC values and wide genetic distances indicated the large variability among maize germplasm. Cluster analysis divided the 20 maize accessions into three groups. Coefficient cofenetic value (r) was 0.85 indicated a good fit based on the genetic similarity value. As many as 30 inbred heterotic recombinants were derived by incorporating 20 QPM and Provit-A with genetic distance of ≤0.65. The SSRs proved to be reliable and is practical technique for revealing the relationship among specialty maize genotypes.

scholarly journals Genetic Diversity of Local Maize Germplasm of Tana Toraja South Sulawesi Using SSR (Simple Sequence Repeat) Markers

2018 ◽  
Vol 2 (3) ◽  
pp. 144
Author(s):  
Ramlah Ramlah ◽  
Isna Rasdianah Aziz ◽  
Cut Muthiadin ◽  
Mashuri Masri ◽  
Muhammad Khalifah Mustami ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Agricultural Research ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Maize Germplasm ◽  
South Sulawesi ◽  
Simple Sequence

Plant genetic diversity is an emerging variation in a crop group caused by its genetic factors. Local corn germplasm as a source of plant genes that are able to adapt to the local environment. The purpose of this research is to obtain information on genetic variation of Tana Toraja local maize germ plasm using SSR (Simple Sequence Repeat) marker. This research was conducted at Balitsereal Molecular Biology Laboratory, Agricultural Research Agency in Maros Regency, South Sulawesi. A total of 4 local maize populations were analyzed by laboratory experimental method with observation with NTSYS pc 2.1 program. The results showed that the average number of alleles was 3.72 alleles per locus and the polymorphism rate of 0.53 with the genetic similarity coefficient was in the range of 0.47 to 0.85. 2 main clusters formed in the genetic similarity coefficient 0.47. Klaster I is Local DallePondan and Local Purple. Klaster II is Local Bebo and Kandora. The genetic distance is in the range of 0.15 to 0.74 with an average genetic distance of 0.46. From the data obtained shows that the 4th germplasm of the population of Tana Toraja Local maize diteleti has a very informative level of genetic diversity. Genetic diversity of local maize germplasm of Tana Toraja, can be used as a source of genes in the assembly of improved varieties in the future.

scholarly journals KERAGAMAN GENETIK 22 AKSESI PADI LOKAL TORAJA UTARA BERBASIS MARKA SIMPLE SEQUENCE REPEATS (SSR)

2019 ◽  
Vol 5 (2) ◽  
pp. 230
Author(s):  
Holy Ekklesia Ladjao ◽  
Rinaldi Sjahril ◽  
Muh. Riadi
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Rice Accession ◽  
Polymorphism Rate ◽  
Simple Sequence

Genetic Diversity of 22 Local Rice Accessions from North Toraja Based on Simple Sequence Repeats (SSR) MarkersABSTRACTOne way to explore the potential of local rice is by the characterization that could obtain genetic diversity of that plants. The aim of this study was to obtain the genetic diversity of 22 local rice accession from North Toraja. Twenty-two of local rice accessions from North Toraja were characterized by 30 SSR markers and using NTSYS pc 2.1 program to analyze genetic diversity. The results showed that twenty-six SSR markers that had been analyzed produced some alelles with a size between 106.75-311 bp, the average number of alleles were 3 and the polymorphism rate was 0.53. On coefficient genetic similarity at 0.38, the population formed three clusters. Cluster I and II were dominated by rice that had no hair on the tip of the grain and cluster III were dominated by rice that had hair on the tip of the grain. There were 105 opportunities to crossing between accessions when the genetic distance was above 0.7.Keywords: genetic diversity, local rice, North Toraja, polymorphism rate, SSR markers ABSTRAKSalah satu cara untuk menggali potensi padi lokal adalah dengan karakterisasi. Dengan adanya kegiatan karakterisasi tersebut maka dapat diketahui bagaimana keragaman genetik dari suatu tanaman. Penelitian ini bertujuan untuk mengetahui keragaman genetik dari 22 aksesi padi lokal Toraja Utara. Duapuluh dua aksesi padi lokal Toraja Utara dikarakterisasi menggunakan 30 marka SSR dan dianalisis keragaman genetiknya menggunakan program NTSYS pc 2.1. Hasil penelitian menunjukkan bahwa duapuluh enam marka SSR yang dianalisis memiliki kisaran ukuran alel antara 106.75-311 bp, dengan jumlah alel rata-rata 3 dan tingkat polimorfisme sebesar 0,53. Koefisien kemiripan genetik 0,38 dan terbentuk 3 klaster. Pada klaster I dan klaster II didominasi oleh padi yang tidak memiliki rambut pada ujung gabahnya, dan pada klaster III didominasi oleh padi yang memiliki rambut pada ujung gabahnya. Selain itu, pada jarak genetik diatas 0,7 terdapat 105 peluang persilangan.Kata Kunci: keragaman genetik, marka SSR, padi lokal, tingkat polimorfisme, Toraja Utara

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.

scholarly journals Evaluation of Genetic Diversity of QPM, Provit-A, and Elite Maize Inbreds Resistant to Downy Mildew Disease Using Simple Sequence Repeats

2020 ◽  
Vol 4 (3) ◽  
pp. 161
Author(s):  
Nining Nurini Andayani ◽  
Muzdalifah Isnaini ◽  
Muhammad Aqil ◽  
Amran Muis ◽  
Marcia Bunga Pabendon ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Downy Mildew ◽  
Simple Sequence Repeats ◽  
Beta Carotene ◽  
Distance Analysis ◽  
Maize Varieties ◽  
Maize Inbreds ◽  
Biology Laboratory ◽  
Simple Sequence ◽  
Downy Mildew Disease

<p>Functional maize tends to be more susceptible to major maize diseases, particularly Downy mildew. Among the functional maize are Quality Protein Maize (QPM) and Provit A maize. The presence of higher amino acid and beta carotene in functional maize might have caused these types of maize more susceptible to Downy mildew disease. The objective of the research was to identify the heterotic pairs among maize inbreds i.e. QPM, Provit A, and local maize varieties resistant to Downy mildew disease using Simple Sequence Repeats (SSR) marker. The research was conducted from April to July 2017 at the Molecular Biology Laboratory of Indonesian Cereals Research Institute. A total of five QPM inbreds, 15 Provit A inbreds, and 11 Downy mildew resistant local varieties of maize were used in the experiment using 34 SSR markers. Results indicated that among 34 SSR locus analysed, variation of allele lengths ranged from 74 bp to 500 bp. A total of 125 alleles ranging from two to nine alleles per locus with an average of 3.68 alleles were generated. The data indicated wide genetic variations among characters. DNA band profile showed that nc130 marker produced the highest PIC (over 0.83) and allele value (8.00). Genetic distance analysis found a total of 21 heterotic genotypes with genetic distance exceeds 0.65. </p>

scholarly journals Detection of Genetic Polymorphism in Seven Barley Hordeum vulgare L. Varieties Using SSR

2020 ◽  
Vol 33 (2) ◽  
pp. 115-124
Author(s):  
Maha R. Khalil ◽  
Hussain A. Almahasneh ◽  
Salam Y. Lawand
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Polymorphism ◽  
Hordeum Vulgare ◽  
Simple Sequence Repeats ◽  
Genetic Similarity ◽  
Hordeum Vulgare L ◽  
Simple Sequence

Investigation was carried out at the laboratory of Biotechnology, Faculty of Agriculture, Damascus University, during the season 2017-2018. Seven varieties were planted to determine the degree of genetic similarity using SSR-technique (Simple Sequence Repeats), and 14 double primers were used for this purpose. The analysis results revealed that all primers showed polymorphism among the evaluated varieties, except Bmag0385. primers produced a total of 42 alleles with a polymorphic percentage of 88.27%. The number of alleles for each primer varied from 1 allele for the primer (Bmac0067) to 7 alleles for the primer (Bmag0006) in average of 3 alleles per primer. Cluster analysis and Dendrogram showed the highest degree of genetic similarity between variety Arabi asuad  and variety Arabi abiad (0.7619). While it was low between variety Fourat4 and variety Arabi abiad (0.3571), and varieties Fourat4 and Fourat3 (0.3571) which indicated wide genetic diversity among them.

scholarly journals Analysis of Genetic Diversity Between Eriobotrya japonica (Thunb.) Lindl. (Rosaceae) Populations Growing in the Aegean Region of Turkey

2020 ◽  
Vol 77 (2) ◽  
pp. 71
Author(s):  
Emre SEVİNDİK ◽  
Kemalcan OKAN ◽  
Fadime EFE
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Random Amplified Polymorphic Dna ◽  
Eriobotrya Japonica ◽  
Analysis Program ◽  
Aegean Region ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

In this study, we performed a genetic diversity using RAPD (Random amplified polymorphic DNA) and ISSR (Inter-simple sequence repeats) markers for some Eriobotrya japonica populations grown in the Aegean region of Turkey. PCR was performed with all DNA samples and primers with ability of scoring band. Phylogenetic analysis and pairwise genetic distance between the populations were calculated by using the PAUP analysis program. According to the RAPD data, a total of 33 bands were obtained and 21 of them were polymorphic. The closest genetic distance (0.09677) was found between Aydın and Nazilli populations, while the most distant value was found 0.44000 between Salihli and Nazilli populations. According to the ISSR data, a total of 43 bands were obtained and 18 of them were polymorphic. The closest genetic distance (0.09302) was found between İzmir and Aydın populations, while the most distant values (0.48276) were found between Denizli and Nazilli populations. As a result of this study, the rate of polymorphism obtained in ISSR technique was found to be lower than the RAPD technique.

scholarly journals Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
Uslan Uslan ◽  
NUR JANNAH
Keyword(s):  
Genetic Diversity ◽  
Zea Mays ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Simple Sequence Repeats ◽  
Zea Mays L ◽  
Sample Collection ◽  
High Genetic Diversity ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

Abstract. Uslan, Jannah N. 2020. Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker. Biodiversitas 21: 1208-1214. Corn (Zea mays L.) is one of the most important food crops in Indonesia. However, the studies described their genetic variation is relatively poor. Therefore, the aim of this study was to analyze the genetic diversity of local corn cultivars from South Amarasi, Kupang District, East Nusa Tenggara (NTT), Indonesia using ISSR markers. The sampling was conducted in 4 different sites in Sub-district of Amarasi, Kupang District. A total of 11 corn cultivars from Sub-district of South Amarasi was collected. DNA isolation was performed by using CTAB Method. Clustering analysis was conducted on MSVP 3.2 software. It was shown that all ISSR-primers used (UBC 811, UBC 814 and UBC 824) were successfully produced polymorphic bands and represents the high genetic diversity of the local corn cultivars. The genetic distance index indicated that several corn cultivars from two different populations were geographically unclustered, although there are samples from several populations that have a low genetic distance. The genetic variation index also showed high genetic diversity among the populations. Further research on the exhaustive sample collection was needed to give an insight into the genetic diversity of local corn cultivars (Zea mays L.) from South Amarasi, Indonesia. Please write implementation of this research

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

Genetic diversity and molecular markers of five snapper species

2007 ◽  
Vol 4 (1) ◽  
pp. 39-46 ◽  
Author(s):  
Liu Li ◽  
Liu Chu-Wu
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Simple Sequence Repeats ◽  
Microsatellite Loci ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Distances ◽  
The Other ◽  
Information Contents ◽  
The Mean ◽  
Simple Sequence

AbstractIn order to protect and develop valuable snappers (Lutjanus spp.), genetic diversity and molecular markers of five species (Lutjanus vitta, L. fulvus, L. fulviflamma, L. sebae and L. stellatus) were detected and analysed using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) techniques. The polymorphic loci ratio (P) (86.00–92.11%), the mean intraspecies genetic distances (D) (0.1775–0.3431) and the intraspecies genetic diversity indexes (Hi) (0.1022–0.1634) were calculated using the RAPD technique. The genetic diversities of L. fulviflamma and L. vitta were richest in terms of P, and D and Hi, respectively. The results of SSR showed that low effective numbers of alleles (1.7893–3.6591), medium average heterozygosities (0.332–0.676) and medium polymorphism information contents (PIC) (0.302–0.641) occurred in five species of snappers, indicating comparatively rich genetic diversity among these fish. Nine molecular markers in the products amplified by primers OPA8 and OPP10, and six molecular markers in 11 microsatellite loci were found to be useful as specific markers to identify five species of snappers. Two neighbour-joining (NJ) dendrograms based on the results of RAPD and SSR suggested that L. stellatus and L. sebae are closely related and clustered in one branch, with L. vitta, L. fulviflamma and L. fulvus in the other.

Assessment of genetic diversity in Narbon vetch (Vicia narbonensis L.) germplasm using morphological and molecular markers

2018 ◽  
Vol 69 (9) ◽  
pp. 904 ◽  
Author(s):  
Siwar Bouabid ◽  
H. Chennaoui Kourda ◽  
A. Boussaha ◽  
M. Ben Naceur ◽  
A. Zoghlami Khélil
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Germplasm Management ◽  
Vicia Narbonensis ◽  
High Level ◽  
Differentiation Index ◽  
Simple Sequence

Narbon vetch (Vicia narbonensis L.) is a promising forage legume with good resistance to cold and drought. The assessment of genetic diversity of Narbon vetch is an essential component in germplasm management. In this study, we analysed the genetic diversity of 13 local and introduced Narbon vetch accessions from three continents using 27 morphological traits and 13 simple sequence repeat (SSR) markers. Significant differences among accessions for morphological and phenological traits were observed. The SSR markers showed a total of 126 alleles with a mean number of two alleles per locus. Polymorphic information content values were in the range of 0.772–0.915 with an average of 0.858. A high level of diversity (Nei’s genetic differentiation index of 59) was observed among accessions. Analysis of genetic distances separated the studied accessions into three groups based on both morphological and SSR markers. Cluster analysis of the SSR markers separated the accessions into three groups according to geographical origin. The Tunisian populations shared the same morphological traits but differed genetically from each other and were similar to those from Lebanon. A significant correlation was detected between morphological traits and SSR markers. The results suggested that SSR markers can be used to efficiently distinguish Narbon vetch accessions and estimate their genetic diversity.

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