scholarly journals Morphologic and cytoplasmic assessments of bulb onion (Allium cepa L.) landraces

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 167-180
Author(s):  
Esra Cebeci ◽  
Huseyin Padem ◽  
Ali Gokce
Keyword(s):  
Climatic Conditions ◽  
Breeding Program ◽  
Local Source ◽  
Group Method ◽  
Pair Group ◽  
Current Trends ◽  
Bulb Onion ◽  
Allium Cepa L ◽  
New Varieties ◽  
Analysis System

Today climate change threatens to reduce crop yield and harming the food security. Local landraces have adaptation skills to shifting climatic conditions. Using of this local source in plant breeding programs becoming an alternative strategy. In this study, 97 landraces were collected to initiate the bulb onion breeding program eligible for the current trends. Collected materials were morphologically characterized using 21 descriptors, derived from UPOV (International Union for the Protection of New Varieties of Plants). Clustering which was conducted by the NTSYS (Numerical Taxonomy and Multivariate Analysis System) program using UPGMA (Unweighted Pair Group Method of Arithmetic Averages) method, showed that the genetic similarity rate of the landraces was calculated between 0.06-0.96. Hybrid onion breeding program depends on the cytoplasmic-genic male sterility (CMS) system. Thus, the PCR-markers were applied to identify the cytoplasm types of the landraces. Among landraces N-cytoplasm was found in 78 accessions and S-cytoplasm was found in 19 accessions. At the end of the study, a qualified gene pool has been established consisted of characterized onion genotypes which will might be used in further breeding studies.

scholarly journals GENETIC VARIABILITY OF Rottboellia cochinchinensis POPULATIONS IN SUGARCANE FIELDS

2016 ◽  
Vol 34 (3) ◽  
pp. 475-484 ◽  
Author(s):  
A.R. SCHIAVETTO ◽  
D. PERECIN ◽  
L.R. PINTO ◽  
C.A.M. AZANIA ◽  
F.S. ZERA ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genetic Similarity ◽  
Sao Paulo ◽  
The State ◽  
Group Method ◽  
Jaccard Coefficient ◽  
São Paulo ◽  
Pair Group ◽  
Analysis System ◽  
Rottboellia Cochinchinensis

ABSTRACT The hypothesis assumed was the existence of biotypes within populations, which has been the cause of difficulties in itchgrass control by farmers. For that, the genetic variability of three populations of Rottboellia cochinchinensis in sugarcane fields in the state of São Paulo was investigated by using the Amplified Fragment Length Polymorphism (AFLP) technique. Six primers were used to obtain molecular characterization data. AFLP gels were analyzed based on marker presence (1) and absence (0). Using NTSYs (Numerical Taxonomy and Multivariate Analysis System) software, the genetic similarity was calculated by the Jaccard coefficient and, from that, a dendrogram was built through the UPGMA (Unweighted Pair Group Method Arithmetic averages) method, besides determining the isopolymorphic marks. The average genetic similarities seen in the region was 0.742 for Igarapava, 0.793 for Mococa and 0.808 for Piracicaba. Between regions it was 0.730 (Igarapava vs Mococa), 0.735 (Mococa vs Piracicaba) and 0.694 (Igarapava vs Piracicaba). In line with the dendrogram, it is possible to detect the formation of two groups, one with 8 plants from Igarapava and Mococa and the other with 21 plants from Igarapava, Mococa and Piracicaba, as well as the presence of 1 discriminant individual from Piracicaba. It can be concluded that the genetic similarity among itchgrass populations from the state of São Paulo was high (72%), which denotes that the difficulties in chemical management are not only due to different biotypes but also due to other characteristics linked to tolerance of the species to herbicides. However, biotype existence cannot be discarded because of the polymorphic marks generating 22% average genetic variability.

scholarly journals Molecular Characterization of Macrophomina phaseolina, the Incitant of Coleus forskohlii Revealed by RAPD Markers

2012 ◽  
Vol 5 (1) ◽  
pp. 44-50 ◽  
Author(s):  
Chathuri Mudalige ◽  
ST Girisha ◽  
VB Raghavendra ◽  
MH Niranjan ◽  
K Ravikumar ◽  
...  
Keyword(s):  
Root Rot ◽  
Rapd Analysis ◽  
Macrophomina Phaseolina ◽  
Climatic Conditions ◽  
Similarity Coefficient ◽  
Group Method ◽  
Coleus Forskohlii ◽  
Severe Problem ◽  
Pair Group ◽  
Pathogenicity Tests

Coleus forskohlii belong to family lamiaceae is one of the commercial plants grown extensively in the country, the chemical found in the Coleus which has both medicinal application and gives great economy to the industrial organizations. Unfortunately, these plants are being highly succumbed to serious diseases like wilt and root rot caused by a fungus, hence the growers and industrialists are facing severe problem in safeguarding this crop in the field irrespective of the agro climatic conditions. Root rot disease, is one of the major diseases of Coleus forskohlii which, is caused by Macrophomina phaseolina, Pathogen variability was studied at both morphological and molecular level using cultural characteristics and Rapid Amplification of Polymorphic DNA (RAPD) analysis respectively. Totally thirty two isolates were isolated from roots of Coleus forskohlii. In RAPD 165 bands were obtained out of them 121 bands (73.3%) were polymorphic with a similarity coefficient of 0.48-0.66. Clusters analysis of RAPD data when Unweighted Pair Group Method with Arithmetic Mean (UPGMA) Tree constructed using NTSYS, it showed 6 groups. Among them two were major clusters and 4 were minor clusters with similarity coefficient 0.48-0.66. The pathogenicity of the isolates was tested on Coleus forskohlii plants. Analysis of the pathogenicity tests results revealed that the isolates grouped under two major clusters which were different from the one obtained using RAPD data. The results indicate that the data from RAPD analysis and Pathogenicity tests do not correlate with each other.DOI: http://dx.doi.org/10.3126/ijls.v5i1.5598 International Journal of Life Sciences Vol.5(1) 2011 44-50

scholarly journals Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites

2020 ◽  
Vol 63 (1) ◽  
pp. 165-172
Author(s):  
Bahar Argun Karsli ◽  
Eymen Demir ◽  
Huseyin Goktug Fidan ◽  
Taki Karsli
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Group Method ◽  
Sheep Breeds ◽  
Livestock Species ◽  
Pair Group ◽  
Breeding Programmes ◽  
Study Population

Abstract. Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci. By genotyping 120 individuals belonging to four sheep breeds, a total of 275 different alleles, 37 of which were private alleles, were observed across all loci. The mean number of alleles per breed ranged from 7.28 (Güney Karaman) to 8.09 (Karakas), while allelic richness ranged from 7.22 (Güney Karaman) to 7.87 (Karakas). Mean observed heterozygosity varied from 0.60 (Kangal) to 0.66 (Norduz and Karakas). The lowest pairwise FST value (0.084) was between Kangal and Karakas populations, while the highest pairwise FST value (0.142) was between Norduz and Karakas populations. Polymorphic information content (PIC) values, ranging from 0.71 (ETH10) to 0.91 (OarFCB304), were highly polymorphic (PIC > 0.5) and informative in studied populations. In the present study, the results of phylogenetic analysis were of importance, since all studied populations have been accepted as Akkaraman varieties till today. However, factorial correspondence and structure analysis, pairwise FST values, and an unweighted pair group method with arithmetic mean analysis (UPGMA) dendrogram revealed that Güney Karaman and Norduz populations have became genetically different from the Akkaraman breed due being raised in different parts of Turkey under different climatic conditions together with their breeding practices. Therefore, we recommend that more comprehensive molecular studies should be conducted to clarify genetic differentiation of Akkaraman sheep varieties.

scholarly journals The Genetic Variations And Relationship of Madura Tobacco (Nicotiana tabacum L.) Based on Molecular Characteristics

2017 ◽  
Vol 21 (2) ◽  
pp. 70
Author(s):  
Fitri Nadifah ◽  
Budi Setiadi Daryono
Keyword(s):  
Nicotiana Tabacum ◽  
Genetic Similarity ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Molecular Characteristics ◽  
Pair Group ◽  
Nicotiana Tabacum L ◽  
New Genotype ◽  
Analysis System ◽  
Relationship Of

Madura has at least 22 genotypes of local tobaccos (Nicotiana tabacum L.). This diversity could potentially produce new genotype of tobaccos with superior characters. However, information of the genetic diversity of Madura tobaccos is still limited. The aim of this study was to determine the genetic variation and relationship of 24 genotypes of Madura tobaccos with Random Amplified Polymorphic DNA (RAPD) analysis. In this research we were used 6 single primers for amplification: (OPA-18, OPB-12, OPB-14, OPC-1, OPC-8 and OPC-19) and 2 mixture primers ((OPB-12+OPC-8) and (OPC-1+OPC-19)). Genetic similarity and clustering was analyzed with Unweighted Pair Group Method Arithmetic (UPGMA) method with Numerical Taxonomy and Multivariate Analysis System (NTSYS) version 2.10 software. From this research we found that OPA18425, OPB12450, OPC8500, (OPC19+OPC1)550 and OPC8800 can be used as specific markers. Polymorphic bands percentage with mixture primers was relatively equal with single primers (<60%). The dendogram showed that Madura tobacco genotypes consist of 2 main clusters: cluster A (22 genotypes) and cluster B (2 genotypes: Bukabu Sa’ang and Prancak-95). Madura tobaccos had high genetic similarity between genotypes ranging from 0.80-1.00.

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

scholarly journals ANALISIS DIVERSITAS GENETIK AKSESI KELAPA SAWIT KAMERUN BERDASARKAN MARKA SSR

2020 ◽  
Vol 19 (4) ◽  
pp. 194 ◽  
Author(s):  
I MADE TASMA ◽  
SEKAR ARUMSARI
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Information Content ◽  
Ssr Markers ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Group Method ◽  
Pair Group ◽  
Elaeis Guineensis Jacq ◽  
Analysis System

<p>ABSTRAK<br />Diversitas genetik aksesi kelapa sawit Indonesia saat ini sangat<br />rendah. Dalam usaha meningkatkan keragaman genetik telah dilakukan<br />eksplorasi plasma nutfah di pusat keragaman genetik kelapa sawit di<br />Kamerun. Tujuan dari penelitian ini untuk mengetahui diversitas genetik<br />dan tingkat polimorfisme berdasarkan marka SSR aksesi-aksesi kelapa<br />sawit Kamerun. Bahan tanaman yang digunakan 49 aksesi kelapa sawit<br />Kamerun, Afrika yang ditanam di Kebun Sumber Daya Genetik (SDG)<br />Sawit Sijunjung, Sumatera Barat. DNA genomik diisolasi dari tiap<br />individu aksesi menggunakan protokol isolasi DNA untuk tanaman<br />bergetah. DNA dianalisis menggunakan 20 marka SSR. Dendrogram<br />kekerabatan dikonstruksi menggunakan metode Unweighted Pair Group<br />Method Arithmetic (UPGMA) melalui software NTSYS-pc (Numerical<br />Taxonomy and Multivariate Analysis System) versi 2.1-pc. Hasil penelitian<br />menunjukkan nilai polimorfisme information content (PIC) marka SSR<br />tinggi sebesar 0,80 (berkisar 0,63-0,91). Jumlah alel yang terdeteksi per<br />marka SSR berkisar antara 4-15 alel per lokus SSR (rata-rata 8,75).<br />Analisis filogenetik 49 aksesi menghasilkan diversitas genetik 12,5-<br />54,72% (kemiripan genetik 55,28-87,50%). Pada diversitas genetik<br />54,72%, aksesi Kamerun terbagi menjadi tujuh kelompok masing-masing<br />terdiri dari 9, 28, 4, 2, 1, 2, dan 3 aksesi. Aksesi dengan diversitas genetik<br />tinggi dan berada pada klaster berbeda, potensial digunakan sebagai calon<br />tetua dalam program pemuliaan kelapa sawit.<br />Kata kunci: Elaeis guineensis Jacq., diversitas genetik, plasma nutfah,<br />marka SSR</p><p>ABSTRACT<br />Genetic diversity of the Indonesian oil palm collection is very low.<br />To improve their genetic variability, exploration from the oil palm center<br />of origins has been done in Kamerun. The objectives of this study were to<br />determine genetic and polymorphism level of the SSR markers Cameroon-<br />originated oil palm accessions. Genetic materials used were 49 Cameroon-<br />originated oil palm accessions collected at Sijunjung Oil Palm Germplam<br />Collection Station, West Sumatera. Genomic DNA was isolated using a<br />protocol for isolating DNA from leaves rich with latex. DNA was analyzed<br />using 20 SSR markers. A dendogram was constructed using the<br />Unweighted Pair Group Method Arithmetic (UPGMA) method through the<br />Numerical Taxonomy and Multivariate Analysis System software<br />(NTSYS-pc) version 2.1-pc. Results showed that the polimorfisme<br />information content (PIC) values of the SSR markers used was high, 0.80<br />(range from 0.63-0.91). The average number of the SSR alleles detected<br />was also high, 8.75 alleles (range from 4-15 alleles per SSR locus).<br />Phylogenetic analysis of the 49 oil palm accessions resulted genetic<br />diversity of 12.5-54.72% (genetic similarity of 55.28-87.50%). At genetic<br />diversity 54.72%, the 49 accessions were divided into seven clusters, each<br />consisted of 9, 28, 4, 2, 1, 2, and 3 accesions, respectively. Accessions<br />with high genetic diversity and located at different clusters may be useful<br />as parent candidates in the future oil palm breeding programs.<br />Key words: Elaeis guineensis Jacq., genetic diversity, germplasm, SSR<br />markers</p>

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

2021 ◽  
Vol 186 (2) ◽  
pp. 237-244
Author(s):  
M. Domán ◽  
L. Makrai ◽  
Gy. Lengyel ◽  
R. Kovács ◽  
L. Majoros ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Molecular Diversity ◽  
Genetic Relatedness ◽  
Group Method ◽  
Pair Group ◽  
Degree Of Separation ◽  
Avian Origin ◽  
Species Specific ◽  
Sequence Types ◽  
Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

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