SSR cross-amplification and variation within coffee trees (Coffea spp.)

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1071-1081 ◽  
Author(s):  
V Poncet ◽  
P Hamon ◽  
J Minier ◽  
C Carasco ◽  
S Hamon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Null Allele ◽  
Polymorphic Locus ◽  
Coffea Canephora ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Allele Number ◽  
Primer Sets ◽  
Polymorphism Level ◽  
Potential Use

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was –11% for PSE and –9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.Key words: microsatellite, Coffea, transferability, genetic diversity.

scholarly journals Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1842
Author(s):  
Marcos Paulo Carrera Menezes ◽  
Amparo Martinez Martinez ◽  
Edgard Cavalcanti Pimenta Filho ◽  
Jose Luis Vega-Pla ◽  
Juan Vicente Delgado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Allele Number ◽  
Hair Samples ◽  
The Mean ◽  
Polymerase Chain ◽  
Single Sequence ◽  
Brazilian Populations

The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.

scholarly journals Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

2011 ◽  
Vol 57 (6) ◽  
pp. 717-724 ◽  
Author(s):  
Jiandong Yang ◽  
Zhihe Zhang ◽  
Fujun Shen ◽  
Xuyu Yang ◽  
Liang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Giant Panda ◽  
Population Decline ◽  
Management Strategies ◽  
Ailuropoda Melanoleuca ◽  
High Genetic Diversity ◽  
Giant Pandas ◽  
Allele Number ◽  
High Level

Abstract Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A), Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort.

scholarly journals Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

2010 ◽  
Vol 10 (4) ◽  
pp. 298-304 ◽  
Author(s):  
Tesfahun Alemu Setotaw ◽  
Eveline Teixeira Caixeta ◽  
Guilherme Ferreira Pena ◽  
Eunize Maciel Zambolim ◽  
Antonio Alves Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

scholarly journals KERAGAMAN GENETIK 64 AKSESI KUNYIT ASAL INDONESIA BERDASARKAN MARKA P450-BASED ANALOGUE (PBA)

2020 ◽  
Vol 31 (2) ◽  
pp. 123
Author(s):  
Tresna Kusuma Putri ◽  
Putri Ardhya Anindita ◽  
Noladhi Wicaksana ◽  
Tarkus Suganda ◽  
Vergel Concibido ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Accurate Result ◽  
Similarity Index ◽  
The Other ◽  
Central Laboratory ◽  
Informative Marker ◽  
P450 Gene ◽  
Allele Number ◽  
Primer Sets ◽  
Marker Cluster

<em>Turmeric is a rhizome producing plant with many utilization such as for consumption, medicine, and colorant industries. The development of superior turmeric varieties in Indonesia needs to be supported by genetic diversity information availability. Despite its potential, genetic diversity information of Indonesian turmeric has not been widely observed. A molecular marker is used to address genetic diversity information with the accurate result due to minimum environmental influences. PBA can detect the P450 gene as a functional marker, which is related to the synthesis of secondary metabolites in a wide genome area.  Thus, it can be used as an alternative marker to identify genetic diversity. This research aimed to obtain genetic diversity information of 64 turmeric accessions using eight primer sets of P450-Based Analogue (PBA). The study was conducted in the Central Laboratory of Padjadjaran University from June 2019 to January 2020. Results showed that the full 133 bands were detected with a range of allele number 8 - 45 bands and an average of 22.3 bands per allele. PIC analysis showed six primer sets of PBA had high polymorphisms ranged from 0.90 to 0.98, hence categorized </em><em>PBA as a highly informative marker. Cluster analysis divided 64 turmeric accessions into two main clusters based on a similarity index ranged from 0.01 to 0.83. The accession of CL-GTL01 origins from Gorontalo had a low similarity coefficient of 0.01 to the other 64 accessions cluster. On the other hand, CL-NTB01 dan CL-PPB01 had the highest similarity index of 0.83. Based on the PIC value, the total number of polymorphic bands, and genetic distance, it can be concluded that local Indonesian turmeric had wide diversity based on PBA marker.</em>

scholarly journals Genetic Variability of 15 Robusta Coffee Genotypes Selected by Farmer Based on SSRs Markers

2014 ◽  
Vol 1 (2) ◽  
pp. 87
Author(s):  
Syafaruddin Syafaruddin ◽  
Enny Randriani ◽  
Dani Dani ◽  
Indah Sulistyorini ◽  
M. B. Pabendon
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Coffea Canephora ◽  
Coffee Plantations ◽  
Robusta Coffee ◽  
Allele Number ◽  
Grafting Technique ◽  
Ssrs Markers ◽  
Biology Laboratory ◽  
Research Institute

<p>Robusta coffee (Coffea canephora) has been grown widely in Indonesia, especially in Bengkulu Province. For the last few decades, some farmers have been selected and developed several Robusta clones through plagiotropic shoot grafting technique to replace earlier coffee populations which were derived from seed. Hence, it would reduce the genetic diversity of Robusta coffee at farmer’s field. To understand the genetic variability among 15 Robusta coffee genotypes selected by farmer, it is important to perform molecular analysis. Leaf samples of 15 Robusta coffee genotypes selected by farmer were collected from smallholder Robusta coffee plantations in Bengkulu Province. Genetic diversity analysis was conducted in the Germplasm, Breeding, and Biotechnology Laboratory of Indonesian Industrial and Beverage Crops Research Institute (IIBCRI), and Molecular Biology Laboratory, Indonesian Cereals Research Institute (ICERI). DNA samples were amplified using 34 SSRs markers. The result showed that 23 out of 34 SSRs markers had high polymorphism levels. Allele number per locus ranged from 2-8 with an average of 4 alleles per locus. Dendrogram analysis based on genetic similarity was obtained with score of about 0,44-0,79, and r score = 0,92 (good fit). Based on cluster analysis as well as PCoA analysis, there are three distinct groups of genotypes. Those three groups can be distinguished by specific character of leaf morphotype. Nevertheless, the majority of genotypes were clustered together into the single group. This indicates narrow genetic diversity among Robusta genotypes that selected by farmer.</p><p>Kopi Robusta telah dikembangkan secara luas di Indonesia, khususnya di Provinsi Bengkulu. Beberapa dekade terakhir sebagian petani telah menyeleksi dan mengembangkan beberapa genotipe dengan teknik sambung tunas plagiotrop untuk merehabilitasi populasi kopi Robusta asal biji. Oleh sebab itu, terdapat peluang terjadinya penurunan keragaman genetik kopi Robusta di lahan petani. Analisis molekuler perlu dilakukan untuk mengevaluasi keragaman genetik antar 15 genotipe kopi Robusta hasil seleksi petani. Kegiatan analisis keragaman genetik dilaksanakan di Laboratorium Plasma Nutfah, Pemuliaan, dan Bioteknologi, Balai Penelitian Tanaman Industri dan Penyegar (Balittri), Sukabumi dan Laboratorium Biologi Molekuler, Balai Penelitian Tanaman Serealia (Balitsereal), Maros. DNA diamplifikasi dengan menggunakan 34 marka SSR. Hasil penelitian menunjukkan bahwa 23 dari 34 marka SSR yang digunakan mampu menghasilkan tingkat polimorfisme yang tinggi. Jumlah alel berada pada kisaran 2-8 alel per lokus dengan rata-rata 4 alel per lokus SSR. Analisis dendrogram berdasarkan kemiripan genetik diperoleh dengan skor sekitar 0,44-0,79 dan skor r = 0,92 (good fit). Berdasarkan hasil analisis gerombol dan analisis komponen utama diketahui bahwa terdapat tiga kelompok genotipe. Masing-masing kelompok dapat dibedakan berdasarkan karakter morfotipe daun. Meskipun demikian, sebagian besar genotipe diklasifikasikan ke dalam satu kelompok. Ini menandakan bahwa keragaman genetik klon-klon kopi Robusta hasil seleksi petani cenderung rendah.</p><p>Keywords: Coffea canephora, klon plagiotropik, kehilangan genetik</p>

scholarly journals Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit

2016 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
I Made Tasma ◽  
Ahmad Warsun ◽  
Dani Satyawan ◽  
Syafaruddin Syafaruddin ◽  
Budi Martono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Germ Plasm ◽  
Elaeis Guineensis ◽  
Study Finding ◽  
Multivariate System ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
Polymorphism Level

<p>Genetic diversity of the<br />Indonesian oil palm collection remains low and collection<br />enrichness through exploration activities from the center of<br />origins is required. In 2009, 103 oil palm accessions from<br />Cameroon were collected at the National Oil Palm Genetic<br />Resources Collection located at the District of Sijunjung,<br />West Sumatera. The objectives of the present study were to<br />analayze the 50 Cameroon-originated oil palm accessions in<br />order to: (1) determine polymorphism levels of the SSR<br />markers used; (2) understand diversity levels of the oil palm<br />accessions tested; and (3) analyze accessions potentially<br />used for germ plasm collection. Fifty oil palm accessions<br />were used in this study. DNA was isolated from leaves of the<br />selected individual plants representing each of the<br />accessions. DNA was analyzed with 12 SSR markers. A<br />dendrogram was constructed using the UPGMA through<br />Numerical Taxonomy and Multivariate System program<br />version 2.1-pc. Results showed that SSR markers used<br />demonstrated the average number of alleles per locus of 3.6<br />(2-6). The polymorphism level was 0.53 (0.21-0.73). The<br />phylogenetic analysis resulted nine clusters with genetic<br />diversity between two accessions ranged from 4-82%. Ten<br />accessions (20%) showed low genetic diversity (&lt;10%) but<br />the accessions demonstrated high diversity in flowering<br />time. Eleven accessions showed medium diversity level (27-<br />42%). Five accessions demonstrated high genetic diversity<br />level (45-82%). A confirmation study using more SSR<br />markers is recommended. This study finding may be useful<br />in planning the oil palm germ plasm collection activities.</p>

scholarly journals Genetic variability in populations of Pilosocereus catingicola (Gürke) Byles & Rowley subsp. salvadorensis (Werderm.) Zappi (Cactaceae)

2020 ◽  
Vol 9 (8) ◽  
pp. e126985521
Author(s):  
Fabiana dos Anjos Barbosa ◽  
Alex da Silva Barbosa ◽  
Gláucia Diojânia Azevêdo Medeiros ◽  
Alberício Pereira de Andrade ◽  
Mailson Monteiro do Rêgo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Locus ◽  
Genetic Erosion ◽  
Jaccard Coefficient ◽  
Binary Matrix ◽  
High Genetic Diversity ◽  
Hierarchical Grouping ◽  
The Matrix ◽  
Ctab Method

Studies on genetic diversity of cacti are important to elucidate evolutionary events and ecological characteristics of populations vulnerable to genetic erosion. The objective of this study was to evaluate the genetic diversity among individuals of Pilosocereus catingicola subsp. salvadorensis occurring in three populations located in the Caatinga do Agreste region of Paraiba, using RAPD markers. For the extraction of DNA, tissues of the parenchyma and cladodium of the stem of the individuals were used by the 2% CTAB method and amplified using 05 primers. The obtained marks were converted into a binary matrix, from which the matrix of genetic dissimilarity was constructed using the arithmetic complement of the Jaccard coefficient and the construction of the dendrogram, by the UPGMA method. All markers tested amplified, being 82.4% polymorphic locus and 10.6% monomorphic for the Arara population; 84.4% polymorphic and 15.6% monomorphic for the Areial population, the Boa Vista population did not show monomorphism, resulting in 100% polymorphism. The averages of heterosigose observed (0.372, 0.492 and 0.135) show that there are genetic divergences within the populations. The primers used were effective in identifying polymorphism in the species. The populations evaluated in this study showed high genetic diversity, both within and between the population, originating fifteen groups among the 120 individuals from the UPGMA hierarchical grouping analysis, and it was possible to discriminate the populations.

scholarly journals Evaluation of the Conservation Status of the Croatian Posavina Horse Breed Based on Pedigree and Microsatellite Data

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2130
Author(s):  
Ante Ivanković ◽  
Giovanni Bittante ◽  
Miljenko Konjačić ◽  
Nikolina Kelava Ugarković ◽  
Mateja Pećina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Meat Production ◽  
Phenotypic Data ◽  
High Genetic Diversity ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
The Status ◽  
The Mean ◽  
Economic Use

The Croatian Posavina horse (CPH) is native Croatian breed under a conservation program and under various programs of economic use (ecosystem services, agrotourism, and meat production). The aim of this study was to analyze the status of the CPH population through an analysis of their pedigree (28,483 records), phenotype (292 licensed stallions, 255 mares), and genetic structure (292 licensed stallions). The average generation interval was 8.20 years, and the number of complete generations was 1.66. The effective number of founders and ancestors was 138 and 107, respectively, with a ratio of 1.29, and the genetic conservation index was 4.46. As for the morphometric characteristics, the average withers height of the stallions was 142.79 cm, the chest circumference was 194.28 cm, and the cannon bone circumference was 22.34. In mares, the withers height, chest, and cannon bone circumference were lower (139.71 cm, 190.30 cm, and 20.94 cm, respectively). Genetic microsatellite analysis of the 29 sire-lines showed high genetic diversity, expressed as the mean allele number (7.7), allele richness (4.0), and expected heterozygosity (0.740). There was no evidence of high inbreeding or a genetic bottleneck. The genetic and phenotypic data indicate that the CPH is an important and diverse reservoir of genetic diversity and can be conserved because of its special characteristics (adaptability).

Development of genomic microsatellite markers in Coffea canephora and their transferability to other coffee species

Genome ◽  
2007 ◽  
Vol 50 (12) ◽  
pp. 1156-1161 ◽  
Author(s):  
Valérie Poncet ◽  
Magali Dufour ◽  
Perla Hamon ◽  
Serge Hamon ◽  
Alexandre de Kochko ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genomic Library ◽  
Polymorphic Locus ◽  
Coffea Canephora ◽  
Genetic Studies ◽  
Critically Endangered Species ◽  
Allele Number ◽  
Coffea Species ◽  
High Level ◽  
Coffee Species

Of the 103 accepted Coffea species, 70% are threatened with extinction but only a few of them have been studied. A set of 40 polymorphic microsatellite markers was developed using a GA/GT-enriched Coffea canephora genomic library. Amplification of these markers was tested in accessions of C. heterocalyx (a Critically Endangered species) and C. pseudozanguebariae (a Vulnerable species) belonging to different African geographical clades. All microsatellites were polymorphic in C. canephora, with a mean allele number per polymorphic locus of more than 3 (at least 9 genotypes were tested). Observed and expected heterozygosities calculated for C. canephora and C. pseudozanguebariae varied from 0.10 to 0.91 and from 0.20 to 0.77, respectively. In total, 38 primer pairs (95%) were amplified in C. heterocalyx and C. pseudozanguebariae, indicating their high level of transferability across the genus Coffea. This large marker set will be useful for more extensive genetic studies of threatened Coffea species.

scholarly journals Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Zhi Li ◽  
Weibin Xu ◽  
Jing Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
In Situ Conservation ◽  
Grass Shrimp ◽  
The Other ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Two Populations

Abstract Background The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. Results Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. Conclusion This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

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