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 Determination of Three Main Chlorogenic Acids in Water Extracts of Coffee Leaves by Liquid Chromatography Coupled to an Electrochemical Detector

Antioxidants ◽  
2018 ◽  
Vol 7 (10) ◽  
pp. 143 ◽  
Author(s):  
Rocío Rodríguez-Gómez ◽  
Jérôme Vanheuverzwjin ◽  
Florence Souard ◽  
Cédric Delporte ◽  
Caroline Stevigny ◽  
...  
Keyword(s):  
Liquid Chromatography ◽  
Coffea Arabica ◽  
Limit Of Detection ◽  
Coffea Canephora ◽  
Antioxidant Compounds ◽  
Chlorogenic Acids ◽  
Coffea Species ◽  
Coffee Species ◽  
Coffea Liberica

Coffee is a beverage widely consumed in the world. The coffee species most commercialized worldwide are Arabica (Coffea arabica) and Robusta (Coffea canephora). Roasted coffee beans are the most used, but coffee leaves are also consumed as infusion in several countries for traditional medicinal purposes. They contain several interesting phenolic antioxidant compounds mainly belonging to chlorogenic acids (CGAs). In the present work, a liquid chromatography-electrochemical detection (LC-EC) method was developed for the determination of three main chlorogenic acid isomers, namely 3-, 4-, and 5-caffeoylquinic acids (CQA), in coffee leaves aqueous extracts. Samples from eight coffee species, namely; Coffea arabica, Coffea canephora, Coffea liberica, Coffea humilis, Coffea mannii, Coffea charrieriana, Coffea anthonyi, and Coffea liberica var. liberica, were grown and collected in tropical greenhouses. Linearity of the calibration graphs was observed in the range from the limit of quantification to 1.0 × 10−5 M, with R2 equal to 99.9% in all cases. High sensitivity was achieved with a limit of detection of 1.0 × 10−8 M for 3-CQA and 5-CQA (i.e., 3.5 µg/L) and 2.0 × 10−8 M for 4-CQA (i.e., 7.1 µg/L). The chromatographic profile of the samples harvested for each Coffea species was studied comparatively. Obtained raw data were pretreated for baseline variations and shifts in retention times between the chromatographic profiles. Principal Component Analysis (PCA) was applied to the pretreated data. According to the results, three clusters of Coffea species were found. In the water sample extracts, 5-CQA appeared to be the major isomer, and some species contained a very low amount of CQAs. Fluctuations were observed depending on the Coffea species and harvesting period. Significant differences between January and July were noticed regarding CQAs content. The species with the best CQAs/caffeine ratio was identified. The LC-EC data were validated by liquid chromatography-high resolution mass spectrometry (LC-HRMS).

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 Microsatellites Cross-Species Amplification across Some African Cichlids

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Etienne Bezault ◽  
Xavier Rognon ◽  
Karim Gharbi ◽  
Jean-Francois Baroiller ◽  
Bernard Chevassus
Keyword(s):  
Microsatellite Markers ◽  
Oreochromis Niloticus ◽  
Molecular Genetic ◽  
Point Of View ◽  
Genetic Studies ◽  
African Cichlid ◽  
Wide Range ◽  
The Mean ◽  
High Level ◽  
African Cichlids

The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.

Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Konrad Celiński ◽  
Ewa Pawlaczyk ◽  
Aleksandra Wojnicka-Półtorak ◽  
Ewa Chudzińska ◽  
Wiesław Prus-Głowacki
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Pinus Mugo ◽  
Genetic Studies ◽  
Transfer Rates ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
European Mountain ◽  
High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthio camelus) genome

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 833-840 ◽  
Author(s):  
Bo Tang ◽  
Yin Hua Huang ◽  
Li Lin ◽  
Xiao Xiang Hu ◽  
Ji Dong Feng ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genomic Library ◽  
Enriched Library ◽  
Genetic Studies ◽  
Pcr Screening ◽  
Struthio Camelus ◽  
Parentage Testing ◽  
Isolation And Characterization ◽  
Length Polymorphisms

Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.

scholarly journals A study on genetic diversity of bagrid catfish (Hemibagrus guttatus Lacepede, 1803) using microsatellite markers

2018 ◽  
Vol 16 (1) ◽  
pp. 59-65
Author(s):  
Bùi Hà My ◽  
Nguyễn Thị Hương ◽  
Nguyễn Hữu Đức ◽  
Trần Thị Thúy Hà
Keyword(s):  
Microsatellite Markers ◽  
Economic Value ◽  
Low Frequency ◽  
Wild Populations ◽  
Genetic Characteristics ◽  
Allele Number ◽  
Expected Heterozygosity ◽  
Artificial Breeding ◽  
The Mean ◽  
High Level

Bagrid catfish (Hemibagrus guttatus Lacepede, 1803) is a wild species of high economic value in Northern Vietnam. Artificial reproduction of bagrid catfish requires sources of quality fingerlings in terms of genetics. In fact, bagrid catfish is endangered due to overhunting. Until now, studying on bagrid catfish was mainly focused on biology characterictics and artificial breeding. In this study, three microsatellite markers were used to assess the genetic characteristics of four bagrid catfish populations (three wild populations collected in Tuyên Quang, Phu Tho, Ha Giang and a cultured population in Hai Duong). These markers were registed Genbwith the code of KJ873116, KJ873117 and NC 023976 for HM7, HM8 and SS1, respectively. All of the loci showed high level of polymorphism with 16 alleles in total which were 5 at locus HM7, 5 at locus HM8, and 6 at locus SS1. Total allele number in population collected in Ha Giang was higher than that of Tuyen Quang, Phu Tho and Hai Duong populations. The mean of number of observed alleles (Na = 3,83 ± 0,24) was higher than the mean number of effective alleles (Ne = 2,14 ± 0,13) and low frequency alleles (< 0,1) were observed in all loci. The value of the expected heterozygosity (He = 0,38- 0,63) was lower than that of the observed heterozygosity (Ho = 0,51-0,71). FIS value was low and the genetic differences between four populations was insignificant as FST < 0,05. The results provide useful information for breeding program and conservation of the bagrid catfish in the future.

The way of value of Correlation of genomic DNA microsatellite loci and live weight of Chukchi reindeer

2020 ◽  
pp. 27-32
Author(s):  
V. Dodokhov ◽  
N. Pavlova ◽  
T. Rumyantseva ◽  
L. Kalashnikova
Keyword(s):  
Microsatellite Markers ◽  
Agricultural Production ◽  
Live Weight ◽  
Biodiversity Loss ◽  
Tribal Community ◽  
High Germination ◽  
Wide Range ◽  
The Mean ◽  
High Level ◽  
Dna Microsatellite

The article presents the genetic characteristic of the Chukchi reindeer breed. The object of the study was of the Chukchi reindeer. In recent years, the number of reindeer of the Chukchi breed has declined sharply. Reduced reindeer numbers could lead to biodiversity loss. The Chukchi breed of deer has good meat qualities, has high germination viability and is adapted in adverse tundra conditions of Yakutia. Herding of the Chukchi breed of deer in Yakutia are engaged only in the Nizhnekolymsky district. There are four generic communities and the largest of which is the agricultural production cooperative of nomadic tribal community «Turvaurgin», which was chosen to assess the genetic processes of breed using microsatellite markers: Rt6, BMS1788, Rt 30, Rt1, Rt9, FCB193, Rt7, BMS745, C 143, Rt24, OheQ, C217, C32, NVHRT16, T40, C276. It was found that microsatellite markers have a wide range of alleles and generally have a high informative value for identifying of genetic differences between animals and groups of animal. The number of identified alleles is one of the indicators of the genetic diversity of the population. The total number of detected alleles was 127. The Chukchi breed of deer is characterized by a high level of heterozygosity, and the random crossing system prevails over inbreeding in the population. On average, there were 7.9 alleles (Na) per locus, and the mean number of effective alleles (Ne) was 4.1. The index of fixation averaged 0.001. The polymorphism index (PIC) ranged from 0.217 to 0.946, with an average of 0.695.

scholarly journals Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

2021 ◽  
Author(s):  
Júlia Halász ◽  
Noémi Makovics-Zsohár ◽  
Ferenc Szőke ◽  
Sezai Ercisli ◽  
Attila Hegedűs
Keyword(s):  
Simple Sequence Repeat ◽  
Principal Component ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Allele Number ◽  
Genetic Potential ◽  
Ssr Loci ◽  
High Level ◽  
Diversity Studies ◽  
Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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