scholarly journals Microsatellites in the analysis of wheat genetic diversity

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 1047-1063
Author(s):  
Ankica Kondic-Spika ◽  
Milica Nicic ◽  
Ljiljana Brbaklic ◽  
Dragana Trkulja ◽  
Dragana Miladinovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Ssr Markers ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
Null Alleles ◽  
Wheat Genotypes ◽  
Rare Alleles ◽  
High Level

Microsatellite markers (SSR) were used to study wheat genetic diversity. A set of 87 wheat genotypes was analysed with four SSR markers. Primers used for the amplification of adequate microsatellite loci (Xgwm) are according to R?DER et al. (2002). Results were obtained using Applied Biosystems 3130 genetic analyser. Total of 28 alleles were determined, i.e. average of 7 alleles per marker. Number of alleles for individual markers ranged from six (Xgwm3) to eight (Xgwm18). The presence of two null alleles for Xgwm18 and Xgwm155 was found. There were five rare alleles (frequency <2%). Polymorphism information content (PIC) values ranged from 0.52 for Xgwm408 to 0.80 for Xgwm18. Mean PIC value was 0.69 for all markers, which signifies a high level of the detected polymorphism. According to the data collected through the analysis of four markers, most genotypes can be grouped in clusters. The results show usefulness of microsatellite markers in detecting polymorphism, identifying genotypes and assessing genetic diversity.

scholarly journals Genetic diversity of Tibetan goats of Plateau type using microsatellite markers

2011 ◽  
Vol 54 (2) ◽  
pp. 188-197 ◽  
Author(s):  
Y. Wang ◽  
J. Wang ◽  
X.-D. Zi ◽  
C.-R. Huatai ◽  
X. Ouyang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
The Other ◽  
Allele Number ◽  
The Mean ◽  
Black Goat ◽  
Historical Origins

Abstract. The 10 microsatellite markers (XBM7, XBM11, XBM16, XBM19, XBM24, XBM31, XBM84, TGLA53, SRCRSP-10 and ILS005) were selected to investigate the genetic diversity of Tibetan goat of Plateau type (NM, n=108), and the other 5 goat populations, i.e., Tibetan goat of Valley type (TG, n=36), Baiyu black goat (BY, n=36), Jianchang black goat (JC, n=36), Meigu goat (MG, n=36) and Xinjiang goat (XJ, n=32) were served as control. The mean polymorphism information content, heterozygosity and effective allele number of these 6 populations were 0.660/0.777/4.476, 0.716/0.797/4.9416, 0.631/0.673/3.061, 0.649/0.680/3.125, 0.629/0.680/3.125 and 0.561/0.793/4.840 respectively. The allele frequencies of Tibetan goat of plateau type in 10 microsatellite loci were greatly different with other 5 goat populations. The 6 goat populations were grouped into three distinct clusters: the Tibetan goat cluster (NM goat and TG goat), Sichuan goat cluster (JC goat, MG goat and BY goat), and Xinjiang goat cluster (XJ goat). These 3 distinct clusters were finally clustered together. The genetic differences among populations were in accordance with their geographical and historical origins.

scholarly journals Genetic diversity and differentiation in reef-buildingMilleporaspecies, as revealed by cross-species amplification of fifteen novel microsatellite loci

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2936 ◽  
Author(s):  
Caroline E. Dubé ◽  
Serge Planes ◽  
Yuxiang Zhou ◽  
Véronique Berteaux-Lecellier ◽  
Emilie Boissin
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Natural Populations ◽  
454 Sequencing ◽  
Genetic Distances ◽  
Null Alleles ◽  
Future Research ◽  
Significant Linkage ◽  
Pacific Species

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

scholarly journals  Evaluation of 11 microsatellite loci for their use in paternity testing in Yugoslav Pied cattle (YU Simmental cattle)

2010 ◽  
Vol 55 (No. 6) ◽  
pp. 221-226 ◽  
Author(s):  
J. Stevanovic ◽  
Z. Stanimirovic ◽  
V. Dimitrijevic ◽  
M. Maletic
Keyword(s):  
Microsatellite Markers ◽  
Information Content ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
Mean Value ◽  
Paternity Testing ◽  
Cattle Population ◽  
The Mean ◽  
Simmental Cattle

Eleven microsatellite loci (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA126, TGLA122, INRA023, ETH3, ETH225, BM1824) were evaluated for their use in paternity testing in the Yugoslav Pied cattle (YU Simmental cattle) population in Serbia. A total of 40 animals were tested. At the 11 tested loci, a total of 91 alleles were detected. The mean number of alleles per locus was 8.273. Polymorphism information content (PIC) values ranged from 0.58 to 0.88 with the mean value of 0.72. The most informative loci were: TGLA53 (14 alleles, PIC = 0.88), TGLA227 (11 alleles, PIC = 0.82), INRA023 (11 alleles, PIC = 0.86), BM2113 (9 alleles, PIC = 0.80). Combined power of discrimination (CPD) for the 11 microsatellite loci was 0.999. The results of the present study confirm that the analysed set of 11 microsatellite markers recommended by ISAG is suitable for paternity testing in Yugoslav Pied cattle in Serbia.

scholarly journals Genetic structure of the carp population (Cyprinus carpio carpio) grown in the aquaculture in the Republic of Belarus

2021 ◽  
Vol 65 (1) ◽  
pp. 68-75
Author(s):  
V. A. Lemesh ◽  
V. Yu. Ageyets ◽  
A. Yu. Nosova ◽  
V. N. Kipen ◽  
N. I. Tsar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Cyprinus Carpio ◽  
Microsatellite Loci ◽  
High Genetic Diversity ◽  
Total Percentage ◽  
Cyprinus Carpio Carpio ◽  
Rare Alleles ◽  
The Republic ◽  
High Level

In this study, we presented a panel of 14 microsatellite loci (MFW1, MFW2, MFW6, MFW9, MFW10, MFW11, MFW13, MFW16, MFW20, MFW24, MFW26, MFW28, MFW29 and Cid0909), with which we studied the genetic structure of Cyprinus carpio carpio of the breed “Izobelinsky” in the Republic of Belarus. Four offshoots of carp were included in the study: two mirrory (“Smes’ zerkal’naya”, “Tri prim”) and two scaly (“Smes’ cheshujchataya”, “Stolin XVIII”).As a result, it was found that the carp breed “Izobelinsky” exhibits a high level of in-breed genetic variability. In the studied microsatellite loci, 231 alleles were identified, 62 % of the total number of alleles were rare alleles with a frequency of occurrence of less than 5.0 %. The number of effective alleles (Ne) at the loci ranged from 3.082 (MFW10) to 9.754 (MFW26). The Shannon biodiversity index (I) was 2.082 ± 0.075. The highest value of the expected heterozygosity index (He) was noted for the MFW26 locus (0.897), the lowest – for the MFW10 locus (0.676).The greatest genetic diversity is characteristic of the scaly carp “Smes’ cheshujchataya” and “Stolin XVIII”. The highest total percentage of rare alleles was determined for fishes from “Stolin XVIII”. The minimum values of this parameter were found for specimens of the carp “Smes’ zerkal’naya” and “Tri prim”.The results of this study indicate a fairly high genetic diversity of four offshoots of the carp breed “Izobelinsky”, which was established using the marker loci optimally selected for analysis. This makes it possible to differentiate the layering among themselves.

scholarly journals Microsatellite loci variability in apple cultivars developed at VIR

2021 ◽  
Vol 182 (3) ◽  
pp. 151-158
Author(s):  
A. V. Shlyavas ◽  
A. A. Trifonova ◽  
I. S. Chepinoga ◽  
A. S. Sidnin ◽  
K. V. Boris
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Collection Management ◽  
Breeding Programs ◽  
Rare Alleles ◽  
Pcr Products ◽  
Apple Cultivars ◽  
Place Of Origin ◽  
High Level ◽  
Traits For Breeding

Background. Microsatellite (SSR) markers are now widely used both for studying genetic diversity in fruit crop collections, including apple (Malus × domestica Borkh.), and for genotyping individual accessions. The apple collection held by VIR, being the largest in Russia, contains cultivars bred at five experiment stations of VIR. These cultivars not only meet the requirements of horticulture in the region of their origin, but also are interesting as sources of valuable traits for breeding programs. However, these cultivars have not previously been studied using microsatellite markers. Materials and methods. A set of 10 SSR markers (CH02c02b, CH03d01, CH01f03b, CH02d08, CH02c02a, CH05e03, CH02c09, CHVf1, CH01h01, COL) was used for genotyping 35 apple cultivars developed at VIR and four parental forms. Fluorescently labeled PCR products were separated by capillary electrophoresis on ABI Prism 3130xl.Results. In 35 apple cultivars from VIR, 97 alleles were identified at ten studied loci. The number of alleles per locus varied from 5 (CH02c02b) to 17 (CH02c02a). The frequency of unique alleles was 26,8%, with 12,4% for rare alleles. Polymorphism information content (PIC) values varied from 0,49 (CH02c02b) to 0,91 (CH02c02a) and averaged 0,76. Expected and observed heterozygosity levels averaged 0,79 and 0,56, respectively. Cluster analysis did not reveal a clear division of cultivars according to the place of origin (experiment stations of VIR), but revealed clustering according to pedigrees.Conclusion. A high level of polymorphism was observed in 35 apple cultivars from VIR using ten SSR markers. The obtained data on the allelic composition of the studied cultivars can be used for their identification and contribute to more efficient collection  management. Further studying and SSR genotyping of VIR’s apple collection and comparison with the data obtained in the presented work can help to identify the origin of cultivars with unknown pedigrees.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)

2016 ◽  
Vol 7 (2) ◽  
pp. 76
Author(s):  
Dwinita Wikan Utami ◽  
Sutoro Sutoro ◽  
Nurul Hidayatun ◽  
Andari Risliawati ◽  
Ida Hanarida
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Heading Date ◽  
Germplasm Collection ◽  
Dna Fingerprint ◽  
Early Maturity ◽  
Plant Variety ◽  
Variety Protection ◽  
Genetic Analyzer

<p>Genetic Diversity of 96 Accession of Rice Germplasm<br />Using 30 SSR Markers Linked to Heading Date Genes (HD<br />Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun,<br />Andari Risliawati, and Ida Hanarida. Rice with early<br />maturity is one of an important genetic resources in rice<br />germplasm collection. Characterization and identification of<br />genetic diversity is an important issue for plant variety protection.<br />Molecular identification by microsatellite markers<br />using Genetic Analyzer enables resolve of this issue. The<br />objective of this research is to identify the genetic diversity of<br />96 rice accessions based on their specific DNA fingerprint<br />using microsatellite markers. A total of 96 accessions consisting<br />of a diverse variety of maturity classification were<br />genotyped with 30 SSR markers linked to HD genes which<br />spread out in 12 chromosomes of rice geneome. The total<br />297 alleles were detected indicated the level of marker<br />informativeness. RM5607 generated 7 allele with the size<br />range from 103 to 197 and the highest PIC at 0.90. RM3571<br />(linked to HD12 gene) has a significant value associated with<br />varieties which have early maturity trait. Clustering analysis<br />showed the cluster based on Sub Species genome background<br />and on early maturity trait.</p>

scholarly journals Genetic diversity in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
Author(s):  
Francisco Elias Ribeiro ◽  
Luc Baudouin ◽  
Patricia Lebrun ◽  
Lázaro José Chaves ◽  
Claudio Brondani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Cape Verde ◽  
Coconut Palm ◽  
Different Populations ◽  
The Mean ◽  
High Level ◽  
Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

scholarly journals Study of the gene pool of the winter rye Secale cereale L. of the Republic of Belarus using microsatellite markers

2021 ◽  
Vol 66 (2) ◽  
pp. 215-222
Author(s):  
V. S. Mandrusova ◽  
I. S. Gordej ◽  
O. M. Lyusikov ◽  
V. E. Shimko ◽  
I. A. Gordej
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Gene Pool ◽  
Winter Rye ◽  
Interpopulation Variability ◽  
Content Index ◽  
Secale Cereale L ◽  
New Varieties ◽  
The Republic

In this work, the genetic diversity of the modern gene pool of the winter rye (S. cereal L.) of the Republic of Belarus from 20 actual breeding samples was investigated using 15 microsatellite (SSR) markers to develop divergent crossing combinations in breeding for heterosis. It was shown that the formed set of SSR markers is highly effective – the informational content index (PIC) varied from 0.50 to 0.83 and averaged 0.72. The most effective microsatellite markers (SCM28, SCM43, SCM101 and SCM102) were identified and can be successfully used to study the genetic diversity of rye. It has been established that the modern gene pool of the winter rye of the Republic of Belarus is generally characterized by fairly wide genetic diversity (interpopulation variability) – all collection samples are characterized by a unique allelic composition of the studied microsatellite loci. Based on investigation results, a hierarchical clustering dendrogram was constructed, which made it possible to determine the most genetically divergent combinations of crosses. The information obtained can be used for the development of an effective scheme allowing to develop new varieties and hybrids in the practical breeding of rye for heterosis.

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