An assessment of genetic variation in vulnerable Borneo Ironwood Eusideroxylon zwageri Teijsm. & Binn. in Sarawak using SSR markers

Borneo Ironwood Eusideroxylon zwageri Teijsm. & Binn. has high market value for its valuable and durable timber, which has put it at risk due to illegal logging. This study analysed E. zwageri genetic variation using four microsatellite markers in populations at Nirwana Rehabilitation Forest (NRF), and Tatau, Sarawak. We found that 20.1% of total genetic variation corresponded to differences between populations, while 79.9% was attributed to differences among individuals from the same population. The Tatau population had lower genetic diversity compared to NRF, and both populations showed depressed heterozygosity indicative of inbreeding. Allelic data were also used to confirm variety level differences proposed by earlier workers, and three informal varieties: zwageri, grandis, and exilis were recognized in the study area. It is expected that the results from this study could serve as baseline data for conservation of this vulnerable species.

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

Jurnal AgroBiogen ◽

10.21082/jbio.v7n2.2011.p76-84 ◽

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

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

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

Proceedings of the National Academy of Sciences of Belarus Biological Series ◽

10.29235/1029-8940-2021-66-2-215-222 ◽

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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Genetic variation analysis of superior cotton varieties of Gossypium hirsutum through microsatellite markers

International Journal of Plant Biology ◽

10.4081/pb.2017.6996 ◽

2017 ◽

Vol 8 (1) ◽

Author(s):

Dede Nuraida ◽

Yusuf Abdurrajak ◽

Moh Amin ◽

Utami S. Hastutik

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gossypium Hirsutum ◽

Microsatellite Markers ◽

Size Range ◽

Allele Frequencies ◽

Variation Analysis ◽

Ctab Method

This study was conducted in order to obtain information on genetic variation in populations rated as superior cotton (Gossypium hirsutum L.) varieties in Balittas Malang, Indonesia. The samples used 10 varieties of cotton Kanesia series and 2 other superior varieties that are LRA 5166 and ISA 205A. Indicators of genetic diversity are the number of alleles per locus, allele frequencies, and heterozygosity values. DNA was isolated from the leaves of 3- week-old seedlings using the CTAB method. Amplification was performed using 5 SSRs primer pairs of the JESPR series. The results showed five microsatellite loci, yielding 12 alleles with a size range of 80–500 bp, with an average number of alleles per locus of 4.60. The average values of heterozygosity of the five loci was high, at 0.71. Based on the number of alleles, allele frequencies and heterozygosity values, the genetic variation sampled in the superior cotton varieties studied here is quite high.

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Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽

10.7717/peerj.2504 ◽

2016 ◽

Vol 4 ◽

pp. e2504 ◽

Cited By ~ 1

Author(s):

Katarzyna Bilska ◽

Monika Szczecińska

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Conservation Genetics ◽

Ssr Markers ◽

Full Range ◽

Mantel Test ◽

Evolutionary Potential ◽

Functional Variation ◽

Genetics Research ◽

Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽

10.1017/s0031182002002020 ◽

2002 ◽

Vol 125 (7) ◽

pp. S51-S59 ◽

Cited By ~ 50

Author(s):

J. CURTIS ◽

R. E. SORENSEN ◽

D. J. MINCHELLA

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Molecular Markers ◽

Microsatellite Markers ◽

Natural Populations ◽

Mitochondrial Marker ◽

Tropical Regions ◽

Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

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Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers

Genome ◽

10.1139/g98-130 ◽

1999 ◽

Vol 42 (3) ◽

pp. 420-431 ◽

Cited By ~ 35

Author(s):

Gen-Lou Sun ◽

Oscar Díaz ◽

Björn Salomon ◽

Roland von Bothmer

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Microsatellite Markers ◽

Correlation Coefficients ◽

Geographic Isolation ◽

Elymus Caninus ◽

Distance Matrices ◽

High Level ◽

Mantel’S Test ◽

Similarity Matrices

Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker.Key words: Elymus caninus, genetic diversity, isozymes, RAPDs, microsatellites.

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Evaluation of genetic diversity of honey bee in Ukraine analyzed by the SSR-markers

Faktori eksperimental'noi evolucii organizmiv ◽

10.7124/feeo.v26.1241 ◽

2020 ◽

Vol 26 ◽

pp. 56-60

Author(s):

D. I. Hryhorchuk ◽

A. M. Rabokon ◽

A. S. PostovoitovA ◽

N. M. Pirko ◽

Ya. V. Pirko ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Honey Bee ◽

Ssr Markers ◽

Honey Bees ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Analysis Method ◽

Ssr Analysis ◽

Silver Nitrate Staining

Aim. The aim of the work was to analyze current genetic structure of honey bee populations in Ukraine that belong to different subspecies: A. meliffera meliffera, A. meliffera carnica, A. meliffera macedonica using microsatellite markers. Methods. SSR-analysis was used for evaluation of the honey bee polymorphism. Amplified fragments were fractionated by electrophoresis in non-denaturing polyacrylamide gel. DNA bands were detected using silver nitrate staining. Results. The analysis of the sample of honey bees (workers and male-bees) collected from different regions of Ukraine was performed by using two SSR-markers (Ac011 and A007). In this sample reasonably high polymorphism was observed, especially for the SSR-marker A007. Conclusions. It was estimated that SSR-analysis method can be applied in molecular-genetic analysis of honey bees for evaluation of genetic diversity and cross-subspecies hybridization. Keywords: microsatellite markers, Apis meliffera, PIC (Polymorphism Information Content).

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Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2020/v3i430094 ◽

2020 ◽

pp. 46-58 ◽

Cited By ~ 1

Author(s):

Ahmed Medhat Mohamed Al-Naggar ◽

Mohamed Abd El-Maboud Abd El-Shafi ◽

Mohamed Helmy El-Shal ◽

Ali Hassan Anany

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Ssr Markers ◽

Triticum Aestivum L ◽

Genetic Progress ◽

High Genetic Diversity ◽

Breeding Programs ◽

High Polymorphism Information Content ◽

Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

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Regional Polymorphism Assessment of Myanmar ‘Sein Ta Lone’ Mango (Mangifera indica Linn) from Sintgaing Township Based on Microsatellite Markers

Horticultural Biotechnology Research ◽

10.25081/hbr.2019.v5.5447 ◽

1970 ◽

pp. 17-22

Author(s):

May Sandar Kyaing ◽

Sein Sandar May Phyo

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Microsatellite Markers ◽

Mangifera Indica ◽

Germplasm Management ◽

Upgma Dendrogram ◽

Expected Heterozygosity ◽

Upgma Cluster Analysis ◽

Relationship Of

This study was conducted to explore the genetic diversity and relationship of Sein Ta Lone mango cultivars among 20 commercial orchards in Sintgaing Township, Mandalay region. Nine microsatellite (SSR) markers were used to detect genetic polymorphism in a range from (3 to 6) alleles with (4.33) alleles per marker in average. Six out of nine microsatellite markers gave the PIC values of greater than (0.5). Among them, SSR36 held the highest PIC values of (0.691) while MiSHRS39 and MN85 possessed the least PIC values of (0.368) and (0.387) respectively. The genetic diversity was expressed as unbiased expected heterozygosity (UHe) value with an average of (0.561). The genetic relationship was revealed by (UPGMA) dendrogram in a range of (0.69 to 1.00). Based on UPGMA cluster analysis, three main clusters were classified among three different locations. This study was intended to help cultivar characterization and conservation for proper germplasm management with the estimation of genetic variation and relationship in the existing population of Sein Ta Lone mangoes in Sintgaing Township by microsatellite markers.

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Assessment of genetic variation in Bapedi sheep using microsatellite markers

South African Journal of Animal Science ◽

10.4314/sajas.v50i2.15 ◽

2020 ◽

Vol 50 (2) ◽

pp. 318-324

Author(s):

A. Maqhashu ◽

N.O. Mapholi ◽

H.A. O’Neill ◽

K.A. Nephawe ◽

F.V. Ramukhithi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Microsatellite Markers ◽

South African ◽

Agricultural Research ◽

Germplasm Conservation ◽

Genetic Distances ◽

Fixation Index ◽

Indigenous Sheep ◽

Agricultural Research Council

This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep. Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep

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