Keragaman Genetik 50 Aksesi Plasma Nutfah Kedelai Berdasarkan Sepuluh Penanda Mikrosatelit

Genetic Diversity of 50 Soybean Accessions Based on Ten Microsatellite Markers. Chaerani, Nurul Hidayatun, and Dwinita W. Utami. Soybean accessions in germplasm collection have increased in number as a result of exploration, introduction as well as development or release of new commercial varieties. This complicates accurate and reliable evaluation of an accession for purposes of utilization in breeding program and discrimination of a new commercial variety for purposes of plant variety protection. The aims of this study were to identify the genetic diversity of soybean germplasm to complement the existing phenotypic database as the basis for efficient management and accurate discrimination of commercial varieties, and to identify potential parents for hybridizations. Fifty soybean accessions consisting of 12 released varieties, 32 local varieties, and 6 introductions were analyzed using microsatellite DNA markers based on semi-automatic sizing system. A total of 86 alleles were detected with the number of alleles per locus ranged from 4 to 16. Rare alleles were detected at a rate of 53% which was shown by 68% of the genotypes. Informativeness of the microsatellite markers as measured by the average gene diversity (D) or polymorphism information content (PIC) was 0.60 and 0.58, respectively. A heterozygosity level of 0.09 as detected by seven loci was observed among 64% of the genotypes. The average genetic distance among the genotypes was 0.56, which indicated the relatively low polymorphism among the analyzed soybean germplasm. Four microsatellites that showed a high D or PIC value (over 0.75) were able to discriminate between accession reliably. Each soybean accession had different DNA microsatellite fingerprint which can be used for accurate discrimination to complement the previous conventional characterizations. UPGMA clustering separated the 50 accessions into 10 major clusters, which showed no clear pattern of clustering according to varietal group or geographical origin. Genetic similarity data identified five clusters and 15 genotypes with highest intercluster or inter-genotype genetic distances which are potential candidates to be exploited as parents in hybridizations for development of new commercial varieties.

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Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

Author(s):

S Islam ◽

MS Haque ◽

RM Emon ◽

MM Islam ◽

SN Begum

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Genetic Distance ◽

Microsatellite Markers ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Triticum Aestivum L ◽

Allele Number ◽

Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

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Analysis of Genetic Diversity within Nepalese Maize Populations Using SSR Markers

Nepal Journal of Science and Technology ◽

10.3126/njst.v11i0.4082 ◽

1970 ◽

Vol 11 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Dil Bahadur Gurung ◽

Maria Luz C George ◽

Quirino D Dela Cruz

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Gene Diversity ◽

Genetic Distances ◽

Maize Breeding ◽

Maize Populations ◽

Maize Varieties ◽

Ssr Loci ◽

Average Gene ◽

Hybrid Maize

Information on genetic diversity and relationships among breeding materials is necessary for hybrid maize breeding. Four open-pollinated varieties were analyzed using SSR markers to determine the genetic diversity within the varieties. In each variety, 15 individuals were genotyped with 30 SSR markers. Average heterozygosity percentage of the varieties was 45.07%, ranging from 35.23% in Rampur Composite to 54.64% in Khumal Yellow, indicating the higher level of heterozygosity in these two varieties. An average PIC value across all the polymorphic SSR loci was 0.50; which ranged from 0.47 in Manakamana-2 to 0.52 in Khumal Yellow and Arun-4. At the genotype level, the range was from 0.07 in umc1161 to 0.84 in umc1136. The total number of alleles detected was 415 for 30 SSR markers in 60 genotypes. The unique and common alleles detected respectively were 27 and 71. The average number of alleles per locus was 3.45 among the varieties, ranging from 3.21in Manakamana-2 to 3.76 in Khumal Yellow. Average gene diversity across the varieties was 0.54 and ranged from 0.51 in Manakamana-2 to 0.56 in Khumal Yellow and Arun-4. The genetic similarity coefficient of all individuals among the varieties was seen at 0.35.The MRD values were higher between Arun-4 and Manakamana-2 (0.290) and low between Khumal Yellow and Rampur Composite (0.221). Estimate of genetic distances among the varieties showed that Rampur Composite, Khumal Yellow, and Manakamana-2 were closely related sharing the similar genetic backgrounds, whereas Arun-4 was genetically more distantly related. Efforts are being made for the development and evaluation of inbred lines from these distantly related maize varieties for developing high yielding maize hybrids. Key Words: genetic diversity; maize hybrid; SSR markers DOI: 10.3126/njst.v11i0.4082Nepal Journal of Science and Technology 11 (2010) 1-8

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Genetic diversity between Italian and Greek buffalo populations

Animal Genetic Resources Information ◽

10.1017/s1014233900001383 ◽

2001 ◽

Vol 29 ◽

pp. 31-40 ◽

Cited By ~ 6

Author(s):

B. Moioli ◽

A. Georgoudis ◽

F. Napolitano ◽

G. Catillo ◽

S. Lucioli ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Genetic Distances ◽

Allele Frequency Distribution ◽

Average Gene Diversity ◽

Polymorphic Microsatellite ◽

Average Gene ◽

Degree Of Differentiation ◽

Two Populations ◽

Global Project

SummaryThe present study is a first step of a global project aiming at the estimation of the genetic distances and relationships among buffalo breeds and sub-populations and the investigation of the production potential and adaptability of different buffalo genotypes in various environments.Genetic diversity of Italian and Greek buffalo populations was estimated on the basis of allele frequencies at nine polymorphic microsatellite loci: CSSM43, CSSM38, DRB3, D21S4, CYP21, CSSM47, CSSM60, CSSM36 and CSSM33. The number of detected alleles per locus varied from two (D21S4) to thirteen (CSSM47). Allele frequency distribution was similar in the two populations, which have the same alleles at the highest frequency at all loci, except loci CSSM47 and CSSM60. Average gene diversity over all loci was 0.60. Across-loci average gene diversity increased with the number of alleles. Observed average heterozygosity was 0.167 and 0.177 in the Italian and Greek populations, respectively. The degree of differentiation between Italian and Greek buffalo was moderate and estimated at 0.021 ± 0.009.

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The Use of DNA Microsatellite Markers for Genetic Diversity Identifi cation of Soybean (Glycine max (L) Meriil.) as a Supplementary Method in Reference Collections Management

Indonesian Journal of Biotechnology ◽

10.22146/ijbiotech.9306 ◽

2016 ◽

Vol 19 (2) ◽

pp. 136 ◽

Cited By ~ 1

Author(s):

Nina Agusti Widaningsih ◽

Edi Purwanto ◽

N. Nandariyah ◽

R. Reflinur

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Morphological Characteristics ◽

Morphological Characters ◽

Practical Applications ◽

Plant Collection ◽

New Varieties ◽

Variety Protection ◽

Dna Microsatellite ◽

Biology Laboratory

Large number of new soybean varieties are mostly derived from crosses of elite genotypes resulted ina narrowing of both the genetic diversity and the phylogenetic relationship between soybean varieties. Thus,discrimination among soybean varieties is becoming more diffi cult, especially when morphological traits wereapplied. In Plant Variety Protection (PVP) system, new varieties of soybeans including granted PVP right, localand breeding varieties registered in PVP offi ce were frequently increased, implicate on increasingly the numberof soybean varieties collections. To assist the management of varieties collections, a standard fi ngerprinting datais further needed. In comparison to the management of plant collection in the fi eld, molecular marker systemswhich are rapid, reliable, informative and relatively simple are continually sought for practical applications ingermplasm conservation, management and enhancement. This study aimed to identify the genetic diversity andphylogenetic relationship of soybean varieties that have earned PVP Right as well as local varieties and breedingvarieties registered in the PVP offi ce using microsatellite or simple sequence repeats (SSR) markers.This study was conducted in Molecular Biology laboratory, Indonesian Center for Agricultural Biotechnologyand Genetic Resources Research and Development (ICABIOGRAD) Bogor, from February to May 2013. The datawere analyzed using the genetic analysis package NTSYSpc 2.02i and PowerMarker V3.25. The result showed arelatively narrow genetic diversity among 45 varieties of soybean analyzed in present study which were indicatedby the small number of genotypes and total number of alleles (NA), and the low value of gene diversity and PICvalues (<0.75). Cluster analysis showed that the grouping varieties are not related to morphological characters butrelated to phylogeny relationship between varieties. Despite the group of varieties were not clustered in accordancewith morphological characteristics, SSR marker can be a powerful tool for discriminating varieties, so that it couldbe useful for initial varieties identity in conjunction with genetic diversity analysis.

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Genetic diversity in table grapes based on RAPD and microsatellite markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011000900010 ◽

2011 ◽

Vol 46 (9) ◽

pp. 1035-1044 ◽

Cited By ~ 9

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.

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

PeerJ ◽

10.7717/peerj.2936 ◽

2017 ◽

Vol 5 ◽

pp. e2936 ◽

Cited By ~ 13

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.

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High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.723706 ◽

2021 ◽

Vol 12 ◽

Author(s):

Amali Malshani Samaraweera ◽

Ranga Liyanage ◽

Mohamed Nawaz Ibrahim ◽

Ally Mwai Okeyo ◽

Jianlin Han ◽

...

Keyword(s):

Genetic Diversity ◽

Sri Lanka ◽

Microsatellite Markers ◽

Allelic Diversity ◽

Genetic Distances ◽

Population Substructure ◽

High Genetic Diversity ◽

Naked Neck ◽

Local Chicken ◽

Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

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Comparison of Genetic Diversity in Naturally Regenerated Norway Spruce Stands and Seed Orchard Progeny Trials

Forests ◽

10.3390/f10100926 ◽

2019 ◽

Vol 10 (10) ◽

pp. 926 ◽

Cited By ~ 3

Author(s):

Dainis Ruņģis ◽

Solveiga Luguza ◽

Endijs Bāders ◽

Vilnis Šķipars ◽

Āris Jansons

Keyword(s):

Genetic Diversity ◽

Norway Spruce ◽

Gene Diversity ◽

Seed Orchard ◽

Seed Orchards ◽

Spruce Stands ◽

Ssr Loci ◽

Naturally Regenerated Stands ◽

Average Gene ◽

Environmental Events

Forest ecosystems in Europe are expected to experience changes in temperature and water regimes associated with increased risks of extreme environmental events and disasters. Genetic diversity and relatedness has been linked to resilience of forest stands and landscapes. Genetic diversity indicators were compared between a Norway spruce population naturally regenerated after extensive windthrow and Norway spruce progeny populations derived from two seed orchards. In addition, genetic diversity in an undisturbed stand in a long established national park and a spruce genetic resource stand were analyzed. Populations were genotyped at 11 simple sequence repeat (SSR) loci. Average genetic diversity indicators were similar across populations. However, the total number of alleles, average number of alleles over all loci, effective number of alleles, average gene diversity, and average allelic richness were highest in the naturally regenerated population and lowest in one of the seed orchard progeny populations. The genetic diversity in progeny from seed orchards used for stand renewal is comparable to the genetic diversity in naturally regenerated stands. However, fluctuations in seed production between years can have a large impact on genetic diversity in seed orchard progeny. The use of improved Norway spruce germplasm deployed via clonal seed orchards for forest renewal can maintain similar levels of genetic diversity compared to naturally regenerated stands, while also increasing production and timber quality.

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Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

Journal of Scientific Research ◽

10.3329/jsr.v4i3.10416 ◽

2012 ◽

Vol 4 (3) ◽

pp. 757-767 ◽

Cited By ~ 1

Author(s):

M. M. Hassan ◽

A. K. M. Shamsuddin ◽

M. M. Islam ◽

K. Khatun ◽

J. Halder

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Gene Diversity ◽

Allele Number ◽

Rice Landraces ◽

Efficient Management ◽

Ssr Loci ◽

Pattern Of Variation ◽

Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

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