Characterization of Genetic Diversity of Stone Fruit Rootstocks Used in Chile by Means of Microsatellite Markers

Stone fruit (Prunus L.) production in Chile covers ≈43,000 ha and includes a wide variety of soils and climates requiring a large diversity of rootstocks. The most commercially important rootstock cultivars are 26 genotypes from three different taxonomic groups belonging to the subgenera Amygdalus (L.) Benth. Hook. (peach group), Prunus Focke [= Prunophora (Neck.)] Focke (plum group), and Cerasus (Adans.) Focke (cherry group) with eight, seven, and 10 individuals, respectively. To determine their genetic diversity, characterization by microsatellite markers [simple sequence repeat (SSR)] was conducted. Of a total of 20 SSR markers evaluated, 12 generated amplified products that were consistent in the three taxonomic groups. The number of alleles per marker ranged from 18 for PSM-3 to four in CPPCT-002. Clustering analysis, by both traditional hierarchical and model-based approaches, indicate that all genotypes are clustered in their respective taxonomic groups, including the interspecific hybrids. Genetic diversity, measured as the average distances (expected heterozygosity) between individuals in the same cluster, was higher in Cerasus (0.78) followed by Prunus (0.72) and Amygdalus (0.64). Total number of alleles observed was 133, of which 14, 33, and 35 from six, 10, and 10 loci were unique for the peach, plum, and cherry rootstock groups, respectively. Alleles shared among peach/plum, plum/cherry, and peach/cherry rootstock genotypes were 13, 14, and 18 from nine, seven, and seven loci, respectively. Only six alleles from five loci were common to the three taxonomic groups. In addition, to develop a rootstock identification system based on SSR markers, a minimum set of three markers (PMS-3, BPPCT-037, and BPPCT-036) able to differentiate the 26 genotypes was identified. This study is the first step toward establishing a stone fruit rootstock breeding program in Chile.

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Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262114000112 ◽

2014 ◽

Vol 12 (3) ◽

pp. 323-329 ◽

Cited By ~ 1

Author(s):

Guillermo Padilla ◽

Rafel Socias i Company ◽

Amando Ordás

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Average Value ◽

La Palma ◽

Expected Heterozygosity ◽

Commercial Cultivars ◽

Soft Shell ◽

Genetic Profiles ◽

Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

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Molecular characterization of China aster (Callistephus chinensis (L.) Nees) genotypes using SSR markers

Israel Journal of Plant Sciences ◽

10.1163/22238980-bja10037 ◽

2021 ◽

pp. 1-10

Author(s):

Veluru Bhargav ◽

Rajiv Kumar ◽

Anuradha Sane ◽

T. Manjunatha Rao ◽

T. Usha Bharathi ◽

...

Keyword(s):

Genetic Diversity ◽

Association Mapping ◽

Ssr Markers ◽

Crop Improvement ◽

Flower Color ◽

Target Populations ◽

Genome Wide ◽

China Aster ◽

Simple Sequence

Abstract Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement.

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MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

Bangladesh Journal of Plant Breeding and Genetics ◽

10.3329/bjpbg.v21i1.17041 ◽

2008 ◽

Vol 21 (1) ◽

pp. 01-06 ◽

Cited By ~ 1

Author(s):

A. K. M. Khorsheduzzaman ◽

M. Z. Alam ◽

M. M. Rahman ◽

M. A. K. Mian ◽

M. I. H. Mian ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Banding Pattern ◽

Genomic Dna ◽

Molecular Level ◽

Narrow Range ◽

Solanum Melongena ◽

Pcr Amplification ◽

Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccards coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

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Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Plants ◽

10.3390/plants10030487 ◽

2021 ◽

Vol 10 (3) ◽

pp. 487

Author(s):

Trinity P. Hamm ◽

Marcin Nowicki ◽

Sarah L. Boggess ◽

William E. Klingeman ◽

Denita Hadziabdic ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Diversity Index ◽

Molecular Tools ◽

Closely Related Species ◽

Future Studies ◽

Expected Heterozygosity ◽

Large Genus ◽

Simple Sequence

The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA sequencing and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.

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Transferability and Characterization of Microsatellite Markers from Byrsonima Cydoniifolia A. Juss. (MALPIGHIACEAE) in Seven Related Taxa from Cerrado Biome Reveal Genetic Relationships

10.21203/rs.3.rs-238340/v1 ◽

2021 ◽

Author(s):

Vanessa Bernardes ◽

Devanir M. Murakami ◽

Nair Bizão ◽

Tamara N. Souza ◽

Marcos J. da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Divergence ◽

High Efficiency ◽

Population Studies ◽

Genetic Relationships ◽

Species Occurrence ◽

Genetic Population ◽

Expected Heterozygosity

Abstract Byrsonima Rich. is one of the largest genera of the Malpighiaceae family, with 97 species occurrence in Brazil. In this study, 17 microsatellite markers previously developed and characterized in Byrsonima cydoniifolia A. Juss. were tested for seven related taxa. All species tested here are native to Brazil, and of these species four are endemic. Cross-amplification as successfully optimized with high efficiency for all species. Microsatellite markers panels ranged from 11 (64,8%) transfered markers in B. viminifolia to 6 (35.2%) in B. umbellata. All loci were genotyped for 16 individuals of each species, except for B. viminifolia (14 individuals), then the polymorphic loci were characterized. The total number of alleles per locus across tested species ranged from 5 (B. linearifolia) to 8 (B. subterranea) alleles. B. umbellata showed lower values of observed and expected heterozygosity (Ho = 0.312; He = 0.436) and B. subterranea presented the highest values (Ho = 0.687; He = 0.778). A greater number of microsatellite markers should be developed for B. umbellata, once that the markers set transferred is reasonably informative, due to the greatest genetic divergence between species. The microsatellite marker panels transferred to the species B. intermedia, B. verbascifolia, B. laxiflora, B. subterranea, B. viminifolia and B. linearifolia are very informative, with a high combined probability of exclusion of paternity (Q ≥ 0.976) and the low combined probability of identity (I ≤ 9.91x10− 6), potentially suitable for future genetic-population studies, supporting strategies for maintaining the genetic diversity and for exploration of Byrsonima species as genetic resources.

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Microsatellite Markers in Hazelnut: Isolation, Characterization, and Cross-species Amplification

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.4.543 ◽

2005 ◽

Vol 130 (4) ◽

pp. 543-549 ◽

Cited By ~ 56

Author(s):

Nahla V. Bassil ◽

R. Botta ◽

S.A. Mehlenbacher

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Geographical Origin ◽

Genome Mapping ◽

Polymorphic Information Content ◽

Corylus Avellana ◽

Expected Heterozygosity ◽

Gaa Repeats ◽

Microsatellite Alleles ◽

Simple Sequence

Three microsatellite-enriched libraries of the european hazelnut (Corylus avellana L.) were constructed: library A for CA repeats, library B for GA repeats, and library C for GAA repeats. Twenty-five primer pairs amplified easy-to-score single loci and were used to investigate polymorphism among 20 C. avellana genotypes and to evaluate cross-species amplification in seven Corylus L. species. Microsatellite alleles were estimated by fluorescent capillary electrophoresis fragment sizing. The number of alleles per locus ranged from 2 to 12 (average = 7.16) in C. avellana and from 5 to 22 overall (average = 13.32). With the exception of CAC-B110, di-nucleotide SSRs were characterized by a relatively large number of alleles per locus (≥5), high average observed and expected heterozygosity (Ho and He > 0.6), and a high mean polymorphic information content (PIC ≥ 0.6) in C. avellana. In contrast, tri-nucleotide microsatellites were more homozygous (Ho = 0.4 on average) and less informative than di-nucleotide simple sequence repeats (SSRs) as indicated by a lower mean number of alleles per locus (4.5), He (0.59), and PIC (0.54). Cross-species amplification in Corylus was demonstrated. These microsatellite markers were highly heterozygous and polymorphic and differentiated among genotypes of C. avellana irrespective of geographical origin. They will aid in fingerprinting genotypes of the european hazelnut and other Corylus species, genome mapping, and genetic diversity assessments.

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Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

10.21203/rs.3.rs-1204134/v1 ◽

2022 ◽

Author(s):

Huiling Wang ◽

Kuan Yang ◽

Liwei Guo ◽

Lifen Luo ◽

Chi He ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Yunnan Province ◽

Polymorphic Information Content ◽

Polyacrylamide Gel Electrophoresis ◽

Panax Notoginseng ◽

Expected Heterozygosity ◽

Ssr Primers ◽

Polymorphic Microsatellite ◽

Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

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Genetic Diversity Assessment in Pea (Pisum sativum L.) using Microsatellite Markers

International Journal of Bio-resource and Stress Management ◽

10.23910/1.2021.2374a ◽

2021 ◽

Vol 12 (5) ◽

pp. 402-408

Author(s):

Hanuman Ram ◽

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Ssr Markers ◽

Molecular Diversity ◽

Polymorphic Information Content ◽

Association Studies ◽

Pisum Sativum L ◽

Diversity Assessment ◽

Potential Use ◽

Simple Sequence

The present study was conducted on genetic diversity analyses among 24 pea genotypes during 2017–2018 to assess the molecular diversity of pea genotypes using SSR markers. Out of 62, eleven markers were found to be polymorphic and the polymorphic information content (PIC) of the simple sequence repeat (SSR) markers ranged from 0.19 to as high as 0.64. Molecular profiling of these genotypes using 11 SSRs distributed throughout the genome generated 32 alleles with a mean of 2.91 alleles per locus. The genetic dissimilarity based on simple matching coefficient for 24 genotypes ranged from 0.00 to 0.91 with an average of 0.52. Cluster analyses grouped 24 genotypes into two major clusters with one outlier and supported by principal coordinate analysis (PCoA) in which genotypes were distributed across four quadrangles. Analysis of molecular variance (AMOVA) showed significant estimated value at degree of 1000 permutations. Percentage of variability was higher among individual (67%) than among populations (11%). Percentage of variability within individual was also higher (22%) than among populations (11%). Pop1 (I=0.707, He=0.446, and uHe=0.466) shows higher diversity than pop2 (I=0.630, He=0.381 and uHe=0.398). The percentage of polymorphic loci per population (PPL) ranged from 81.82% (pop2) to 90.91% (pop1) with an average of 86.36%. The present study demonstrates the utility of microsatellite markers for estimating molecular diversity as well as genotype identification in pea. This study also suggests a potential use of these markers in further association studies.

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GENETIC DIVERSITY OF EGYPTIAN ARABIAN HORSES FROM EL-ZAHRAA STUD BASED ON 14 TKY MICROSATELLITE MARKERS

Slovenian Veterinary Research ◽

10.26873/svr-1041-2020 ◽

2021 ◽

Vol 58 (2) ◽

Author(s):

Mary Sargious ◽

Ragab El-Shawarby ◽

Mohamed Abo-Salem ◽

Elham EL-Shewy ◽

Hanaa Ahmed ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Parentage Assignment ◽

Expected Heterozygosity ◽

Bioinformatics Software ◽

Pcr Products ◽

Arabian Population ◽

Genetic Analyzer

The objectives of this study were, firstly, to conduct genetic characterization of Egyptian Arabian horses based on 14 TKY microsatellite markers, secondly, to investigate the powerfulness of these 14 TKY markers for parentage assignment of Arabian horses. A total of 101 horse samples including (Arabian = 71, Thoroughbred = 19 and Nooitgedacht = 11) were analysed by 14 TKY microsatellite markers. The PCR products were electrophoresed on Genetic analyzer 3500 with the aid of Liz standard. The basic measures of the allele’s size and genetic diversity were computed using bioinformatics software. The polymorphism of the TKY markers across the Arabian population showed moderate values for genetic diversity parameters; number of allele (NA) =8.143, effective number of allele (Ne) = 3.694, observed heterozygosity (HO) = 0.599, expected heterozygosity (HE) = 0.691, polymorphic Information Content (PIC) = 0.636 and Inbreeding coefficient (FIS)= 0.128. The combined probability of exclusion (CPE) value of the 14 TKY microsatellite loci of our Arabian horses was 0.9999. The results from current study confirm the applicability and efficiency of TKY microsatellite panel for evaluating the genetic diversity and parentage assignment of Egyptian Arabian horses.Key words: Arabian horses; genetic diversity; microsatellite; TKY markers GENSKA RAZNOVRSTNOST EGIPČANSKIH KONJ ARABSKE PASME IZ KOBILARNE EL-ZAHRAA NA PODLAGI 14 MIKROSATELITSKIH OZNAK TKY Izvleček: Nameni raziskave so bili genetska karakterizacija egipčanskih konj arabske pasme na podlagi 14 mikrosatelitskih označevalecv TKY ter raziskava moči 14 označevalcev TKY za dodelitev staršev arabskih konj. S pomočjo 14 mikrosatelitskih označevalcev TKY je bilo analiziranih 101 vzorcev konj (arabski = 71, čistokrvni = 19 in konji Nooitgedacht = 11). Produkte PCR so analizirali s pomočjo elektroforeze na genskem analizatorju 3500 s pomočjo Liz standarda. Osnovne mere velikosti alela in genske raznovrstnosti so bile izračunane s pomočjo programske opreme za bioinformatiko. Polimorfizem označevalcev TKY v arabski populaciji je pokazal zmerne vrednosti za parametre genske raznolikosti; število alelov (NA) = 8,143, efektivno število alelov (Ne) = 3,694, opazovana heterozigotnost (HO) = 0,599, pričakovana heterozigotnost (HE) = 0,691, polimorfna informacijska vsebina (PIC) = 0,636 in Inbriding koeficient (FIS) = 0,128. Skupna vrednost verjetnosti izključitve (CPE) 14 mikrosatelitskih lokusov TKY njihovih arabskih konj je bila 0,9999. Rezultati te raziskave potrjujejo uporabnost in učinkovitost mikrosatelitske plošče TKY za oceno genetske raznovrstnosti in starševske pripadnosti egipčanskih arabskih konj.Ključne besede: arabski konji; genska raznolikost; mikrosatelit; markerji TKY

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Primer Note: A novel set of EST-SSR markers in Tamarix: a resource to characterize this genus

Silvae Genetica ◽

10.1515/sg-2013-0013 ◽

2013 ◽

Vol 62 (1-6) ◽

pp. 104-109 ◽

Cited By ~ 3

Author(s):

S. Terzoli ◽

E. Cattan ◽

M. Sabatti ◽

R. Valentini ◽

A. Zilberstain ◽

...

Keyword(s):

Ssr Markers ◽

Expressed Sequence Tag ◽

Genetic Characterization ◽

Ecological Impact ◽

Expected Heterozygosity ◽

Desert Habitat ◽

The Mean ◽

Expressed Sequence ◽

Simple Sequence

Abstract Both the negative and positive ecological impact of Tamarix plants is controversial, and thus a more comprehensive understanding is necessary. Tamarisks are invasive in many countries but the inter-specific transferability that characterizes simple sequence repeats (SSRs) could be harnessed to track the spread of specific genotypes or to study invasive populations. Thirteen polymorphic SSR markers, derived from expressed sequence tag (EST), were identified by first screening 26 samples of T. aphylla, T. jordanis, T. nilotica, and T. tetragyna and then 33 unidentified tamarisks from Yotvata, Israel. The mean number of alleles per locus ranged from two to 14 and the mean expected heterozygosity was 0.415. These EST-SSR markers will undoubtedly be useful in the genetic characterization of the genus Tamarix due to their high cross-species transferability which enables the estimation of the genetic diversity among and within different species, that are adapted to the same desert habitat under severe environmental constraints.

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