Analysis of genetic diversity in the core collection of red clover (Trifolium pratense) with isozyme and RAPD markers

Nuñas are a type of common bean (Phaseolus vulgaris) that possess the unusual characteristic of popping or expanding their cotyledonary tissue when heated. Numerous landraces of nuña beans were domesticated in the Andean region of South America (Peru, Bolivia, and Ecuador) and have been grown and consumed in this region since antiquity. The practical consideration in the domestication of nuñas in the high Andes was likely due to the greater energy efficiency in cooking toasted vs. boiled seeds.The Phaseolus germplasm bank at CIAT (Centro Internacional de Agricultura Tropical) has developed a core collection of Andean beans that includes numerous nuña landraces. Based on the wide range of phaseolin types observed among nuña landraces, it has been hypothesized that nuñas may represent a greater source of genetic diversity compared to other landraces and cultivars of common bean. Eighty nuña accessions and 120 nonpopping common bean accessions were randomly sampled from the CIAT Andean germplasm core collection. The 200 accessions were characterized for 140 mapped RAPD markers. The objectives of our research were to 1) understand the genetic structure of nuña bean accessions relative to other Andean common beans, and 2) to measure the genetic distance and genetic diversity between nuña and other Andean bean populations.

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Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/9/2012-cjgpb ◽

2013 ◽

Vol 49 (No. 1) ◽

pp. 36-47 ◽

Cited By ~ 4

Author(s):

M. Studnicki ◽

W. Mądry ◽

J. Schmidt

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Dactylis Glomerata ◽

Sampling Strategy ◽

Sampling Strategies ◽

Core Collections ◽

The Core ◽

Entire Collection ◽

The Mean ◽

Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

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Genetic variation among cultivars of red clover (Trifolium pratense L.) detected by RAPD markers amplified from bulk genomic DNA

Euphytica ◽

10.1007/bf00022293 ◽

1996 ◽

Vol 89 (3) ◽

pp. 355-361 ◽

Cited By ~ 2

Author(s):

Prasert Kongkiatngam ◽

Marcia J. Waterway ◽

Bruce E. Coulman ◽

Marc G. Fortin

Keyword(s):

Genetic Variation ◽

Genomic Dna ◽

Rapd Markers ◽

Trifolium Pratense ◽

Red Clover ◽

Trifolium Pratense L

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Genetic diversity in red clover (Trifolium pratense L.) revealed by morphological and microsatellite (SSR) markers

Euphytica ◽

10.1007/s10681-007-9534-z ◽

2007 ◽

Vol 160 (2) ◽

pp. 189-205 ◽

Cited By ~ 40

Author(s):

Paula Menna Barreto Dias ◽

Bernadette Julier ◽

Jean-Paul Sampoux ◽

Philippe Barre ◽

Miguel Dall’Agnol

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Trifolium Pratense ◽

Red Clover ◽

Trifolium Pratense L

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The Formation of Test Arrays and a Core Collection in Cucumber Using Phenotypic and Molecular Marker Data

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.127.4.558 ◽

2002 ◽

Vol 127 (4) ◽

pp. 558-567 ◽

Cited By ~ 14

Author(s):

Jack E. Staub ◽

Fenny Dane ◽

Kathleen Reitsma ◽

Gennaro Fazio ◽

Anabel López-Sesé

Keyword(s):

Genetic Diversity ◽

Heat Stress ◽

Disease Resistance ◽

Downy Mildew ◽

Core Collection ◽

Genetic Relationships ◽

Population Variation ◽

Fruit Rot ◽

Plant Introductions ◽

The Core

Genetic relationships among 970 cucumber (Cucumis sativus L.) plant introductions (PIs) in the U.S. National Plant Germplasm System (NPGS) were assessed by observing variation at 15 isozyme loci. Allozyme frequency data for these PIs were compared to allozyme variation in heirloom and modern (H&M) cultivars released from 1846-1985 (H&M cultivars; 178 accessions), and experimental commercial (EC) germplasm (EC germplasm; 82 accessions) in use after 1985. Multivariate analysis defined four distinct groups of accessions (Groups A-D), where Group A consisted of PIs received by the NPGS before 1992, Group B contained PIs from India and China obtained by NPGS after 1992, Group C consisted of EC germplasm, and Group D contained H&M cultivars. Morphological, abiotic stress (water and heat stress tolerance) and disease resistance evaluation data from the Germplasm Resources Information Network (GRIN) for the PIs examined were used in conjunction with estimates of population variation and genetic distance estimates to construct test arrays and a core collection for cucumber. Disease resistance data included the evaluation of angular leafspot [Pseudomonas lachrymans (E.F. Smith) Holland], anthracnose [Colletotrichum lagenarium (Ross.) Ellis & Halst], downy mildew [Pseudoperonospora cubensis (Berk. & Curt) Rostow], rhizoctonia fruit rot (Rhizoctonia solani Kuhn), and target leafspot [Corynespora cassiicola (Berk. & Curt) Wei] pathogenicity. The test arrays for resistance-tolerance to angular leafspot, anthracnose, downy mildew, rhizoctonia fruit rot, target leafspot, and water and heat stress consisted of 17, 16, 17, 16, 17, 16, and 16 accessions, respectively. The core collection consisted of accessions in these test arrays (115) and additional 32 accessions that helped circumscribe the genetic diversity of the NPGS collection. The core collection of 147 accessions (115 + 32) represents ≈11% of the total collection's size (1352). Given estimates of genetic diversity and theoretical retention of diversity after sampling, this core collection could increase curatorial effectiveness and the efficiency of end-users as they attempt to identify potentially useful germplasm.

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Genetic diversity characterization of cassava cultivars (Manihot esculenta Crantz).: I) RAPD markers

Genetics and Molecular Biology ◽

10.1590/s1415-47571998000100018 ◽

1998 ◽

Vol 21 (1) ◽

pp. 105-113 ◽

Cited By ~ 31

Author(s):

Carlos Colombo ◽

Gérard Second ◽

Tereza Losada Valle ◽

André Charrier

Keyword(s):

Genetic Diversity ◽

Multivariate Analysis ◽

Genetic Variability ◽

Manihot Esculenta ◽

Core Collection ◽

Rapd Markers ◽

Manihot Esculenta Crantz ◽

Important Resource ◽

Flour Production

RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil’s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.

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Analysis of genetic diversity and structure in a genebank collection of red clover (Trifolium pratense L.) using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262116000034 ◽

2016 ◽

Vol 15 (4) ◽

pp. 376-379 ◽

Cited By ~ 3

Author(s):

Mamta Gupta ◽

Vikas Sharma ◽

Sunil K. Singh ◽

Rakesh K. Chahota ◽

Tilak R. Sharma

Keyword(s):

Genetic Diversity ◽

Trifolium Pratense ◽

Fragment Size ◽

Red Clover ◽

Principal Component ◽

Model Based Clustering ◽

Average Value ◽

Genetic Diversity And Structure ◽

Trifolium Pratense L ◽

High Level

AbstractGenetic diversity of a red clover global collection was assessed using 36 simple sequence repeat (SSR) primers representing all seven linkage groups (LGs). The number of fragments amplified ranged from 1 to 6 for all the primers. Primer RCS0060 detected highest number of fragments, whereas four SSRs viz., RCS0899, RCS1594, TPSSR40 and RCS6927 amplified single fragment. Size range of amplicons generated by all the primers varied from 100 to 400 bp. Polymorphism information content values ranged from 0.301 to 0.719 with an average value of 0.605. LG wise diversity analysis showed that LG 3 was most diverse (I = 0.65, Ht = 0.44), whereas LG-1 showed minimum diversity (I = 0.48, Ht = 0.26) for the microsatellites used. Bayesian model-based clustering inferred three genetically distinct populations in the red clover germplasm holding and showed considerable admixture in individuals within clusters. Neighbour-joining analysis showed intermixing of accessions within groups. Principal component analysis plot complemented the clustering shown by Structure and distinguished three populations to greater extent. Analysis of molecular variance showed that 91% of the genetic variation was residing within populations, while 9% variation was among populations. Overall, the results showed that a high level of genetic diversity is prevailing in this worldwide collection of red clover, which can be exploited for its genetic improvement through breeding approaches.

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Development of the Northern European Ribes core collection based on a microsatellite (SSR) marker diversity analysis

Plant Genetic Resources ◽

10.1017/s1479262111000980 ◽

2012 ◽

Vol 10 (1) ◽

pp. 70-73 ◽

Cited By ~ 5

Author(s):

Kristiina Antonius ◽

S. Karhu ◽

H. Kaldmäe ◽

G. Lacis ◽

R. Rugenius ◽

...

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Ssr Marker ◽

Selection Process ◽

Northern Europe ◽

Diversity Analysis ◽

Molecular Analyses ◽

The Core ◽

Northern European

The purpose of the study was to support the selection process of the most valuable currant and gooseberry accessions cultivated in Northern Europe, in order to establish a decentralized core collection and, following the selection, to ensure sufficient genetic diversity in the selected collection. Molecular analyses of the material from nine project partners were run at seven different laboratories. The results were first analysed for each partner separately, and then combined to ensure sufficient genetic diversity in the core collection.

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Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

Plant Genetic Resources ◽

10.1017/s1479262113000373 ◽

2013 ◽

Vol 12 (1) ◽

pp. 112-119 ◽

Cited By ~ 6

Author(s):

Jong-Hyun Park ◽

Sundan Suresh ◽

Gyu-Taek Cho ◽

Nag-Gor Choi ◽

Hyung-Jin Baek ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Simple Sequence Repeat ◽

Core Collection ◽

Sesamum Indicum ◽

Group Method ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

The Core ◽

Simple Sequence

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

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Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.726152 ◽

2021 ◽

Vol 12 ◽

Author(s):

Debjani Roy Choudhury ◽

Ramesh Kumar ◽

Vimala Devi S ◽

Kuldeep Singh ◽

N. K. Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Tamil Nadu ◽

East Coast ◽

Snp Markers ◽

The Core ◽

Core Set ◽

Population Structure Analysis ◽

The Mean

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.

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