Characterisation of Genetic Diversity in ICARDA Core Collection of Cultivated Barley (Hordeum vulgare L.)

Out of the total accessions of cultivated barley, held at ICARDA, a subset core collection consisting of 153 accessions originating from different countries was established. Genetic diversity of the core collection was studied using AFLP markers. The accessions were grouped into different geographic sub-regions and the total genetic variation was estimated using Popgene software. Genetic distance matrix was computed and hierarchical unrooted tree was performed using Phylip software package. Our results demonstrate that the AFLP markers were highly informative and were useful in generating a meaningful classification of the cultivated barley that we determined as a subset of core collection.    

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Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity.

Genetics ◽

10.1093/genetics/119.4.981 ◽

1988 ◽

Vol 119 (4) ◽

pp. 981-990

Author(s):

S Jana ◽

L N Pietrzak

Keyword(s):

Genetic Diversity ◽

Eastern Mediterranean ◽

Hordeum Spontaneum ◽

Hordeum Vulgare L ◽

Closely Related Species ◽

Mediterranean Countries ◽

Isozyme Loci ◽

Cultivated Barley ◽

Multilocus Associations ◽

High Degree

Abstract Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species.

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

Cropp Breeding and Applied Biotechnology ◽

10.12702/1984-7033.v08n03a04 ◽

2008 ◽

Vol 8 (3) ◽

pp. 202-211 ◽

Cited By ~ 4

Author(s):

P.M.B. Dias ◽

V.F. Pretz ◽

M. Dall’Agnol ◽

M.T. Schifino-Wittmann ◽

J.A. Zuanazzi

Keyword(s):

Genetic Diversity ◽

Core Collection ◽

Rapd Markers ◽

Trifolium Pratense ◽

Red Clover ◽

The Core

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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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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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Genetic Diversity and Structure of Core Collection of Huangqi (Astragalus) Developed by Genomic Simple Sequence Repeat Markers

10.21203/rs.3.rs-1218329/v1 ◽

2022 ◽

Author(s):

Fanshu Gong ◽

Yaping Geng ◽

Pengfei Zhang ◽

Feng Zhang ◽

Xinfeng Fan ◽

...

Keyword(s):

Genetic Diversity ◽

Simulated Annealing ◽

Core Collection ◽

Phylogenetic Trees ◽

Simulated Annealing Algorithm ◽

Therapeutic Effects ◽

Core Collections ◽

The Core ◽

Genetic Diversity And Structure ◽

Annealing Algorithm

Abstract Huangqi (Astragalus) is a versatile herb that possesses several therapeutic effects against a variety of diseases, especially lung diseases. The aim of this study was to establish a core collection of Astragalus germplasm resources based on molecular 10 SSR markers. Based on 380 samples of Astragalus collected from different areas, five different methods were utilized to construct the core collection of Astragalus, including PowerCore-based M strategy, CoreFinder-based M strategy, Core Hunter-based stepwise sampling, PowerMarker-based simulated annealing algorithm based on allele maximization, and PowerMarker-based simulated annealing algorithm based on maximizing genetic diversity. Of the constructed Astragalus core collections, the CoreFinder-based M strategy was found to be the most suitable approach as it reserved all the alleles and most of the genetic diversity parameters were higher than those of the initial collection. Additional analyses demonstrated that the genetic diversity of the core collection matched the properties of the initial collection. Further, the phylogenetic trees indicated that the population structure of the core collection was similar to that of the initial collection. In addition, our results showed that the optimal grouping value of K was 2. The construction of a core collection is beneficial for the understanding, management, and utilization of Astragalus. Moreover, this study will act as a valuable reference for constructing core collections for other plants or fungi.

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Evaluation of the USDA National Clonal Pyrus Germplasm Collection for Resistance to Podosphaera leucotricha

HortScience ◽

10.21273/hortsci.41.3.717 ◽

2006 ◽

Vol 41 (3) ◽

pp. 717-720 ◽

Cited By ~ 1

Author(s):

Maryna Serdani ◽

Robert A. Spotts ◽

Jill M. Calabro ◽

Joseph D. Postman ◽

Annie P. Qu

Keyword(s):

Genetic Diversity ◽

Powdery Mildew ◽

Core Collection ◽

Germplasm Collection ◽

Economic Losses ◽

Podosphaera Leucotricha ◽

Breeding Programs ◽

Natural Field ◽

Resistant Cultivars ◽

The Core

Powdery mildew (PM) occurs worldwide and is prevalent on susceptible cultivars wherever pears are grown, causing economic losses due to russeted fruit and an increased need for fungicides. A core subset of the Pyrus germplasm collection at the USDA National Clonal Germplasm Repository in Corvallis, Ore., was evaluated for resistance to Podosphaera leucotricha, the causal agent of PM, using greenhouse and field inoculations of potted trees. The core collection consists of about 200 cultivars and species selections, representing most of the genetic diversity of pears and includes 31 Asian cultivars (ASN), 122 European cultivars (EUR), 9 EUR × ASN hybrids and 46 pear species selections. Three trees of each core accession were grafted on seedling rootstocks. In 2001–02, trees were artificially inoculated in a greenhouse, grown under conditions conducive for PM, and evaluated for symptoms. The same trees were subsequently evaluated for PM symptoms from natural field infections during 2003 and 2004. In the greenhouse, 95% of EUR and 38% of ASN were infected with PM. Average PM incidence (percent of leaves infected) in the greenhouse (8% for ASN and 30% for EUR) was much higher than incidence in the field (2% for ASN and 5% for EUR) during 2003. Symptoms were also more severe in the greenhouse, with 46% of ASN and 83% of EUR with PM symptoms having a mean PM incidence of >10%. In the field, 42% and 22% of EUR and 23% and 13% of ASN were infected with P. leucotricha in 2003 and 2004, respectively. Field infection was very low during both years, with percentage leaves infected in ASN and species selections significantly different from EUR. In the field, 6% of ASN with PM symptoms had a mean PM incidence >10% during both years, while 15% and 2% of EUR accessions with PM symptoms had a mean PM incidence >10% in 2003 and 2004 respectively. These results should be very useful to pear breeding programs to develop improved PM resistant cultivars in the future, by using accessions with consistent low PM ratings.

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Geographic differentiation in isozyme genotypes of Himalayan barley (Hordeum vulgare)

Genome ◽

10.1139/g91-108 ◽

1991 ◽

Vol 34 (5) ◽

pp. 704-709 ◽

Cited By ~ 8

Author(s):

T. Konishi ◽

S. Matsuura

Keyword(s):

Genetic Diversity ◽

Hordeum Vulgare ◽

Isozyme Variation ◽

Geographic Differentiation ◽

Hordeum Vulgare L ◽

Phosphogluconate Dehydrogenase ◽

Allelic Distribution ◽

Northern Regions ◽

History Of ◽

Cultivated Barley

Isozyme variation among Himalayan barley (Hordeum vulgare L.) landraces was surveyed at seven loci, using 650 accessions collected from different regions. Large genetic diversities were detected at the Est1, Est2, and Est4 loci for esterase and at the Aat3 locus for aspartate aminotransferase. However, only a few variations were observed at the Pgd1 and Pgd2 loci for phosphogluconate dehydrogenase, and no variation was found at the Aat2 locus. The allelic combinations observed were not randomly distributed in the Himalayas: a geographic trend was closely related to covered and naked types of barley. The covered barleys were frequently distributed in southern regions of the Himalayas and were characterized principally by the Al-Fr-At genotype at the Est1-Est2-Est4 multilocus, combined with the Mo allele at the Aat3 locus. The naked barleys were found mainly in northern regions, and most of them possessed the genotypes Ca-Un-Nz or Pr-Fr-At, together with the Eg allele. Such a nonrandom allelic distribution provides useful information for further analysis aimed at considering the history of cultivated barley in the Himalayas.Key words: Himalayan barley, genetic diversity, isozymes, geographic distribution.

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