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

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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Evaluation of a Diverse, Worldwide Collection of Wild, Cultivated, and Landrace Pepper (Capsicum annuum) for Resistance to Phytophthora Fruit Rot, Genetic Diversity, and Population Structure

Phytopathology ◽

10.1094/phyto-02-14-0031-r ◽

2015 ◽

Vol 105 (1) ◽

pp. 110-118 ◽

Cited By ~ 10

Author(s):

R. P. Naegele ◽

A. J. Tomlinson ◽

M. K. Hausbeck

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phytophthora Capsici ◽

The United States ◽

Fruit Rot ◽

Sources Of Resistance ◽

Plant Introductions ◽

Genetic Clusters ◽

Commercial Breeding ◽

Moderately Resistant

Pepper is the third most important solanaceous crop in the United States and fourth most important worldwide. To identify sources of resistance for commercial breeding, 170 pepper genotypes from five continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats. Partial resistance and isolate-specific interactions were identified in the population at both 3 and 5 days postinoculation (dpi). Plant introductions (PIs) 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when pepper varieties were grouped by predefined categories of disease resistance, continent, and country of origin. Moderately resistant or resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.

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Reactions in the Annual Medicago spp. Core Germ Plasm Collection to Phoma medicaginis

Plant Disease ◽

10.1094/pdis.2003.87.5.557 ◽

2003 ◽

Vol 87 (5) ◽

pp. 557-562 ◽

Cited By ~ 9

Author(s):

Nichole R. O'Neill ◽

Gary R. Bauchan ◽

Deborah A. Samac

Keyword(s):

Disease Resistance ◽

Leaf Spot ◽

Core Collection ◽

Germ Plasm ◽

Severity Scale ◽

Forage Crop ◽

The Core ◽

Phoma Medicaginis ◽

Disease Severity Scale ◽

Annual Medicago

The annual Medicago spp. core collection, consisting of 201 accessions, represents the genetic diversity inherent in 3,159 accessions from 36 annual Medicago spp. This germ plasm was evaluated for resistance to spring black stem and leaf spot caused by Phoma medicaginis. Spring black stem and leaf spot is a major destructive disease in perennial alfalfa (Medicago sativa) grown in North America, Europe, and other temperate regions. Disease control is based principally on the use of cultivars with moderate levels of resistance. Evaluation of the core collection was conducted using standardized environmental conditions in growth chambers, and included the M. sativa standard reference cultivars Ramsey (resistant) and Ranger (susceptible). The degree of resistance found among accessions within species was variable, but most annual species and accessions were susceptible. Most accessions from 10 species exhibited high disease resistance. These included accessions of M. constricta, M. doliata, M. heyniana, M. laciniata, M. lesinsii, M. murex, M. orbicularis, M. praecox, M. soleirolii, and M. tenoreana. Most of the accessions within M. arabica, M. minima, M. lanigera, M. rotata, M. rugosa, M. sauvagei, and M. scutellata were highly susceptible. Disease reactions among some accessions within species were highly variable. On a 0-to-5 disease severity scale, ratings ranged from 0.67 (PI 566873) to 4.29 (PI 566883) within accessions of M. polymorpha. Most of the M. truncatula accessions were susceptible, with a mean of 3.74. Resistant reactions were similar to those found in incompatible interactions with P. medicaginis and alfalfa, which have been associated with specific genes leading to the production of isoflavonoid phytoalexins. The large genetic variability in annual Medicago spp. offers potential for locating and utilizing disease resistance genes through breeding or genetic engineering that will enhance the utilization of Medicago spp. as a forage crop.

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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 diversity and population structure analyses in the Alpine plum (Prunus brigantina Vill.) confirm its affiliation to the Armeniaca section

10.1101/2020.08.12.247718 ◽

2020 ◽

Author(s):

Liu Shuo ◽

Decroocq Stephane ◽

Harte Elodie ◽

Tricon David ◽

Chague Aurelie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Genetic Relationships ◽

Allelic Diversity ◽

Wild Relatives ◽

Ex Situ ◽

Conservation Measures ◽

Geographical Regions

AbstractIn-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.

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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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Development and Utilization of a Core Collection in Theobroma cacao based on RAPD Marker-based Estimates of Genetic Distance

HortScience ◽

10.21273/hortsci.32.3.513c ◽

1997 ◽

Vol 32 (3) ◽

pp. 513C-513

Author(s):

Jane M. Marita ◽

José Luis Pires ◽

W. Martin Aitken ◽

James Nienhuis

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Random Sampling ◽

Theobroma Cacao ◽

Core Collection ◽

Genetic Relationships ◽

Rapd Marker ◽

Sources Of Resistance ◽

Resistant Varieties ◽

Broom Disease

An increased need to understand the genetic relationships among cacao (Theobroma cacao) germplasm exists to identify cultivars that possess resistance to witches' broom disease (caused by Crinipellis perniciosa). Loss of production due to witches' broom disease in important cacao-growing areas, such as Bahia, Brazil, has generated a strong demand for disease-resistant varieties. Varieties based on single sources of resistance have been released; however, other genotypes are needed to enlarge the genetic diversity of cultivars in breeding programs. A core collection has been created to represent the range of genetic diversity available among the more than 600 cacao accessions at Centro de Pesquisa do Cacau (CEPEC). The cacao core facilitates access to the collection and is intended to enhance its use. This core collection was created from RAPD marker-based estimates of genetic distance among a subset of 270 accessions from the entire collection. The subset was sampled based on 1) witches' broom disease resistance data, 2) random sampling of the collection, and 3) random sampling of recently acquired accessions. Differences in RAPD marker frequencies were used to identify accessions in a witches' broom disease breeding program that contribute to the genetic diversity of the collection as a whole. In addition, differences in RAPD marker frequency allowed the comparison between accessions in the original collection and those acquired from new geographic regions that may expand the collection's genetic diversity.

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Genetic diversity of the floury race of maize Avati Morotî from the Guaraní tribe in Paraguay

Spanish Journal of Agricultural Research ◽

10.5424/sjar/2016143-9214 ◽

2016 ◽

Vol 14 (3) ◽

pp. e0707 ◽

Cited By ~ 3

Author(s):

Orlando Noldin ◽

Pedro Revilla ◽

Bernardo Ordás

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variability ◽

Core Collection ◽

Polymorphic Locus ◽

Genetic Relationships ◽

South American ◽

Large Variability ◽

Marginal Areas ◽

Simple Sequence

Avati Morotî is a race of floury maize widely used by the Guarani people in South America, whose variability and potential value for breeding has been neglected so far. The objective of this research was to explore the genetic variability within the main Paraguayan race Avati Morotî. We studied the genetic variability available in the 20 accessions of Paraguayan Avati Morotî included in the South American core collection made by CIMMYT. Thirty individuals per accession were genotyped with 30 SSR (simple sequence repeat); we determined genetic diversity and made a cluster analysis in order to define genetic relationships among accessions. Mean of polymorphic loci (0.96), alleles per locus (3.57), alleles per polymorphic locus (3.65), expected (0.48) and observed (0.43) heterozygosity, and coefficient of consanguinity (0.12) revealed that Avati Morotî contains a genetic diversity comparable to the most variable maize races of maize. The cluster analysis classified the 20 populations in eight groups, five of them with a single accession, and a large group representing a central pool of germplasm. These results indicate that there is a large variability available in this race, and encourage the collection of more samples of Avati Morotî, particularly in marginal areas that were scarcely sampled.

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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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