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

HortScience ◽  
2006 ◽  
Vol 41 (3) ◽  
pp. 717-720 ◽  
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.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Genetic diversity of table grape based on morphoagronomic traits

2011 ◽  
Vol 68 (1) ◽  
pp. 42-49 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Cosme Damião Cruz ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Clustering Analysis ◽  
Germplasm Collection ◽  
Table Grape ◽  
Cluster Method ◽  
Breeding Programs ◽  
Method Analysis ◽  
Vitis Spp ◽  
Grape Cultivars

The conservation and characterization of grape (Vitis spp) genetic resources in germplasm banks have been the basis of its use in breeding programs that result in development of new cultivars. There are at least 10,000 grape cultivars kept in germplasm collection. The genetic diversity in 136 table grape accessions from the state of Bahia, Brazil, was evaluated. Continuous and discrete morphoagronomic traits were assessed. The clustering analysis by the Tocher otimization method resulted in 30 clusters (considering continuous morphoagronomic traits), and 9 clusters (taking into consideration multicategorical traits). There was no agreement between clusters obtained by both, continuous or discrete phenotypic descriptors, independent of the cluster method analysis used. A satisfactory genetic variability among the table grape accessions was observed.

scholarly journals Genotypic Characterization of the U.S. Peanut Core Collection

2020 ◽  
Vol 10 (11) ◽  
pp. 4013-4026
Author(s):  
Paul I. Otyama ◽  
Roshan Kulkarni ◽  
Kelly Chamberlin ◽  
Peggy Ozias-Akins ◽  
Ye Chu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Regional Distribution ◽  
Country Of Origin ◽  
Snp Array ◽  
Germplasm Collection ◽  
Genotypic Diversity ◽  
Cultivated Peanut ◽  
Food And Feed ◽  
Genetic Clustering

Cultivated peanut (Arachis hypogaea) is an important oil, food, and feed crop worldwide. The USDA peanut germplasm collection currently contains 8,982 accessions. In the 1990s, 812 accessions were selected as a core collection on the basis of phenotype and country of origin. The present study reports genotyping results for the entire available core collection. Each accession was genotyped with the Arachis_Axiom2 SNP array, yielding 14,430 high-quality, informative SNPs across the collection. Additionally, a subset of 253 accessions was replicated, using between two and five seeds per accession, to assess heterogeneity within these accessions. The genotypic diversity of the core is mostly captured in five genotypic clusters, which have some correspondence with botanical variety and market type. There is little genetic clustering by country of origin, reflecting peanut’s rapid global dispersion in the 18th and 19th centuries. A genetic cluster associated with the hypogaea/aequatoriana/peruviana varieties, with accessions coming primarily from Bolivia, Peru, and Ecuador, is consistent with these having been the earliest landraces. The genetics, phenotypic characteristics, and biogeography are all consistent with previous reports of tetraploid peanut originating in Southeast Bolivia. Analysis of the genotype data indicates an early genetic radiation, followed by regional distribution of major genetic classes through South America, and then a global dissemination that retains much of the early genetic diversity in peanut. Comparison of the genotypic data relative to alleles from the diploid progenitors also indicates that subgenome exchanges, both large and small, have been major contributors to the genetic diversity in peanut.

scholarly journals A Modified Roger’s Distance Algorithm for Mixed Quantitative–Qualitative Phenotypes to Establish a Core Collection for Taiwanese Vegetable Soybeans

2021 ◽  
Vol 11 ◽  
Author(s):  
Chung-Feng Kao ◽  
Shan-Syue He ◽  
Chang-Sheng Wang ◽  
Zheng-Yuan Lai ◽  
Da-Gin Lin ◽  
...  
Keyword(s):  
Core Collection ◽  
Dietary Habits ◽  
Phenotypic Traits ◽  
Variable Rate ◽  
Vegetable Soybean ◽  
Breeding Programs ◽  
The Core ◽  
Entire Collection ◽  
Redundant Accessions ◽  
High Diversity

Vegetable soybeans [Glycine max (L.) Merr.] have characteristics of larger seeds, less beany flavor, tender texture, and green-colored pods and seeds. Rich in nutrients, vegetable soybeans are conducive to preventing neurological disease. Due to the change of dietary habits and increasing health awareness, the demand for vegetable soybeans has increased. To conserve vegetable soybean germplasms in Taiwan, we built a core collection of vegetable soybeans, with minimum accessions, minimum redundancy, and maximum representation. Initially, a total of 213 vegetable soybean germplasms and 29 morphological traits were used to construct the core collection. After redundant accessions were removed, 200 accessions were retained as the entire collection, which was grouped into nine clusters. Here, we developed a modified Roger’s distance for mixed quantitative–qualitative phenotypes to select 30 accessions (denoted as the core collection) that had a maximum pairwise genetic distance. No significant differences were observed in all phenotypic traits (p-values > 0.05) between the entire and the core collections, except plant height. Compared to the entire collection, we found that most traits retained diversities, but seven traits were slightly lost (ranged from 2 to 9%) in the core collection. The core collection demonstrated a small percentage of significant mean difference (3.45%) and a large coincidence rate (97.70%), indicating representativeness of the entire collection. Furthermore, large values in variable rate (149.80%) and coverage (92.5%) were in line with high diversity retained in the core collection. The results suggested that phenotype-based core collection can retain diversity and genetic variability of vegetable soybeans, providing a basis for further research and breeding programs.

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

2013 ◽  
Vol 49 (No. 1) ◽  
pp. 36-47 ◽  
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.

scholarly journals Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers

2012 ◽  
Vol 30 (1) ◽  
pp. 112-118 ◽  
Author(s):  
Maria do Desterro M dos Santos ◽  
Carlos Francisco Ragassi ◽  
Maria Esther de N Fonseca ◽  
Anne Gizelle R Buzar ◽  
Valter R Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Germplasm Collection ◽  
Rio Grande ◽  
Breeding Programs ◽  
Tropical Regions ◽  
Low Genetic Diversity ◽  
Tropical Conditions ◽  
Average Similarity ◽  
Onion Germplasm

Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7%) were monomorphic and 102 (16.3%) were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical'), for which the genetic origin (with few exceptions) can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in relation to main 'Baia Periforme' group. This germplasm displayed a relatively low genetic diversity, with the predominance of materials originated from the base population 'Baia Periforme'. There are, however, some accessions, which can add genetic diversity to this germplasm and they can be exploited by onion breeding programs aiming to develop cultivars for tropical regions of the world.

A PEACH GERMPLASM COLLECTION FOR INCREASING THE GENETIC DIVERSITY IN EUROPEAN BREEDING PROGRAMS

2015 ◽  
pp. 125-129 ◽  
Author(s):  
M.L. Badenes ◽  
M. Cambra ◽  
M.M. López ◽  
I. Batlle ◽  
I. Iglesias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Germplasm Collection ◽  
Breeding Programs

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

2008 ◽  
Vol 8 (3) ◽  
pp. 202-211 ◽  
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

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

2002 ◽  
Vol 127 (4) ◽  
pp. 558-567 ◽  
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.

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

2012 ◽  
Vol 10 (1) ◽  
pp. 70-73 ◽  
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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