Development of the core collection through advanced maximization strategy with heuristic approach in cashew (Anacardium occidentale L.)

2018 ◽  
Vol 16 (4) ◽  
pp. 367-377 ◽  
Author(s):  
G. S. Mohana ◽  
M. G. Nayak
Keyword(s):  
Core Collection ◽  
Heuristic Approach ◽  
Gene Bank ◽  
Morphometric Characters ◽  
The Core ◽  
Efficient Management ◽  
Entire Collection ◽  
Validation Parameters ◽  
Separate Block ◽  
Clustering Approach

AbstractICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

scholarly journals Genotype Heterogeneity in Accessions of a Winter Barley Core Collection Assessed on Postulated Specific Powdery Mildew Resistance Genes

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 513
Author(s):  
Antonín Dreiseitl
Keyword(s):  
Resistance Genes ◽  
Core Collection ◽  
Powdery Mildew Resistance ◽  
Gene Bank ◽  
Winter Barley ◽  
The Core ◽  
Genotype Identification ◽  
Environmentally Safe ◽  
Mla Locus ◽  
Resistance Tests

Gene bank accessions are necessary for implementing many research and breeding projects. However, a great number of accessions are contaminated or confused. If such accessions are used, the results obtained from these projects are inaccurate and non-reproducible. There are methods that allow almost perfect genotype identification; nevertheless, they are relatively recent and results cannot be compared with the characteristics of the original accessions. Growing resistant cultivars is an environmentally safe and cheap way of disease management and knowledge of diverse resistance genes and their combinations can be used to identify varieties and verify their authenticity and homogeneity. For this purpose, all 172 accessions of the core collection (CC) of the Czech winter barley (Hordeum vulgare) gene bank, originating from 35 countries, were studied. For resistance tests, 51 reference isolates of Blumeria graminis f. sp. Hordei, collected in all nonpolar continents over a period of 63 years and representing the global virulence/avirulence diversity of the pathogen, were used. Only 25 barley accessions were homogeneous (genetically uniform), whereas 147 accessions were heterogeneous due to presence of different genotypes. In total, 17 resistance genes were found singly or in combinations; 76.3% of accessions with identified resistance genes carried alleles at the Mla locus. To purify the CC, progenies of individual plants must be multiplied and authenticity and homogeneity of the seed should be confirmed with resistance tests, and subsequently can be studied with more advanced methods.

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.

Establishment of a cassava (Manihot esculenta Crantz) core collection based on agro-morphological descriptors

2012 ◽  
Vol 10 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Ranjana Bhattacharjee ◽  
Dominique Dumet ◽  
Paul Ilona ◽  
Soyode Folarin ◽  
Jorge Franco
Keyword(s):  
Manihot Esculenta ◽  
Core Collection ◽  
Phenotypic Diversity ◽  
Crop Improvement ◽  
International Institute ◽  
Environment Interaction ◽  
Manihot Esculenta Crantz ◽  
Linear Discriminant ◽  
The Core ◽  
Entire Collection

International Institute of Tropical Agriculture maintains 2544 cassava accessions (Manihot esculenta Crantz) from 28 countries in its field bank. Being vegetatively propagated, this poses challenges in maintenance in terms of cost as well as in labour requirements. A core collection representing the range of phenotypic diversity present in the entire collection would enhance the conservation aspects and increase the potential for its exploitation in crop improvement programmes. The present study aimed to establish a core collection using 40 agro-morphological traits evaluated at two locations using a different number of accessions in each location. To meet the challenges generated by the types of variables and include maximum diversity in the core collection, a sequential strategy based on five major concepts was used: hierarchical multiple factor analysis allowing the mixture of variables of different kinds; three-way analysis that included the effect of genotype × environment interaction in the clustering process; linear discriminant function to assign all those individuals who were included in one location but not in the other to the groups that were generated from the common number of accessions evaluated in both locations; and D-allocation method to select samples from each cluster. The representativeness of the core subset to the entire collection was further estimated by comparing means and variances, range, and distances between accessions. The established cassava core collection consisted of 428 accessions that conserved 15% higher phenotypic diversity with no redundancies. The phenotypic diversity represented in this core collection will be a guide to users of cassava germplasm in their crop improvement programmes.

Cowpea [Vigna unguiculata (L.) Walp.] core collection defined by geographical, agronomical and botanical descriptors

2007 ◽  
Vol 5 (03) ◽  
pp. 113-119 ◽  
Author(s):  
V. Mahalakshmi ◽  
Q. Ng ◽  
M. Lawson ◽  
R. Ortiz
Keyword(s):  
Core Collection ◽  
International Institute ◽  
Pests And Diseases ◽  
The Core ◽  
Land Race ◽  
Drought Tolerant ◽  
Selection Processes ◽  
World Collection ◽  
Entire Collection ◽  
The Tropics

Cowpea is a drought-tolerant food legume grown in the savannah regions of the tropics and subtropics. The International Institute for Tropical Agriculture (IITA) holds the world collection of 15,003 cultivated cowpea from 89 countries in its genebank. In excess of 12,000 accessions were characterized for 28 agrobotanical descriptors. The entire collection was first stratified by country of origin and biological status. Land race accessions (10,227) with information on origin and characterization data were grouped using clustering procedures. The clustering analysis was based on Euclidean distances between and among accessions. Accessions within each country were then grouped hierarchically, according to their similarity. The number of clusters selected for countries varied from 2 to 20, depending on the size of collection for that country. A percentage number of accessions (5–25%) was chosen from each country, based on the size of the collection and its proximity to the centre of diversity. The number of accessions from each cluster in a country was then chosen randomly, based on the predetermined percentage. In countries where the numbers of accessions were few ( < 10), the percentage chosen from those countries would be higher and may go up to 100% to ensure that at least one accession was chosen from every country. Accessions with no characterization information were treated as a group, and accessions were chosen randomly, based on their geographical distribution. In the process of selection, 200 accessions that are known to be resistant to pests and diseases and not originally chosen through the selection processes were, nevertheless, kept as part of the core collection. Following these procedures, a total of 1701 accessions of landraces were chosen from the entire collection. Using the same procedures, a subset of 225 accessions was chosen from 1422 advanced cultivars and breeding or research lines. A third subset of 130 accessions was chosen from 838 accessions that either lack information on origin or biological status, and six accessions of wild and weedy forms from the available 64 wild and weed accessions were added. Thus a core collection of 2062 accessions of cowpea was constituted. The diversity in the core collection was similar to that of the entire collection and correlated traits that may be linked were also preserved in the core collection. This core collection of cowpea provides an opportunity for further exploitation of the cowpea germplasm for improvement of this crop.

scholarly journals Establishing a core collection of foxtail millet to enhance the utilization of germplasm of an underutilized crop

2008 ◽  
Vol 7 (02) ◽  
pp. 177-184 ◽  
Author(s):  
Hari D. Upadhyaya ◽  
R. P. S. Pundir ◽  
C. L. L. Gowda ◽  
V. Gopal Reddy ◽  
S. Singh
Keyword(s):  
Core Collection ◽  
Diversity Index ◽  
Foxtail Millet ◽  
Qualitative Traits ◽  
The Core ◽  
Underutilized Crop ◽  
Entire Collection ◽  
Breeding Programmes ◽  
Precise Assessment ◽  
Germplasm Accessions

Foxtail millet (Setaria italica(L.) Beauv.) is one of the ten small millets and is cultivated in 23 countries. The foxtail millet is valued as a crop of short duration, which is good as food, feed and fodder. In general, grain yield levels of foxtail millet are low in comparison with other staple cereals. The greater use of diverse germplasm in breeding is suggested as a means to improve the productivity of this crop. The International Crops Research Institute for the Semi-Arid Tropics genebank is presently holding 1474 cultivated germplasm accessions from 23 countries. To utilize this diversity in research, a core collection (10% of the entire collection) was established using the taxonomic and qualitative traits data. The germplasm accessions were stratified into three taxonomic races (Indica, Maxima and Moharia). Principal coordinate analysis was performed on 12 qualitative traits for each of the biological races, separately that resulted in the formation of 29 clusters. From each cluster, 10% of the accessions were selected to constitute a core collection of 155 accessions. The composition and diversity of the core collection was validated by the χ2-tests of the frequencies of origin, races, subraces and data on qualitative traits. The analysis of the quantitative traits for mean, range, variance, Shannon–Weaver diversity index and phenotypic associations indicated that the diversity from the entire collection was optimally represented in the core collection. The core subset will be evaluated in replicated trials to make a more precise assessment of diversity and further efforts to identify the sources of agronomic and grain nutritional traits for utilization in breeding programmes.

scholarly journals Developing proso millet (Panicum miliaceum L.) core collection using geographic and morpho-agronomic data

2011 ◽  
Vol 62 (5) ◽  
pp. 383 ◽  
Author(s):  
H. D. Upadhyaya ◽  
Shivali Sharma ◽  
C. L. L. Gowda ◽  
V. Gopal Reddy ◽  
Sube Singh
Keyword(s):  
Core Collection ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Germplasm Collection ◽  
Diversity Indices ◽  
Panicum Miliaceum ◽  
Biotic Stresses ◽  
Proso Millet ◽  
Efficient Management ◽  
Entire Collection

Proso millet (Panicum miliaceum L.) is a rich source of protein, minerals, and vitamins, and is an important cereal crop of Asia and Africa. Due to its lowest water and nutrient requirement, it has the potential for agriculture diversification. The development of a core collection would assist in efficient management and enhanced utilisation of proso millet genetic resources. The present investigation was conducted to develop a core collection of proso millet based on geographic information and 20 qualitative and quantitative traits recorded on 833 accessions conserved in the International Crops Research Institute for the Semi-Arid Tropics genebank. The entire germplasm collection was stratified into five groups based on races and data on 20 morpho-agronomic traits were used for clustering following Ward’s method. About 10% (or at least one accession) was randomly selected from each of 101 clusters to constitute a core collection of 106 accessions. Comparisons of means, variances, frequency distribution, diversity indices, and correlation studies indicated that the variation in the entire collection has been preserved in the core collection. This core collection provides a gateway to identify diverse trait-specific germplasm accessions for important agronomic traits and for abiotic and biotic stresses for use in crop improvement research and in crop diversification programs.

scholarly journals Peach palm core collection in Brazilian Amazonia

2015 ◽  
Vol 15 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Michelly de Cristo-Araújo ◽  
Doriane Picanço Rodrigues ◽  
Spartaco Astolfi-Filho ◽  
Charles R. Clement
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Wild Populations ◽  
Germplasm Bank ◽  
Molecular Polymorphism ◽  
Molecular Variance ◽  
Peach Palm ◽  
The Core ◽  
Entire Collection

The Peach palm Active Germplasm Bank has abundant genetic diversity in its holdings. Because it is a live collection, maintenance, characterization and evaluation are expensive, restricting its use. One way to promote more efficient use is to create a Core Collection, a set of accessions with at least 70% of the genetic diversity of the full collection with minimal repetition. The available geographic, molecular marker (RAPD) and morphometric information was systematized and the populations were stratified into wild and domesticated. The Core Collection consists of 10% of the entire collection: 31 accessions of landraces, 5 accessions of non-designated populations and 4 accessions of wild populations. The Core has 92% of the molecular polymorphism and 95% of the heterozygosity of the full collection, with minimal divergence between them by molecular variance. The Core is already receiving priority maintenance, which will contribute to long term conservation.

scholarly journals USE AND ABUSE OF THE CORE COLLECTION CONCEPT IN MANAGEMENT OF PLANT GENETIC RESOURCES

HortScience ◽  
1991 ◽  
Vol 26 (6) ◽  
pp. 794E-794
Author(s):  
James McFerson ◽  
Stephen Kresovich
Keyword(s):  
Core Collection ◽  
Plant Genetic Resources ◽  
Practical Implementation ◽  
Genetic Integrity ◽  
Core Concept ◽  
Crop Species ◽  
The Core ◽  
Germplasm Collections ◽  
Entire Collection ◽  
Definition Of

Indiscriminate growth can lead to germplasm collections that are too large to maintain, too large to use, or both. Curators' budgets do not often increase with collection size, so conservation and utilization activities are hindered. Maintenance of genetic integrity in large collections is practically impossible. Evaluation is restricted to easily-observed traits, potentially limiting utilization. One strategy to improve management of large collections is the core collection concept, proposed by O.H. Frankel in 1984 and subsequently expounded by A.H.D. Brown. It establishes one subset of accessions, the core, selected to represent “with a minimum of repetitiveness, the genetic diversity of a crop species and its relatives”. The other subset, the reserve, includes all accessions not in the core. Both subsets are conserved according to the highest standards feasible, but the core receives priority for characterization and evaluation to facilitate use and provide subsequent directed access to the entire collection. Use and abuse of the core concept will be discussed, including: definition of terms, genetic and statistical assumptions, and practical implementation.

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