Genetic diversity and establishment of a core collection of oil palm (Elaeis guineensisJacq.) based on molecular data

Understanding of genetic diversity and its distribution is essential for promoting the use of genetic resources. The development of core collections using molecular tools has been proposed as a strategy for increasing the economical use and conservation of genetic resources. In this study, we investigated the genetic variation among different geographical origins and potential entries that constituted a core collection of oil palm, using 29 microsatellite markers and by evaluating 788 oil palm accessions. Our results revealed important genetic diversity (HT= 0.759) between oil palm accessions from Angola and Cameroon, which exhibited a low coefficient of genetic differentiation between populations (GST= 0.022). However, the inclusion of oil palm accessions from Indonesia in the analysis resulted in a high coefficient of genetic differentiation between populations (GST= 0.251). We found that the combination of stratified sampling based on a sorting method and a heuristic algorithm was the most effective method for the development of an oil palm core collection set. Using this method, two core collections were identified. The first core collection, comprising 289 entries, contained 271 retained alleles in a sample representing 37% of the entire collection. The second one is a mini core collection, comprising 91 entries, that contained 271 retained alleles with a totalHevalue of 0.72 in a sample representing 11% of the entire collection. The information reported in this study will be of great interest to oil palm researchers because new strategies for breeding programmes can be developed based on these advances.

Download Full-text

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.

Download Full-text

Some recent issues on the conservation of crop genetic resources in developing countries

Genome ◽

10.1139/g99-051 ◽

1999 ◽

Vol 42 (4) ◽

pp. 562-569 ◽

Cited By ~ 11

Author(s):

S Jana

Keyword(s):

Genetic Diversity ◽

Developing Countries ◽

Plant Breeding ◽

Genetic Resources ◽

Core Collection ◽

Ex Situ ◽

Crop Genetic Resources ◽

Core Collections ◽

Global Food Security ◽

Crop Genetic Diversity

Crop genetic resources (CGRs) are renewable resources. These resources are enriched rather than depleted by their use in research and plant breeding. Both at the time of Vavilov and, later, in the early 1970s, when concerted international efforts to collect and preserve CGRs started with the initiatives of the International Board for Plant Genetic Resources (IBPGR), CGRs were considered to be the common heritage of humankind. Now, they are widely accepted as "national heritage." Possible impacts of this nationalization on the utilization and enrichment of global crop genetic diversity and, consequently, on global food security are issues of great significance. At present, efficient management and adequate use of CGRs are more important concerns than their further exploration and collection. To increase the use of preserved CGRs in plant breeding, the formation of core collections, by selecting representative subsets from large ex situ collections of CGRs, was recommended in 1984. Since then, the core-collection strategy has been further justified as a practical approach to genetic resources management, as well as to their conservation. As a cost-saving germplasm-management strategy, the core-collection concept has considerable merit. However, the rapidly increasing popularity of core collections may undermine the genetic wealth stored in national gene banks of both developed and developing countries. Distinction is made between subsets of working collections and core collections. When a small number of CGRs is required for specific plant breeding purposes, a properly formed working collection is more useful than a representative collection. Despite the relative abundance of genetic diversity in crop plants in traditional agroecosystems, maintenance of these agroecosystems is not a realistic long-term alternative for preserving crop genetic diversity and ensuring global food security. What is needed in the "gene-rich" developing countries is the adoption of "biodiversity friendly" plant breeding and agricultural practices.Key words: crop genetic resources, core collection, germplasm conservation, in situ conservation, ex situ conservation, modern landraces.

Download Full-text

Molecular characterization of oil palmElaeis guineensisJacq. materials from Cameroon

Plant Genetic Resources ◽

10.1017/s1479262112000482 ◽

2013 ◽

Vol 11 (2) ◽

pp. 140-148 ◽

Cited By ~ 5

Author(s):

Diana Arias ◽

Carmenza Montoya ◽

Hernán Romero

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Molecular Characterization ◽

Oil Palm ◽

Elaeis Guineensis ◽

Low Frequency ◽

Molecular Data ◽

Ex Situ ◽

Geographical Regions

The narrow genetic base of existing commercial oil palm cultivars has prompted oil palm breeders to give increased importance to augmenting these genetic resources because the sustainable development of the crop depends largely on the availability of genetic diversity and its use. Therefore, the purpose of this study was to conduct a molecular characterization of anex situcollection of oil palmElaeis guineensisJacq. populations from the Republic of Cameroon using microsatellite molecular markers. Overall, 31 simple sequence repeats were polymorphic, with a total of 223 alleles, 78.4% of which were found at low frequency. The total genetic diversity was relatively high (HT= 0.673). The genetic differentiation between geographical regions was low (GST= 0.023,P= 0.001), and between families it was high (GST= 0.166,P= 0.001), showing greater variation between families than among geographical regions. The molecular data indicate that genetic diversity among the genotypes evaluated is mainly distributed within regions, suggesting that there is no isolation by geographical distance and that all the sampled individuals form a single diverse population. Therefore, it was concluded that a relatively low number of accessions (120 in the analysed case) that includes at least one representative of each family would allow us to efficiently collect almost the entire genetic diversity of Cameroon within the collection studied. This will allow for the efficient use of genetic resources and a reduction in morpho-agronomic characterization costs.

Download Full-text

Enrichment of chickpea genetic resources collection monitored by microsatellites

Czech Journal of Genetics and Plant Breeding ◽

10.17221/49/2008-cjgpb ◽

2009 ◽

Vol 45 (No. 1) ◽

pp. 11-17 ◽

Cited By ~ 4

Author(s):

K. Jomová ◽

M. Benková ◽

J. Kraic

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Slovak Republic ◽

Diversity Index ◽

Polymorphic Information Content ◽

Microsatellite Analysis ◽

Entire Collection ◽

Single Fragment ◽

New Germplasm ◽

New Alleles

A set of 49 chickpea accessions maintained in the collection of the Genebank of the Slovak Republic was analyzed using microsatellite markers. The level of genetic diversity and the effectivity of new germplasm acquisition for the collection enrichment were evaluated. Five primer pairs used generated 50 different amplified alleles. Four of them, TA2, TA5, TR1, and TR7, containing a long TAA-tandem repeat, were polymorphic with 11–13 alleles per locus. A single fragment was obtained from all the accessions with the primer pair CATPER flanking a small microsatellite repetition in the mRNA sequence of chickpea cationic peroxidase. The genetic diversity was expressed as a diversity index (DI) and polymorphic information content (PIC) with values in the range from 0.885 to 0.904 and from 0.972 to 0.991, respectively. Recently acquired new germplasm contributed 13 new alleles to the entire collection, i.e. almost 70% of microsatellite diversity originated from the recently acquired accessions. Remarkable is also, that one accession carries a unique allel, not present in the remaining collection. Microsatellite analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources.

Download Full-text

Evaluation of linkage disequilibrium, population structure, and genetic diversity in the U.S. peanut mini core collection

BMC Genomics ◽

10.1186/s12864-019-5824-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Paul I. Otyama ◽

Andrew Wilkey ◽

Roshan Kulkarni ◽

Teshale Assefa ◽

Ye Chu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Core Collection ◽

Mini Core Collection ◽

The U.S

Download Full-text

SPAR Markers-Assisted Assessment of Genetic Diversity and Population Structure in Finger Millet (Eleusine Coracana (L.) Gaertn) Mini-Core Collection

Journal of Crop Science and Biotechnology ◽

10.1007/s12892-018-0034-0 ◽

2018 ◽

Vol 21 (5) ◽

pp. 469-481 ◽

Cited By ~ 2

Author(s):

Subramani Pandian ◽

Karuppasamy Marichelvam ◽

Lakkakula Satish ◽

Stanislaus Antony Ceasar ◽

Shunmugiah Karutha Pandian ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Core Collection ◽

Finger Millet ◽

Eleusine Coracana ◽

Mini Core Collection

Download Full-text

Genetic diversity among Brazilian okra landraces detected by morphoagronomic and molecular descriptors

Acta Scientiarum Agronomy ◽

10.4025/actasciagron.v42i1.43426 ◽

2019 ◽

Vol 42 ◽

pp. e43426

Author(s):

Luana Rainieri Massucato ◽

Karina Kazue Nakamura ◽

Paulo Mauricio Ruas ◽

Douglas Mariani Zefa ◽

Derly José Henrique da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Quantitative Traits ◽

Genetic Parameters ◽

Molecular Descriptors ◽

Geographical Origin ◽

Molecular Data ◽

Gene Bank ◽

Aflp Markers ◽

Distance Measures ◽

Breeding Programmes

The conservation of okra landraces [Abelmoschus esculentus (L.) Moench] in gene banks is essential for the success of their use in breeding programmes. This study evaluated the genetic diversity among okra landraces in Brazil based on morphoagronomic descriptors and AFLP markers. We studied 30 accessions of the vegetable gene bank of the Universidade Federal de Viçosa. To this end, 17 morphoagronomic descriptors and five combinations of AFLP primers were used. Genetic parameters were estimated for the quantitative traits and the accessions were grouped by Ward’s method, using the Gower’s and Jaccard’s distance measures, respectively, for the morphoagronomic and molecular data. Polymorphisms were observed for all qualitative traits, while the quantitative traits were significant by deviance analysis. The genetic parameters confirmed the existence of variability among accessions, and high accuracy and heritability indices were found for the traits related to fruit and plant height. Ward’s grouping showed no relationship between the clusters formed with the morphoagronomic and molecular data and the geographical origin of the accessions. No association between morphoagronomic descriptors and AFLP markers was observed. The lack of correlation suggests that both approaches of characterization are important to understand and differentiate the okra accessions.

Download Full-text