scholarly journals Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255418
Author(s):  
Siou Ting Gan ◽  
Chin Jit Teo ◽  
Shobana Manirasa ◽  
Wei Chee Wong ◽  
Choo Kien Wong
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oil Palm ◽  
Core Collection ◽  
Elaeis Guineensis ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Fixation Index ◽  
Core Set ◽  
Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

scholarly journals Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 256
Author(s):  
Aida Dervishi ◽  
Jernej Jakše ◽  
Hairi Ismaili ◽  
Branka Javornik ◽  
Nataša Štajner
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Core Collection ◽  
Expressed Sequence Tag ◽  
Fruit Trees ◽  
Ex Situ ◽  
Natural Ecosystems ◽  
Model Based ◽  
Genetic Diversity And Structure

Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.

scholarly journals GENETIC DISTANCE OF 47 ACCESSIONS OF OIL PALM (Elaeis guineensis Jacq.) GERMPLASM FROM CAMEROON BASED ON MORPHOLOGICAL CHARACTER

2019 ◽  
Vol 27 (1) ◽  
pp. 25-40
Author(s):  
Sujadi Sujadi ◽  
Tiara S Wandita ◽  
Nanang Supena ◽  
Yurna Yenni
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Distance ◽  
Palm Oil ◽  
Oil Palm ◽  
Alternative Energy ◽  
Elaeis Guineensis ◽  
Distance Analysis ◽  
Elaeis Guineensis Jacq ◽  
Genetic Distance Analysis

Oil palm (Elaeis guineensis Jacq.) is a plantation commodity that has an important role in various aspects of life in Indonesia, especially the domestic economy. This is supported by the increasing demand for world palm oil for food needs (edible oil), industrial (oleochemical), and alternative energy sources based on biodiesel. The development of the palm oil industry requires several efforts to achieve increased national productivity, one of which is the utilization of quality seeds supported by the availability of genetic resources (germplasm) that have a high level of genetic diversity. Efforts that can be made for the development of oil palm in Indonesia is through the characterization of oil palm intoduction from abroad. Considering this, further research on genetic distance analysis of palm oil accession introduced from Cameroon is based on morphological characters to produce parent elders that can produce heterosis properties. Research conducted at Seed Garden of Adolina PTPN IV and laboratory analysis of plant material of Palm Oil Research Center located on Jl. Brigjen Katamso No. 5, Medan, North Sumatera, which lasted from December 2017 to February 2018. Single observations were made on 47 accession palm oil from Cameroon planted on December 2010 and ten trees from PPKS 540 variety for compare. Data analysis used was a description of the plant to know the character of plant morphology as well as genetic distance analysis. Analysis of genetic distance using PCA analysis and cluster analysis. The results obtained are based on the results of PCA (Principal Component Analysis) reduce the observed character into six major components that have eigen value > 1 and able to explain the material diversity tested for 73.8%. Based on the cluster analysis obtained the genetic distance of 47 accessions of palm oil from Cameroon by 57%. It can be concluded that, when the genetic distance between accessions is further away, the larger the genetic variability between the observed characters. If the genetic diversity is wider the greater the chance for successful selection in increasing the desired gene frequency.

scholarly journals Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
AGUSTIAMAN PURBA ◽  
RAHMAH HAYATI ◽  
LOLLIE A.P. PUTRI ◽  
DIANA CHALIL ◽  
INDRA SYAHPUTRA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Control Strategies ◽  
Cocos Nucifera ◽  
Ganoderma Boninense ◽  
Success Rates ◽  
Genetic Diversity And Structure ◽  
Distinct Individual ◽  
Plantation Crops

Abstract. Purba A, Hayati R, Putri LAP, Chalil D, Afandi D, Syahputra I, Basyuni M. 2020. Genetic diversity and structure of Ganoderma boninense isolates from oil palm and other plantation crops. Biodiversitas 21: 451-456. Oil palm is an economically important plant, which one of the most important sources of vegetable oil in the world. However, oil palm plantation and other crops face the treat basal stem rot (BSR) disease by Ganoderma boninense. A study on genetic diversity and structure of G. boninense is therefore needed in order to formulate improved control strategies for this disease. This work aimed to analyze the genetic diversity and structure of the G. boninense isolates derived from different hosts, 131 oil palm (Elaeis guineensis), six rubber (Hevea brasiliensis), three coconuts (Cocos nucifera), and three lontar palm (Borassus flabellifer). Genetic diversity and population structure of G. boninense isolates were investigated using six SSR markers with GenAlex 6.502 software. Results showed that several microsatellite loci indicated specific primary success rates, such as KT124402, KT124399, and KT124394, depicting high polymorphism content (>75%). This result suggested that these markers were equally effective in determining the polymorphisms of G. boninense isolates. A hierarchical analysis of molecular variance (AMOVA) revealed that genetic diversity mostly found among individuals within a population (88%), then among populations (8%), and within individuals (4%).. Phylogeny analysis showed two clusters of Ganoderma isolates. which was considered variation as dissimilar across with origin. The present study indicated that G. boninense from oil palm was predominantly comprised of a genetically distinct individual.

Molecular characterization of oil palmElaeis guineensisJacq. materials from Cameroon

2013 ◽  
Vol 11 (2) ◽  
pp. 140-148 ◽  
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.

scholarly journals Genetic Diversity and Structure in a Collection of Ancient Spanish Pear Cultivars Assessed by Microsatellite Markers

2010 ◽  
Vol 135 (5) ◽  
pp. 428-437 ◽  
Author(s):  
Carlos Miranda ◽  
Jorge Urrestarazu ◽  
Luis G. Santesteban ◽  
José B. Royo ◽  
Valero Urbina
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Core Collection ◽  
Heterogeneous Material ◽  
Fixation Index ◽  
Factorial Correspondence Analysis ◽  
Model Based Clustering ◽  
Genetic Diversity And Structure ◽  
Ssr Loci ◽  
Different Origins

A collection of 141 old and local Spanish accessions of pear (Pyrus communis) from the Escuela Técnica Superior de Ingeniería Agraria-Universidad de Lleida (ETSIA-UdL) Pear Germplasm Bank in Lleida, Spain, were studied using a set of eight microsatellite markers to estimate the genetic diversity of the collection, to identify the genetic structure and relationships among its accessions, and to establish a representative core collection. An additional set of 13 well-known pear cultivars, currently grown in Spain and which represent a wide genetic diversity, were added as reference. The eight simple sequence repeat (SSR) loci amplified 97 alleles, with nine to 15 alleles per locus, and with the expected heterozygosity ranging from 0.65 to 0.89. All of the accessions except for 16 had at least one of the 48 rare alleles (frequency < 0.05) identified, and seven unique alleles were found in six accessions. Fifteen accessions were identified as synonyms and were excluded from the analysis. Genetic analyses performed by hierarchical clustering, Bayesian model-based clustering, and factorial correspondence analysis supported the existence of three groups among the accessions with moderate [fixation index (FST) = 0.074], but significant, differentiation. As a whole, most of the germplasm (about 75%) curated at the collection showed its genetic distinctness with respect to the main pear cultivars used in European orchards. In fact, most reference cultivars were included in one single cluster that, moreover, had the lowest genetic diversity and allelic richness, in spite of having been chosen as heterogeneous material from different origins. The obtained results were also used to create a core collection with 35 accessions constituting an efficient and accessible entry point in the ETSIA-UdL pear collection for breeding and research communities.

scholarly journals Genetic diversity in oil palm (Elaeis guineensis Jacq) using RAM (Random Amplified Microsatellites)

Bragantia ◽  
2018 ◽  
Vol 77 (4) ◽  
pp. 546-556
Author(s):  
Christian Camilo Castañeda Cardona ◽  
Yacenia Morillo Coronado ◽  
Ana Cruz Morillo Conronado ◽  
Iván Ochoa
Keyword(s):  
Genetic Diversity ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Elaeis Guineensis Jacq

scholarly journals All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 139
Author(s):  
Marlien M. van der Merwe ◽  
Jia-Yee S. Yap ◽  
Peter D. Wilson ◽  
Helen T. Murphy ◽  
Andrew Ford
Keyword(s):  
Genetic Diversity ◽  
Allelic Variation ◽  
Germplasm Conservation ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Ex Situ ◽  
Spatial Distance ◽  
Genetic Connectivity ◽  
Conservation Genomics ◽  
Modelling Framework

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

2015 ◽  
Vol 3 (1) ◽  
pp. 1-11
Author(s):  
Rezq Basheer-Salimia
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Vitis Vinifera L ◽  
Similarity Matrix ◽  
Breeding Programs ◽  
Local Varieties ◽  
Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

scholarly journals Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245965
Author(s):  
Catherine Kiwuka ◽  
Eva Goudsmit ◽  
Rémi Tournebize ◽  
Sinara Oliveira de Aquino ◽  
Jacob C. Douma ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Allelic Variation ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Negative Effects ◽  
Robusta Coffee ◽  
Genetic Diversity And Structure ◽  
Adaptive Diversity ◽  
Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

Sign in / Sign up

Export Citation Format

Share Document