scholarly journals Genetic Relationships between Elite Oil Palms from Nigeria and Selected Breeding and Germplasm Materials from Malaysia via Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (2) ◽  
pp. 159 ◽  
Author(s):  
M. N. Okoye ◽  
C. Bakoumé ◽  
M. I. Uguru ◽  
R. Singh ◽  
C. O. Okwuagwu
Keyword(s):  
Ssr Markers ◽  
Oil Palm ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Coefficient Matrix ◽  
High Genetic Diversity ◽  
Breeding Lines ◽  
Natural Oil ◽  
Materials Used

<p>Nine SSR markers were used to study the genetic relationships among 26 elite oil palm materials from Nigeria and Malaysia. The Nigerian elite materials comprised 15 Nigerian Institute for Oil Palm Research (NIFOR) oil palm parental genotypes. The 11 Malaysian genotypes included 2 <em>dura</em> and 2 <em>pisifera</em> advanced breeding lines, 3 palms from natural populations of Nigeria, and 2 from each of the Angola, and Madagascar natural oil palm collections maintained at the Malaysian Palm Oil Board (MPOB). The results revealed a high percentage of polymorphic loci (83.3%) in the entire materials with average polymorphic information content (PIC) of 0.7325. Two SSR markers showed relatively high PIC namely sMg00016 and sMg00179 (0.8018 and 0.8509, respectively). The mean number of alleles varied from 1.333 in Madagascar germplasm material to 4.889 in NIFOR <em>tenera </em>materials (mean = 2.958). The observed heterozygosity varied from 0.167 in Madagascar material to 0.778 in Nigeria germplasm materials (mean = 0.575) and the expected heterozygosity from 0.153 to 0.643. The various oil palm provenances showed significant genetic differentiation (F<sub>ST</sub> = 0.177, P = 0.001) indicating the existence of a genetic structure among the materials used. UPGMA analysis based on Rogers’ dissimilarity coefficient matrix displayed two main clusters, one separating Madagascar accessions from the rest. PCoA showed that the NIFOR breeding parents clustered closely with MPOB’s Nigeria and Angola-derived materials suggesting a common origin of mainland genotypes. The high genetic diversity observed among the MPOB’s germplasm materials highlights the need for proper characterization of entire NIFOR oil palm germplasm with SSR markers to facilitate effective utilization in the breeding programme.</p>

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1365
Author(s):  
Lin Chen ◽  
Tingting Pan ◽  
Huirong Qian ◽  
Min Zhang ◽  
Guodong Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sichuan Basin ◽  
Polymorphic Information Content ◽  
Population Decline ◽  
Natural Populations ◽  
Genetic Population ◽  
Endangered Status ◽  
High Level

Osmanthus serrulatus Rehder (Oleaceae) is an endemic spring-flowering species in China. It is narrowly distributed in the southwestern Sichuan Basin, and is facing the unprecedented threat of extinction due to problems associated with natural regeneration, habitat fragmentation and persistent and serious human interference. Here, the genetic diversity and population structure of 262 individuals from ten natural populations were analyzed using 18 microsatellites (SSR) markers. In total, 465 alleles were detected across 262 individuals, with a high polymorphic information content (PIC = 0.893). A high level of genetic diversity was inferred from the genetic diversity parameters (He = 0.694, I = 1.492 and PPL = 98.33%). AMOVA showed that a 21.55% genetic variation existed among populations and the mean pairwise Fst (0.215) indicated moderate genetic population differentiation. The ten populations were basically divided into three groups, including two obviously independent groups. Our results indicate that multiple factors were responsible for the complicated genetic relationship and endangered status of O. serrulatus. The concentrated distribution seems to be the key factor causing endangerment, and poor regeneration, human-induced habitat loss and fragmentation seem to be the primary factors in the population decline and further genetic diversity loss. These findings will assist in future conservation management and the scientific breeding of O. serrulatus.

Exploring the Genetic Diversity of Some Squash (Cucurbita Maxima L.) Germplasm Using Morphological and Molecular Markers in Erzincan

2021 ◽  
Author(s):  
HALIL IBRAHIM OZTURK ◽  
Veysel Dönderalp ◽  
Hüseyin Bulut ◽  
Recep Korkut ◽  
Arash HOSSEINPOUR ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Ssr Markers ◽  
Molecular Level ◽  
Polymorphic Information Content ◽  
Plant Genetic Resources ◽  
Molecular Characteristics ◽  
Cucurbita Maxima ◽  
High Genetic Diversity ◽  
The Mean

Abstract Background Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. Cucurbita maxima species in the cucurbitaceae family have high genetic diversity, but its genetic diversity at the molecular level is inadequately characterized. Methods and Results To determine the genetic diversity among genotypes of Cucurbita maxima species of squash, which is widely grown in Erzincan, 14 different squash genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple sequence repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. Seven SSR markers yielded a total of 23 polymorphic bands, the number of alleles per marker ranged from 2 to 5, and the mean number of alleles was 3.286. Polymorphic information content (PIC) ranged from 0.00 (GMT-M61) to 0.202 (GMT-P25), and the mean PIC value per marker was 0.130. Cluster analysis using Nei's genetic distance determined that 14 genotypes were divided into 3 major groups. Conclusions The SSR markers used were effective in distinguish among similar winter squash or pumpkin and therefore can be beneficial for consideration of Cucurbita maxima species diversity, screening of genetic resources and their selection.

scholarly journals Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 983-992
Author(s):  
Zelmíra Balázová ◽  
Andrej Trebichalský ◽  
Zdenka Gálová ◽  
Radomíra Hornyák-Gregáňová
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Frequency ◽  
Polymorphic Markers ◽  
Average Value ◽  
Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

scholarly journals Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

scholarly journals Molecular characterization using SSR markers in 50 shrub pea genotypes (Pisum sativum L.) from the GRICAND Collection, Colombia

2019 ◽  
Vol 13 (2) ◽  
pp. 208-218
Author(s):  
Juan Diego Duque-Zapata ◽  
Jaime Eduardo Muñoz ◽  
Oscar Checa-Coral
Keyword(s):  
Pisum Sativum ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Morphological Characteristics ◽  
High Similarity ◽  
Expected Heterozygosity ◽  
Pisum Sativum L ◽  
Simple Sequence

The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.

Molecular Markers (RAPD and SSR) Based Characterisation of Genetic Diversity and Population Structure of Moss Hyophila Involuta

2021 ◽  
Vol 63 (1-2) ◽  
pp. 171-193
Author(s):  
S. Pandey ◽  
A. Alam
Keyword(s):  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Natural Populations ◽  
Reproductive Mode ◽  
Genetic Distances ◽  
Mantel Test ◽  
Resolving Power ◽  
Marker System

Genetic relationships among 24 genotypes of Hyophila involuta collected from five different natural populations of Mount Abu (Rajasthan) is analysed using RAPD and SSR markers. Based on efficiency parameters calculated for each marker system such as polymorphic information content (RAPD = 0.34; SSR = 0.66), marker index (RAPD = 2.78; SSR = 2.62) and resolving power (RAPD = 8.13; SSR = 2.23), the RAPD marker system shows higher values for some indices but microsatellites are more accurately reproducible than RAPD. Moreover, in case of the SSR, the average number of alleles was almost twice compared to RAPD. Mean coefficient of genetic differentiation between populations with RAPD was Gst = 0.269, while with SSR marker was Fst = 0.224. The UPGMA cluster analysis assembled genotypes into two main clusters with diverse levels of sub-clustering within the clusters. Also, the Mantel test showed no significant correlation between geographical and genetic distances. The observed moderately high genetic variability can be explained by efficient spore dispersal. Other factors such as reproductive mode, somatic mutation, continuous propagule recruitment and high degree of intermingling have great impact on the level of genetic variability in moss populations.

scholarly journals Analisis Kekerabatan 50 Aksesi Kelapa Sawit (Elaeis guineensis Jacq.) Asal Kamerun Berdasarkan Marka Mikrosatelit

2016 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
I Made Tasma ◽  
Ahmad Warsun ◽  
Dani Satyawan ◽  
Syafaruddin Syafaruddin ◽  
Budi Martono
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Germ Plasm ◽  
Elaeis Guineensis ◽  
Study Finding ◽  
Multivariate System ◽  
High Genetic Diversity ◽  
Low Genetic Diversity ◽  
Polymorphism Level

<p>Genetic diversity of the<br />Indonesian oil palm collection remains low and collection<br />enrichness through exploration activities from the center of<br />origins is required. In 2009, 103 oil palm accessions from<br />Cameroon were collected at the National Oil Palm Genetic<br />Resources Collection located at the District of Sijunjung,<br />West Sumatera. The objectives of the present study were to<br />analayze the 50 Cameroon-originated oil palm accessions in<br />order to: (1) determine polymorphism levels of the SSR<br />markers used; (2) understand diversity levels of the oil palm<br />accessions tested; and (3) analyze accessions potentially<br />used for germ plasm collection. Fifty oil palm accessions<br />were used in this study. DNA was isolated from leaves of the<br />selected individual plants representing each of the<br />accessions. DNA was analyzed with 12 SSR markers. A<br />dendrogram was constructed using the UPGMA through<br />Numerical Taxonomy and Multivariate System program<br />version 2.1-pc. Results showed that SSR markers used<br />demonstrated the average number of alleles per locus of 3.6<br />(2-6). The polymorphism level was 0.53 (0.21-0.73). The<br />phylogenetic analysis resulted nine clusters with genetic<br />diversity between two accessions ranged from 4-82%. Ten<br />accessions (20%) showed low genetic diversity (&lt;10%) but<br />the accessions demonstrated high diversity in flowering<br />time. Eleven accessions showed medium diversity level (27-<br />42%). Five accessions demonstrated high genetic diversity<br />level (45-82%). A confirmation study using more SSR<br />markers is recommended. This study finding may be useful<br />in planning the oil palm germ plasm collection activities.</p>

scholarly journals Simple-sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea paniculata

HortScience ◽  
2009 ◽  
Vol 44 (1) ◽  
pp. 27-31 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Early Flowering ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 cultivars, breeding lines, and wild-collected accessions of Hydrangea paniculata Sieb. The SSR markers were highly variable among the genotypes, producing a mean of 5.8 alleles per marker. Three cultivars (Boskoop, Compact Grandiflora, and Webb) were either identical to or sports of the popular cultivar Grandiflora. The name ‘Pee Wee’ appears to have been applied to two phenotypically different compact forms of H. paniculata, one of which seems to be a sport of ‘Tardiva’, whereas the other is likely derived from ‘Grandiflora’. No close genetic similarity was observed among several cultivars from a long-term Belgium breeding program, although many had one parent in common. Early-flowering genotypes clustered separately from genotypes that flower in midsummer, but close genetic relationships were not observed among early-flowering cultivars. Two genotypes from Taiwan were genetically similar but were distinctly different from the Japanese genotypes. These, along with the early-flowering genotypes and a new collection from Japan, may represent unexploited sources of germplasm for improvement of H. paniculata.

Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers

Genome ◽  
2001 ◽  
Vol 44 (3) ◽  
pp. 413-425 ◽  
Author(s):  
N Billotte ◽  
A M Risterucci ◽  
E Barcelos ◽  
J L Noyer ◽  
P Amblard ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Ssr Markers ◽  
Oil Palm ◽  
Elaeis Guineensis ◽  
Sequence Data ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Variety Identification ◽  
Palm Species ◽  
Elaeis Guineensis Jacq

The results of the development of oil palm (Elaeis guineensis Jacq.) microsatellite markers are given step by step, from the screening of libraries enriched in (GA)n, (GT)n, and (CCG)n simple-sequence repeats (SSRs) to the final characterisation of 21 SSR loci. Also published are primer sequences, estimates of allele size range, and expected heterozygosity in E. guineensis and in the closely related species E. oleifera, in which an optimal utility of the SSR markers was observed. Multivariate data analyses showed the ability of SSR markers to efficiently reveal the genetic-diversity structure of the genus Elaeis in accordance with known geographical origins and with measured genetic relationships based on previous molecular studies. High levels of allelic variability indicated that E. guineensis SSRs will be a powerful tool for genetic studies of the genus Elaeis, including variety identification and intra- or inter-specific genetic mapping. PCR amplification tests on a subset of 16 other palm species and allele-sequence data showed that E. guineensis SSRs are putative transferable markers across palm taxa. In addition, phenetic information based on SSR flanking region sequences makes E. guineensis SSR markers a potentially useful molecular resource for any researcher studying the phylogeny of palm taxa.Key words: Palmae, SSR, phenetic analysis, phylogeny.

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