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 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 diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Zhi Li ◽  
Weibin Xu ◽  
Jing Dong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
In Situ Conservation ◽  
Grass Shrimp ◽  
The Other ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Polymorphic Microsatellite ◽  
Two Populations

Abstract Background The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. Results Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. Conclusion This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

scholarly journals Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1569
Author(s):  
Agnieszka Fornal ◽  
Katarzyna Kowalska ◽  
Tomasz Zabek ◽  
Agata Piestrzynska-Kajtoch ◽  
Adrianna Musiał ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
World War Ii ◽  
Microsatellite Markers ◽  
Fixation Index ◽  
Parental Genotype ◽  
Native Breed ◽  
Genetic Diversity And Structure ◽  
Genetic Resource Conservation ◽  
The Mean ◽  
Index Value

The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.

scholarly journals Genetic Divergence of Flax Genotypes (Linum Usitatissimum L.) Utilizing Microsatellite Markers

2017 ◽  
Vol 5 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Sumita Nag ◽  
Jiban Mitra
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Linum Usitatissimum ◽  
Rank Correlation ◽  
Natural Fibre ◽  
Similarity Coefficients ◽  
Oilseed Crops ◽  
Linum Usitatissimum L ◽  
Ssr Primers ◽  
Ssr Loci

Flax (Linum usitatissimum L.), stoods in position third, being the largest natural fibre crop and simultaneously one of the five preeminent oilseed crops in the world. SSR/microsatellite markers are extensively utilized for genetic diversity analysis and cultivar identification considering their myriad abundance, co-dominant inheritance, steep polymorphism, reproducibility, and comfort of assay by PCR. Ten microsatellites were amplified in 27 genotypes of Flax. The study was undertaken to assess the genetic diversity in flax and to select most diverse genotypes for future breeding program. Primer efficiency parameters were studied. The 10 SSR loci amplified a total of 41 alleles that were used for genetic analysis. Most primers have PIC value greater than 0.5 and the LU6 marker was highly polymorphic PIC = 0.95. Estimates of RP̅ were highest for the primer LU1 (0.68). The maximum MI was observed for the primer LU10 (3.56). The H and D ranged from 0.26 to 1.78 and 0.36 to 5.40, respectively. According to Spearman rank correlation, PIC and MI were most important parameters in assessing the efficiency of whole set of 10 SSR primers. Dendrogram was constructed using the genetic similarity coefficients using UPGMA. PCo-A was also performed in support. Genetic diversity in Flax was revealed at molecular level.

scholarly journals Genetic Diversity and Structure of Latvian Tilia cordata Populations

2021 ◽  
Vol 75 (4) ◽  
pp. 261-267
Author(s):  
Dainis Edgars Ruņģis ◽  
Baiba Krivmane
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Vegetative Reproduction ◽  
Growth Conditions ◽  
Climatic Conditions ◽  
Tilia Cordata ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Broadleaf Tree ◽  
Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

Evaluation of genetic diversity and structure of Vietnamese goat populations using multi locus microsatellite markers

2017 ◽  
Vol 148 ◽  
pp. 43-50 ◽  
Author(s):  
Le Thi Thuy ◽  
Dinh Van Binh ◽  
Nguyen Trong Binh ◽  
Luu Quang Minh ◽  
Tran Thi Thu Thuy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Diversity And Structure

scholarly journals Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Man Liu ◽  
Xin Hu ◽  
Xu Wang ◽  
Jingjing Zhang ◽  
Xubing Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Medicinal Plant ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Sampling Strategy ◽  
Market Demand ◽  
Conservation Assessment ◽  
Information Index ◽  
Ssr Loci ◽  
Metabolic Data

Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon’s information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.

scholarly journals Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 154 ◽  
Author(s):  
Lucia Lioi ◽  
Diana L. Zuluaga ◽  
Stefano Pavan ◽  
Gabriella Sonnante
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Genotyping By Sequencing ◽  
Fixation Index ◽  
Most Probable Number ◽  
Probable Number ◽  
Individual Snps ◽  
Starting Point ◽  
Genetic Diversity And Structure ◽  
The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

scholarly journals Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Suping Feng ◽  
Helin Tong ◽  
You Chen ◽  
Jingyi Wang ◽  
Yeyuan Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genomic Library ◽  
Trinucleotide Repeats ◽  
The Other ◽  
Diversity Analysis ◽  
Dominant Type ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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