scholarly journals Genetic Differentiation in Moroccan Opuntia ficus-indica Cultivars Using Simple Sequence Repeat (SSR) Markers

2016 ◽  
Vol 8 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Aissam EL FINTI ◽  
Driss TALIBI ◽  
Mouhamed SIDKI ◽  
Abdelhamid E. MOUSADIK
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Opuntia Ficus Indica ◽  
Distance Analysis ◽  
Reference Collection ◽  
Ssr Loci ◽  
Set Up ◽  
Genetic Distance Analysis ◽  
Simple Sequence

Estimation of genetic parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources. In this study, 13 Opuntia ficus-indica cultivars were analyzed using 10 SSR markers selected for studying the genetic diversity among these chosen cultivars. Over the 10 SSR markers, a total of 45 reproducible bands were scored with an average of 4.5 alleles/locus, while the observed heterozygosity (Ho) values of amplified loci ranged from 0.15 (SSR1) to 0.92 (SSR2 and SSR 11). Genetic distance analysis of the 13 cultivars showed a large genetic differentiation (GST = 0.47) and high number of different groups. Most of the accessions were not found to be clustered according to their eco-geographical origin. In addition, each cultivar was characterized by its own multiallelic combination between loci. The results revealed the usefulness of SSR in understanding of genetic diversity in Moroccans Barbary fig cultivars, thus being helpful to set up rational decisions concerning the establishment of a national reference collection.

Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Eline van Zijll de Jong ◽  
Kathryn M Guthridge ◽  
German C Spangenberg ◽  
John W Forster
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Sequence Repeat ◽  
Pasture Grass ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 203
Author(s):  
Siyuan Chen ◽  
Mingliang Dong ◽  
Yan Zhang ◽  
Shuaizheng Qi ◽  
Xuezeng Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Genomic Analysis ◽  
Deciduous Tree ◽  
Genetic Studies ◽  
Ssr Loci ◽  
Nonspecific Amplification ◽  
Close Relatives ◽  
Simple Sequence

Liquidambar formosana (Hamamelidaceae) is a relatively fast-growing deciduous tree of high ornamental value that is indigenous to China. However, few molecular markers are available for the species or its close relatives; this has hindered genomic and genetic studies. Here, we develop a series of transferable expressed sequence tag-simple sequence repeats (EST-SSRs) for genomic analysis of L. formosana. We downloaded the sequence of the L. formosana transcriptome from the National Center of Biotechnology Information Database and identified SSR loci in the Unigene library. We found 3284 EST-SSRs by mining 34,491 assembled unigenes. We synthesized 100 random primer pairs for validation of eight L. formosana individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related Liquidambar species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of Liquidambar. A total of 72 clones of three Liquidambar species were uniquely divided into three main clusters; principal coordinate analysis (PCoA) supported this division. Additionally, a set of 20 SSR markers that did not exhibit nonspecific amplification were used to genotype more than 53 L. formosana trees. The mean number of alleles (Na) was 5.75 and the average polymorphism information content (PIC) was 0.578, which was higher than that of the natural L. formosana population (0.390). In other words, the genetic diversity of the plus L. formosana population increased, but excellent phenotypic features were maintained. The primers will be valuable for genomic mapping, germplasm characterization, gene tagging, and further genetic studies. Analyses of genetic diversity in L. formosana will provide a basis for efficient application of genetic materials and rational management of L. formosana breeding programs.

scholarly journals Genetic structure of populations of several endangered and endemic Dianthus species revealed by microsatellite markers

2018 ◽  
Vol 77 (2) ◽  
pp. 181-188 ◽  
Author(s):  
Anca Butiuc-Keul ◽  
Cornelia Crăciunaș ◽  
Irina Goia ◽  
Anca Farkas ◽  
Liliana Jarda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Genetic Structure Of Populations ◽  
Ssr Loci ◽  
Different Populations ◽  
The Mean ◽  
Simple Sequence

Abstract In order to develop a proper conservation programme for several endangered, rare or endemic species of Dianhtus from Romania, molecular characterization by simple sequence repeat (SSR) markers has been accomplished. Amplification of SSR loci in individuals belonging to different populations of D. callizonus, D. glacialis ssp. gelidus, D. henteri, D. nardiformis and D. tenuifolius revealed 23 polymorphic alleles. D. callizonus and D. tenuifolius showed particular sets of SSR alleles. D. glacialis ssp. gelidus, D. henteri and D. nardiformis proved to share almost the same alleles in most of the loci. The highest genetic diversity was observed in D. glacialis ssp. gelidus and D. tenuifolius in locus MS-DINMADSBOX. Allelic patterns across Dianthus species indicate that the mean number of different alleles was highest in D. glacialis ssp. gelidus, while the number of effective alleles was highest in D. tenuifolius. There are no particular differences in individuals belonging to the same species. Genetic diversity is generally low, ranging from 0.18 (D. callizonus) to 0.44 (D. henteri). Regarding the genetic diversity within populations of the same species, no differences were revealed by the use of the SSR markers tested in the present study.

scholarly journals Genetic Diversity and Differentiation of Relict Plant Liriodendron Populations Based on 29 Novel EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 334 ◽  
Author(s):  
Xiaofei Long ◽  
Yuhao Weng ◽  
Siqin Liu ◽  
Zhaodong Hao ◽  
Yu Sheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Eastern China ◽  
Genetic Distances ◽  
Breeding Strategy ◽  
Western China ◽  
The Usa ◽  
Ssr Loci ◽  
Liriodendron Chinense

Surviving relict populations of species that were more widespread in ancient times can teach us a lot, such as evolution and genetic differentiation. One such relict plant is Liriodendron, of which populations remain in China (L. chinense (Hemsl.) Sarg.) and the USA (L. tulipifera L.). Studying the genetic structure of these populations would give insight into the genetic differentiation and the breeding strategy. In this work, we developed and characterized 29 novel simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) from hybrid Liriodendron (Liriodendron chinense × tulipifera) callus. In total, 29 SSRs with perfect primer-designed were used to assess genetic diversity and differentiation. The set of polymorphic EST-SSR loci was identified in 48 Liriodendron individuals, represented by 35 individuals sampled from 14 provenances of L. chinense and 13 individuals sampled from 5 provenances of L. tulipifera. Our results indicated that L. chinense populations possess slightly higher genetic diversity than L. tulipifera populations. Based on genetic distances, 48 Liriodendron individuals clustered into three groups (the eastern China L. chinense, the western China L. chinense and L. tulipifera), although the STRUCTURE analysis of the Liriodendron populations revealed just two clear genetic clusters (L. chinense and L. tulipifera). Among these 29 novel markers, ESSR119 showed an obvious species-specific characteristic which can be very useful in marker-assisted selection (MAS). In general, all these EST-SSR markers may have agronomic potential and constitute a basis for future studies on the identification, innovation, and even preservation of Liriodendron germplasms.

scholarly journals Combining Quantitative Data on Growth, Wood Density and Other Traits with SSR Markers to Evaluate Genetic Diversity and Structure in a Planted Population of Eucalyptus camaldulensis Dehn.

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1090
Author(s):  
Xiuhua Shang ◽  
Roger J. Arnold ◽  
Zhihua Wu ◽  
Peijian Zhang ◽  
Guo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Quantitative Trait ◽  
Eucalyptus Camaldulensis ◽  
Genetic Distances ◽  
Bark Thickness ◽  
Seed Sources ◽  
Pilodyn Penetration ◽  
Ssr Loci

Eucalyptus camaldulensis Dehn. is one of the most morphologically and genetically variable Eucalyptus species. Growth, Leptocybe invasa Fisher & La Salle susceptibility, pilodyn penetration and other traits up to age 36 months were assessed in a seed source/family trial in China comprising 112 seedlots representing five natural stand and six exotic seed sources. Genetic diversity and population structure of this trial population were also analyzed using 48 simple sequence repeat (SSR) markers. The key objective was to examine whether the genomic data could provide value over information obtained from just quantitative trait data. Significant genetic variation was found among seed sources and among families within seed sources for most quantitative traits. The ratio of variance among seed sources to variance among families within seed sources, based on variances estimated from quantitative trait data, varied from 0.1% (height at 9 months) up to 75.2% (bark thickness). Equivalent ratios estimated from the AMOVA on SSR loci data were similar for height (ages 24 and 36 months) and also pilodyn penetration at 36 months, but not for 9-month height or 36-month bark thickness. From 48 SSR loci examined, the genetic differentiation coefficient (among seed sources) was 0.086, indicating low genetic differentiation among seed sources. While overall genetic diversity in the trial population examined was high, the levels within the different seed sources varied markedly. Prior to this study, genetic distances among families from the three exotic seed sources (from domesticated Indian populations) in the trial, along with their genetic distances from, and relatedness to, families from five natural stand seed sources (Australian) in the trial were unknown. The SSR loci data removed uncertainties and revealed that the exotic sources increased the breadth of genetic origins represented in the trial population—information that could not have been obtained from just the quantitative trait data.

Monitoring genetic diversity across Pinus tabuliformis seed orchard generations using SSR markers

2021 ◽  
Author(s):  
Boning Yang ◽  
Shihui Niu ◽  
Yousry A. El-Kassaby ◽  
Wei Li
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Seed Orchard ◽  
Seed Orchards ◽  
Distance Analysis ◽  
2Nd Generation ◽  
Pinus Tabuliformis ◽  
Genetic Distance Analysis

The maintenance of genetic diversity across seed orchard generations is an important management objective. Here, we used Pinus tabuliformis as a model to explore the extent of genetic diversity across the species’ breeding activities through their corresponding seed orchards generations. We utilized a large number of SSR markers selected from <i></i>Pinus tabuliformis<i></i> transcriptomic data, and then assessed the effect of marker number on genetic diversity and individuals’ genetic relationships across orchards’s generations. In total, we designed 125 simple sequence repeat (SSR) markers, from which 39 SSRs were polymorphic and used in the present study. The genetic diversity and genetic distance parameters tended to increase with thean increase ofin markerloci numbers and a stable trend was reached at 24 SSRs. The selected optimal 24 SSR markers were further used to assess the genetic diversity across seed orchards’s generations, and a decreasing trend was detected with the advancement of orchards’s generations. Genetic distance analysis indicated that individuals in the 2nd generation orchard was more closely related as compared to those of the 1st- and 1.5-generations. This study provided valuable information on the effect of selection and breeding on genetic diversity and highlighted its role for effective seed orchards management.

Genome-wide SSR marker development and application in genetic diversity analysis of the red swamp crayfish, Procambarus clarkii (Girard, 1852) in China

Crustaceana ◽  
2021 ◽  
Vol 94 (2) ◽  
pp. 189-205
Author(s):  
Junxiao Sun ◽  
Guohui Peng ◽  
Lijing Xiong ◽  
Cong Tan ◽  
Yanhe Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Basis ◽  
Molecular Breeding ◽  
Procambarus Clarkii ◽  
Genome Survey ◽  
Red Swamp Crayfish ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract The red swamp crayfish, Procambarus clarkii (Girard, 1852), is currently an economically important aquaculture animal. Its genetic basis has been scarcely reported, however, partly due to the absence of abundant molecular markers in the genome. In this study, Simple Sequence Repeat (SSR) loci were mined, based on genome survey sequencing via the next generation sequence of the red swamp crayfish. A total of 4897 SSR loci were identified, with the most abundant type being the di-nucleotide repeat motifs (75.2%), followed by tri- (20.4%), tetra- (3.8%), penta- (0.5%), and hexanucleotide (0.2%) repeats. In total, 1546 SSR markers were validated to be amplified, and 721 of these were identified as polymorphic SSR markers. Fifty polymorphic SSR markers were randomly selected for the identification of the genetic diversity of the 14 red swamp crayfish populations in China. The expected and observed heterozygosity and polymorphism information content were 0.39, 0.30, and 0.29, respectively, on average. The results indicated a medium genetic diversity among the 14 investigated populations. These probably cluster into three genetic populations. The current study provides abundant genetic markers and information on the 14 populations, which can be helpful for genetic diversity estimation and molecular breeding of the red swamp crayfish.

Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz)

2008 ◽  
Vol 6 (3) ◽  
pp. 208-214 ◽  
Author(s):  
P. Hurtado ◽  
K. M. Olsen ◽  
C. Buitrago ◽  
C. Ospina ◽  
J. Marin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Latin American ◽  
Manihot Esculenta ◽  
Dart Markers ◽  
Diversity Array Technology ◽  
Germplasm Collections ◽  
Array Technology ◽  
Simple Sequence

Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.

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