Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.

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Efficiency of different marker systems for molecular characterization of subtropical carrot germplasm

The Journal of Agricultural Science ◽

10.1017/s0021859609990591 ◽

2010 ◽

Vol 148 (2) ◽

pp. 171-181 ◽

Cited By ~ 3

Author(s):

T. JHANG ◽

M. KAUR ◽

P. KALIA ◽

T. R. SHARMA

Keyword(s):

Genetic Variability ◽

Ssr Markers ◽

Dna Markers ◽

Principal Component ◽

Group Method ◽

Data Set ◽

Breeding Lines ◽

Pair Group ◽

Ssr Loci ◽

Simple Sequence

SUMMARYGenetic variability in carrots is a consequence of allogamy, which leads to a high level of inbreeding depression, affecting the development of new varieties. To understand the extent of genetic variability in 40 elite indigenous breeding lines of subtropical carrots, 48 DNA markers consisting of 16 inter simple sequence repeats (ISSRs), 10 universal rice primers (URPs), 16 random amplification of polymorphic DNA (RAPD) and six simple sequence repeat (SSR) markers were used. These 48 markers amplified a total of 591 bands, of which 569 were polymorphic (0·96). Amplicon size ranged from 200 to 3500 base pairs (bp) in ISSR, RAPD and URPs markers and from 100 to 300 bp in SSR markers. The ISSR marker system was found to be most efficient with (GT)n motifs as the most abundant SSR loci in the carrot genome. The unweighted pair group method with arithmetic mean (UPGMA) analysis of the combined data set of all the DNA markers obtained by four marker systems classified 40 genotypes in two groups with 0·45 genetic similarity with high Mantel matrix correlation (r=0·92). The principal component analysis (PCA) of marker data also explained 0·55 of the variation by first three components. Molecular diversity was very high and non-structured in these open-pollinated genotypes. The study demonstrated for the first time that URPs can be used successfully in genetic diversity analysis of tropical carrots. In addition, an entirely a new set of microsatellite markers, derived from the expressed sequence tags (ESTs) sequences of carrots, has been developed and utilized successfully.

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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia

Biochemical Genetics ◽

10.1007/s10528-021-10090-7 ◽

2021 ◽

Author(s):

Júlia Halász ◽

Noémi Makovics-Zsohár ◽

Ferenc Szőke ◽

Sezai Ercisli ◽

Attila Hegedűs

Keyword(s):

Simple Sequence Repeat ◽

Principal Component ◽

Sequence Repeat ◽

Breeding Programs ◽

Allele Number ◽

Genetic Potential ◽

Ssr Loci ◽

High Level ◽

Diversity Studies ◽

Simple Sequence

AbstractPolyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.

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Application of Microsatellite and Inter Simple Sequence Markers for Certifying Trueness to Type of Grafted Ramets and Clustering of Persian Walnut Varieties

10.21203/rs.3.rs-542091/v1 ◽

2021 ◽

Author(s):

Masoomeh Hosseini Nickravesh ◽

Kourosh Vahdati ◽

fatemeh amini ◽

Reza Amiri ◽

Keith Woeste

Keyword(s):

Ssr Markers ◽

Issr Markers ◽

Principal Coordinate Analysis ◽

Dna Fingerprint ◽

Polymorphic Ssrs ◽

Persian Walnut ◽

Inter Simple Sequence Repeats ◽

Ssr Loci ◽

Ssrs Markers ◽

Simple Sequence

Abstract The utility of seventeen Microsatellite (SSR) markers and fifteen inter simple sequence repeats (ISSR) markers for the identification of twenty eight ramets of 11 varieties of walnut (Juglans regia) was explored. Thirty nine individual genomes were screened using 61 and 38 scorable fragments from SSR and ISSR markers, respectively. The least polymorphic SSR locus was WGA004 (two alleles) and the most polymorphic (5 alleles) was WGA276. Polymorphism information content values ranged from 0.08 (WGA004) to 0.43 (WGA032) in SSR markers and from 0.11 (AGA (AC)7) to 0.49 (CAC(TGT)5) in ISSR markers, with an average of 0.29 and 0.19, respectively. In most cases, grafted varieties with identical names also had the same microsatellites profile. The principal coordinate analysis and clustering (UPGMA) based on the combined marker set emphasized two failures in grafting or off-types, ramets identified as Serr 4 (S4) and Vina 1 (V1). The presence of two off-type ramets in the walnut research orchard emphasizes the importance of using molecular certification for proving true-to-type of walnut orchards. Using 13 polymorphic SSRs, we tabulated a DNA fingerprint chart of 11 walnut varieties. Except for ‘Chandler’, each cultivar could be distinguished using a combination of only two SSR loci. The 13 SSRs markers evaluated in this study could be used in future to identify clones produced from the varieties.

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Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

Genes ◽

10.3390/genes11010011 ◽

2019 ◽

Vol 11 (1) ◽

pp. 11 ◽

Cited By ~ 1

Author(s):

Vadim G. Lebedev ◽

Natalya M. Subbotina ◽

Oleg P. Maluchenko ◽

Tatyana N. Lebedeva ◽

Konstantin V. Krutovsky ◽

...

Keyword(s):

Ssr Markers ◽

Flavonoid Biosynthesis ◽

Flavonoid Pathway ◽

Breeding Programs ◽

Pathogenesis Related ◽

Ssr Loci ◽

Rubus Species ◽

Polymerase Chain ◽

Functional Dna ◽

Primer Annealing

Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat—SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.

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

Notulae Scientia Biologicae ◽

10.15835/nsb839864 ◽

2016 ◽

Vol 8 (3) ◽

pp. 380-385 ◽

Cited By ~ 1

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.

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Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

Forests ◽

10.3390/f10080644 ◽

2019 ◽

Vol 10 (8) ◽

pp. 644 ◽

Cited By ~ 2

Author(s):

Li Dong ◽

Yuhan Sun ◽

Keqi Zhao ◽

Jing Zhang ◽

Yuwei Zhang ◽

...

Keyword(s):

Ssr Markers ◽

Black Locust ◽

Robinia Pseudoacacia ◽

Diversity Analysis ◽

Simple Method ◽

Genetic Diversity Analysis ◽

Ssr Loci ◽

Robinia Pseudoacacia L ◽

Expressed Sequence ◽

Simple Sequence

Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

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Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2007000300011 ◽

2007 ◽

Vol 42 (3) ◽

pp. 377-384 ◽

Cited By ~ 3

Author(s):

Fernanda de Oliveira Pinto ◽

Mirian Perez Maluf ◽

Oliveiro Guerreiro-Filho

Keyword(s):

Ssr Markers ◽

Expressed Sequence Tags ◽

Defense Mechanisms ◽

Leaf Miner ◽

Gene Transcript ◽

Est Database ◽

Hybrid Frequency ◽

Ssr Loci ◽

Expressed Sequence ◽

Simple Sequence

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

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Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers

Crop and Pasture Science ◽

10.1071/cp10165 ◽

2011 ◽

Vol 62 (2) ◽

pp. 177 ◽

Cited By ~ 13

Author(s):

Tadesse Sefera ◽

Bekele Abebie ◽

Pooran M. Gaur ◽

Kebebew Assefa ◽

Rajeev K. Varshney

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Dna Fingerprint ◽

Pedigree Information ◽

Sequence Repeat ◽

Dissimilarity Matrix ◽

Breeding Programs ◽

Simple Sequence ◽

Chickpea Cultivars

The genomic DNA profiles of 48 chickpea cultivars released in nine countries and of historical significance to the chickpea breeding programs at ICRISAT and in Ethiopia were evaluated using 48 simple sequence repeat (SSR) markers. Across the cultivars, a total of 504 alleles representing the 48 SSR loci were detected with frequencies ranging from three to 22 (mean 10.5) alleles per locus. The polymorphism information content (PIC) for the SSR markers varied from 0.37 to 0.91 (mean 0.77). A subset of only three highly informative SSR markers (TA176, TA2, TA180) enabled complete discrimination among all 48 chickpea cultivars tested. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching dissimilarity matrix resolved the 48 cultivars into two major clusters representing desi and kabuli types. These cluster groupings of the cultivars were consistent with the pedigree information available for the cultivars as to the phenotypic classes of chickpea types. Analysis of the temporal patterns of the SSR diversity by classifying 48 chickpea cultivars into four periods of release revealed increasing tendencies in the overall genetic diversity from 0.42 for the earliest varieties developed in the 1970s to 0.62 for those released in the 1980s, and reached a maximum and equivalent level of 0.72 for the varieties developed in the 1990s and 2000s. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprint identification of cultivars.

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

Genome ◽

10.1139/g03-001 ◽

2003 ◽

Vol 46 (2) ◽

pp. 277-290 ◽

Cited By ~ 33

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.

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Genetic variability of Brazilian rice landraces determined by SSR markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2009000700009 ◽

2009 ◽

Vol 44 (7) ◽

pp. 706-712 ◽

Cited By ~ 7

Author(s):

Tereza Cristina de Oliveira Borba ◽

Clistiane dos Anjos Mendes ◽

Élcio Perpétuo Guimarães ◽

Tuliana Oliveira Brunes ◽

Jaime Roberto Fonseca ◽

...

Keyword(s):

Genetic Variability ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Molecular Data ◽

Factorial Correspondence Analysis ◽

Rice Cultivars ◽

Market Demand ◽

Breeding Programs ◽

Rice Landraces ◽

Simple Sequence

The objective of this study was to evaluate the genetic variability of rice (Oryza sativa) landraces collected in Brazilian small farms. Twelve simple sequence repeat (SSR) markers characterized 417 landraces collected in 1986, 1987 and 2003, in the state of Goiás, Brazil. The number of landraces with long and thin grain type increased in the evaluated period, probably due to market demand. Based on the molecular data, the genetic variability increased during this period and, as per to the factorial correspondence analysis, most of the accessions were grouped according to the year of collection. The incorporation of modern rice cultivars in landrace cultivation areas and the selection carried out by small farmers are the most probable factors responsible for increasing landrace genetic variability, during the evaluated period. Genotype exchange between farmers, selection practice and local environmental adaptation are able to generate novel adapted allele combinations, which can be used by breeding programs, to reinitiate the process.

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