Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

ABSTRACT A genome-wide search was performed to identify simple sequence repeat (SSR) loci among the available sequence databases from four strains of Xylella fastidiosa (strains causing Pierce's disease, citrus variegated chlorosis, almond leaf scorch, and oleander leaf scorch). Thirty-four SSR loci were selected for SSR primer design and were validated in PCR experiments. These multilocus SSR primers, distributed across the X. fastidiosa genome, clearly differentiated and clustered X. fastidiosa strains collected from grape, almond, citrus, and oleander. They are well suited for differentiating strains and studying X. fastidiosa epidemiology and population genetics.

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Short Communication Genome-wide identification and characterization of simple sequence repeat loci in grape phylloxera, Daktulosphaira vitifoliae

Genetics and Molecular Research ◽

10.4238/2012.may.15.11 ◽

2012 ◽

Vol 11 (2) ◽

pp. 1409-1416 ◽

Cited By ~ 1

Author(s):

H. Lin ◽

M.S. Islam ◽

D.W. Ramming

Keyword(s):

Simple Sequence Repeat ◽

Short Communication ◽

Sequence Repeat ◽

Daktulosphaira Vitifoliae ◽

Grape Phylloxera ◽

Genome Wide ◽

Identification And Characterization ◽

Simple Sequence

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Molecular characterization of indigenous olive genotypes based on SSR analysis

Genetika ◽

10.2298/gensr1603017u ◽

2016 ◽

Vol 48 (3) ◽

pp. 1017-1025

Author(s):

Hulya Unver ◽

Ebru Sakar ◽

Mehmet Ulas ◽

Sezai Ercisli ◽

Bekir Ak

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Ssr Analysis ◽

Olive Cultivars ◽

Ssr Loci ◽

Similarity Ratio ◽

Repeat Primer ◽

Simple Sequence

Trees of 25 widely grown olive genotypes were analyzed using a set of 10 SSR (simple sequence repeat) primer pairs and to evaluate genetic diversity and reveal inter-cultivar relationships. Two well-known international olive cultivars (Chetoni and Manzanilla) and four widely grown Turkish standard cultivars (Aycalik, Edincik Su, Gemlik, Kilis Yaglik) are also included in the study to compare Kilis genotypes. The 10 polymorphic SSR loci exhibited 4 (UDO4) to 17 alleles (UDO43), with expected heterozygozity (He) ranging from 0.510 to 0.887 and a mean of 0.692 presenting high polymorphism. In this study we did not determine identical genotypes and Polateli4 and Kilis Ya?l?k (0.75), Polateli3 and Polateli7 (0.75) and Polateli6 and Manzanilla (0.70) revealed the highest similarity ratio each other. The most genetically divergent cultivars were Elbeyli8 and Musabeyli5 (0.10); Elbeyli3 and Musabeyli7 (0.15) and Musabeyli6 and Elbeyli7 (0.15), respectively.

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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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Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species

Genomics ◽

10.1016/j.ygeno.2019.09.005 ◽

2020 ◽

Vol 112 (2) ◽

pp. 1554-1564 ◽

Cited By ~ 2

Author(s):

Vandana Jaiswal ◽

Abdul Rawoof ◽

Meenakshi Dubey ◽

Sushil Satish Chhapekar ◽

Vineet Sharma ◽

...

Keyword(s):

Simple Sequence Repeat ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Non Coding Rna ◽

Capsicum Species ◽

Simple Sequence

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Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽

10.1139/b10-019 ◽

2010 ◽

Vol 88 (5) ◽

pp. 537-543 ◽

Cited By ~ 11

Author(s):

Yong-Bi Fu ◽

Gregory W. Peterson

Keyword(s):

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Linum Usitatissimum L ◽

Evolutionary Studies ◽

Expressed Sequence ◽

Simple Sequence ◽

Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

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