Relationships among Peach, Almond, and Related Species as Detected by Simple Sequence Repeat Markers

The genetic relationships among peach [Prunus persica (L.) Batsch], almond [P. dulcis (Mill.) D.A. Webb or P. amygdalus (L.) Batsch] and 10 related Prunus species within the subgenus Amygdalus were investigated using simple sequence repeat (SSR) markers. P. glandulosa Pall. was included as an outgroup. Polymorphic alleles were scored as present or absent for each accession. The number of alleles revealed by the SSR analysis in peach and almond cultivars ranged from one to three whereas related Prunus species showed a range of one to 10 alleles. Results demonstrated an extensive genetic variability within this readily intercrossed germplasm as well as the value of SSR markers developed in one species of Prunus for the characterization of related species. Mean character difference distances were calculated for all pairwise comparisons and were used to construct an unrooted dendogram depicting the phenetic relationships among species. Four main groups were distinguished. Peach cultivars clustered with accessions of P. davidiana (Carr.) Franch. and P. mira Koehne. The second group contained almond cultivars. A third group included accessions of P. argentea (Lam) Rehd., P. bucharica Korschinsky, P. kuramica Korschinsky, P. pedunculata Pall, P. petunikowii Lits., P. tangutica (Spach) Batal., and P. webbii (Spach) Vieh.. P. glandulosa and P. scoparia Batal. were included in a fourth group.

Download Full-text

Cultivar Identification, Pedigree Verification, and Diversity Analysis among Peach Cultivars Based on Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.137.2.114 ◽

2012 ◽

Vol 137 (2) ◽

pp. 114-121 ◽

Cited By ~ 5

Author(s):

Viji Sitther ◽

Dapeng Zhang ◽

Sadanand A. Dhekney ◽

Donna L. Harris ◽

Anand K. Yadav ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Prunus Persica ◽

Genetic Relationships ◽

Genetic Identity ◽

Likelihood Method ◽

Sequence Repeat ◽

Pedigree Structure ◽

Improvement Programs ◽

Simple Sequence

Information on genetic relationships and pedigree structure in germplasm collections is vital to breeders in crop improvement programs. In this study, we assessed genetic identity, kinship distance, and parentage–sibship relationships among 37 peach (Prunus persica) accessions and breeding lines using simple sequence repeat (SSR) markers. Pairwise comparisons based on multilocus SSR profiles led to the identification of two synonymous groups including five accessions. Two pairs of parent–offspring and one full sibling relationships were identified using the likelihood method, and Bayesian cluster analysis partitioned the accessions into groups that were partially compatible with the known pedigree, origin, and flesh color. The 37 accessions were grouped into four clusters, which were largely supported by the known pedigree and origin of these accessions. Although the observed mean heterozygosity was 0.219, mean inbreeding coefficient was 0.635, indicating a high degree of inbreeding among the accessions. Eleven of the 15 SSR markers (73.3%) tested were transferable to nine related Prunus species. Results of the study demonstrate that these SSRs could facilitate the assessment of genetic identity and pedigree structure.

Download Full-text

Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.129.2.0204 ◽

2004 ◽

Vol 129 (2) ◽

pp. 204-210 ◽

Cited By ~ 37

Author(s):

Riaz Ahmad ◽

Dan Potter ◽

Stephen M. Southwick

Keyword(s):

Molecular Markers ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Sweet Cherry ◽

Prunus Persica ◽

Sequence Repeat ◽

Srap Markers ◽

Upgma Cluster Analysis ◽

Commercially Important ◽

Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

Download Full-text

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

Journal of Genetics ◽

10.1007/s12041-011-0018-5 ◽

2011 ◽

Vol 90 (1) ◽

pp. 11-19 ◽

Cited By ~ 8

Author(s):

VIKAS KUMAR SINGH ◽

PRITI UPADHYAY ◽

PALLAVI SINHA ◽

ASHISH KUMAR MALL ◽

SANJAY KUMAR JAISWAL ◽

...

Keyword(s):

Oryza Sativa ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Oryza Sativa L ◽

Genetic Relationships ◽

Sequence Repeat ◽

Male Sterile ◽

Simple Sequence

Download Full-text

Discovery of simple sequence repeat (SSR) markers in hazelnut (Corylus avellana L.) by transcriptome sequencing and SSR-based characterization of hazelnut cultivars

Scandinavian Journal of Forest Research ◽

10.1080/02827581.2020.1797155 ◽

2020 ◽

Vol 35 (5-6) ◽

pp. 227-237

Author(s):

Musa Kavas ◽

Kubilay Yıldırım ◽

Zafer Seçgin ◽

Gökhan Gökdemir

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Transcriptome Sequencing ◽

Corylus Avellana ◽

Sequence Repeat ◽

Corylus Avellana L ◽

Simple Sequence

Download Full-text

Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

Download Full-text

Development and characterization of simple sequence repeat (SSR) markers for the mushroom Flammulina velutipes

Journal of Bioscience and Bioengineering ◽

10.1016/j.jbiosc.2010.04.001 ◽

2010 ◽

Vol 110 (3) ◽

pp. 273-275 ◽

Cited By ~ 14

Author(s):

Ruiying Zhang ◽

Dandan Hu ◽

Jinxia Zhang ◽

Xuemei Zuo ◽

Ruibo Jiang ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Flammulina Velutipes ◽

Sequence Repeat ◽

Simple Sequence

Download Full-text

Cultivation-Independent Analysis of Fungal Genotypes in Soil by Using Simple Sequence Repeat Markers

Applied and Environmental Microbiology ◽

10.1128/aem.01405-07 ◽

2007 ◽

Vol 73 (20) ◽

pp. 6519-6525 ◽

Cited By ~ 19

Author(s):

Kaspar Schwarzenbach ◽

Franco Widmer ◽

Jürg Enkerli

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Fungal Species ◽

Sequence Repeat ◽

Beauveria Brongniartii ◽

Soil Dna ◽

Ssr Analysis ◽

Community Profiling ◽

Independent Analysis ◽

Simple Sequence

ABSTRACT Cultivation-independent analyses of fungi are used for community profiling as well as identification of specific strains in environmental samples. The objective of the present study was to adapt genotyping based on simple sequence repeat (SSR) marker detection for use in cultivation-independent monitoring of fungal species or strains in bulk soil DNA. As a model system, a fungal biocontrol agent (BCA) based on Beauveria brongniartii, for which six SSR markers have been developed, was used. Species specificity of SSR detection was verified with 15 fungal species. Real-time PCR was used to adjust for different detection sensitivities of the six SSR markers as well as for different template quantities. The limit for reliable detection per PCR assay was below 2 pg target DNA, corresponding to an estimated 45 genome copies of B. brongniartii. The cultivation-independent approach was compared to cultivation-dependent SSR analysis with soil samples from a B. brongniartii BCA-treated field plot. Results of the cultivation-independent method were consistent with cultivation-dependent genotyping and allowed for unambiguous identification and differentiation of the applied as well as indigenous strains in the samples. Due to the larger quantities of soil used for cultivation-dependent analysis, its sensitivity was higher, but cultivation-independent SSR genotyping was much faster. Therefore, cultivation-independent monitoring of B. brongniartii based on multiple SSR markers represents a rapid and strain-specific approach. This strategy may also be applicable to other fungal species or strains for which SSR markers have been developed.

Download Full-text