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

2012 ◽  
Vol 137 (2) ◽  
pp. 114-121 ◽  
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.

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

2003 ◽  
Vol 128 (5) ◽  
pp. 667-671 ◽  
Author(s):  
P. Martínez-Gómez ◽  
S. Arulsekar ◽  
D. Potter ◽  
T.M. Gradziel
Keyword(s):  
Ssr Markers ◽  
Related Species ◽  
Simple Sequence Repeat ◽  
Prunus Persica ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Ssr Analysis ◽  
Phenetic Relationships ◽  
Simple Sequence

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.

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

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
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.

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

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 802-810 ◽  
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.

scholarly journals Prospects for Fingerprinting the USDA–ARS Cold-hardy Vitis Germplasm Collection using Simple Sequence Repeat (SSR) Markers

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 620e-620
Author(s):  
Warren F. Lamboy ◽  
Christopher G. Alpha
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Plant Genetic Resources ◽  
Germplasm Collection ◽  
Genetic Identity ◽  
Dna Fragments ◽  
Sequence Repeat ◽  
Cold Hardy ◽  
Types Of Information ◽  
Simple Sequence

Curators of plant genetic resources collections must preserve germplasm possessing known useful characteristics as well as material displaying general genetic diversity. In order to ensure that both types of germplasm are included in a collection, germplasm curators require three fundamental types of information about each accession: taxonomic identity, genetic identity, and genetic relationship. Because simple sequence repeat DNA fragments (SSRs) have been successfully used to determine the genetic identity of grape clones, we conducted a study to determine if SSRs would supply all three types of information for the accessions in the cold-hardy Vitis (grape) germplasm collection. SSR fragments were amplified at six different loci for 23 accessions of cold-hardy grape spanning the range of species diversity in the collection. The minimum number of different alleles found at a locus was 9; the maximum was 26. Heterozygosity values ranged between 0.565 and 0.783, while gene diversity values were in the range 0.785 to 0.944. Two hundred fifty-two pairs of plants out of a possible 253 could be distinguished by their SSR profiles. Nei's genetic identities were computed between all pairs of plants and used in a UPGMA cluster analysis. The relationships obtained did not correspond well to expected relationships based on geography and taxonomy. Four species of grapes were represented by two or more accessions in this study. No DNA fragments found at these six loci served to unambiguously distinguish one species from another. Thus, SSR fragments from the six loci studied were useful in determining genetic identity of accessions, but were not helpful in determining genetic relationships or taxonomic identities. We are searching for additional loci that are informative for these types of information. Meanwhile we highly recommend SSRs for determining genetic identity in germplasm resources collections.

scholarly journals Genetic identity based on simple sequence repeat (SSR) markers for Quinoa (Chenopodium quinoa Willd.)

2019 ◽  
Vol 46 (2) ◽  
pp. 166-178 ◽  
Author(s):  
Maria Romero ◽  
◽  
Angel Mujica ◽  
Edgardo Pineda ◽  
Yesenia Ccamapaza ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Chenopodium Quinoa ◽  
Genetic Identity ◽  
Sequence Repeat ◽  
Identity Based ◽  
Simple Sequence

Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

2007 ◽  
Vol 5 (02) ◽  
pp. 71-81 ◽  
Author(s):  
Serge Tostain ◽  
Clément Agbangla ◽  
Nora Scarcelli ◽  
Cédric Mariac ◽  
Ogoubi Daïnou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Management Practices ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Dioscorea Rotundata ◽  
Tuber Crop ◽  
The Mean ◽  
Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

scholarly journals Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource

HortScience ◽  
2017 ◽  
Vol 52 (12) ◽  
pp. 1655-1660 ◽  
Author(s):  
Noémi Makovics-Zsohár ◽  
Magdolna Tóth ◽  
Dezső Surányi ◽  
Szilvia Kovács ◽  
Attila Hegedűs ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
Principal Component ◽  
Bootstrap Support ◽  
Limited Information ◽  
Sequence Repeat ◽  
Prunus Domestica ◽  
Simple Sequence

The hexaploid European plum (Prunus domestica L.) is an economically important fruit species with limited information on its genetic structure. Our objective was to fingerprint 55 cultivars using seven simple sequence repeat (SSR) markers to estimate the polymorphism level and determine allelic variation and genetic relationships among local and international cultivars. The primer pairs amplified a total of 135 alleles ranging from six to 27 alleles per locus, displaying high polymorphism. All genotypes were clearly distinguished with the seven SSRs used in this study. In a neighbor-joining cluster analysis, cultivars belonging to the same species did not group together. Foreign modern cultivars clustered together, and Hungarian landraces positioned distantly from those. STRUCTURE analysis indicated three genetically distinct groups of the studied genotypes. Each cluster of Hungarian landrace cultivars received strong bootstrap support (89% to 100%). Most genotypes kept under identical name showed different DNA fingerprints. A principal component analysis (PCA) confirmed the information provided by the dendrogram and clarified the origin of ʻFehérszilva’. Our results confirmed the potential of the application of SSR markers in plum breeding.

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