Molecular analysis of genetic relatedness among alfalfa clones differing in levels of self-incompatibility

2000 ◽  
Vol 80 (3) ◽  
pp. 559-564 ◽  
Author(s):  
T. A. Campbell
Keyword(s):  
Simple Sequence Repeat ◽  
Potential Problem ◽  
Genetic Relatedness ◽  
Self Incompatibility ◽  
Use Of Self ◽  
Ssr Analysis ◽  
Heritable Trait ◽  
Breeding Schemes ◽  
Medicago Sativa L ◽  
Simple Sequence

The possibility of increasing hybridity in alfalfa (Medicago sativa L.) cultivars through the use of self-incompatible (SI) parents is being investigated. Prior research has demonstrated that self-incompatibility is a heritable trait and that environmentally stable SI clones can be selected. However, inbreeding depression is very severe in alfalfa, and a potential problem associated with utilizing self-incompatibility to increase hybridity is the purported positive relationship between self-incompatibility and inbreeding. Fifteen stable, partially to fully self-incompatible clones and 18 stable self-compatible (SC) clones were selected from the broad-based population W10-AC3. RAPD, Anchored Microsatellite Priming (AMSP), and Simple Sequence Repeat (SSR) analyses were performed on genomic DNA using 9, 10-mer RAPD primers; the AMSP primers (from the 5' end) CAA(CA)5, CCCC(GA)5, CCG(GA)5, and GCC(GA)5; and eight SSR primer pairs. Based on genetic distance (GD) estimates (computed from RAPD and AMSP markers) and numbers of tri-allelic and tetra-allelic loci from SSR analysis, there is no evidence that SI clones were more closely related than SC clones. Assuming parental GD is positively correlated with heterosis, environmentally stable SI clones with acceptable specific combining ability and separated by large GD's would be a good basis for a hybrid alfalfa system, or for use in other breeding schemes designed to minimize inbreeding while maximizing heterosis. Key words: Anchored microsatellite-priming, heterosis, inbreeding, RAPD, self incompatibility, SSR

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

2007 ◽  
Vol 73 (20) ◽  
pp. 6519-6525 ◽  
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.

Relationships among durum wheat accessions. II. A comparison of molecular and pedigree information

Genome ◽  
2007 ◽  
Vol 50 (4) ◽  
pp. 385-399 ◽  
Author(s):  
M. Maccaferri ◽  
M.C. Sanguineti ◽  
C. Xie ◽  
J.S.C. Smith ◽  
R. Tuberosa
Keyword(s):  
Durum Wheat ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Fragment Length Polymorphism ◽  
Pedigree Information ◽  
Gene Pools ◽  
Haplotype Sharing ◽  
Coefficient Of Parentage ◽  
Wheat Gene ◽  
Simple Sequence

The study of direct ancestry relationships provides information with which to determine essential derivation. SSR profiles were used to determine the pattern of relatedness among 134 durum wheat accessions, representing the most important modern durum wheat gene pools. Simple sequence repeat (SSR)- and amplified fragment length polymorphism (AFLP)-based genetic similarities among cultivars with accurate pedigrees were compared with pedigree-based coefficients of parentage. Sizeable departures of molecular similarities from the expected ones were observed, indicating the unreliability of inferring the pattern of genetic relatedness from the coefficient of parentage. Case studies consisting of parent–progeny cultivar trios and pairs, identified on the basis of their registered pedigree, were studied to evaluate the probability of ancestry of each progeny cultivar, compared with all the remaining accessions. Rare alleles and haplotype sharing were also explored. When the results did not agree with the registered parentages, SSR markers provided information with which to identify the most probable parents (or the corresponding “breeding lineages”) in the collection.

Genetic relatedness among cultivated and wild mulberry (Moraceae: Morus) as revealed by inter-simple sequence repeat analysis in China

2006 ◽  
Vol 86 (1) ◽  
pp. 251-257 ◽  
Author(s):  
Zhao Weiguo ◽  
Zhou Zhihua ◽  
Miao Xuexia ◽  
Wang Sibao ◽  
Zhang Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Pair Group ◽  
Simple Sequence

The genetic diversity of 27 mulberry (Morus spp.) genotypes mainly from China was investigated using inter-simple sequence repeat (ISSR) markers to assist in addressing breeding objectives and conserving existing genetic resources. Of the 22 primers screened, 15 produced highly reproducible ISSR bands. Using these 15 primers, 138 discernible DNA fragments were generated with 126 (91.3%) being polymorphic, indicating considerable genetic variation among the mulberry genotypes studied. Genetic similarity ranged from 0.6014 between Yu 2 and Yu 711 to 0.9493 between Cuizhisang and Dejiang 10. The phenetic dendrogram based on ISSR data generated by the unweighed pair group method with arithmetical averages (UPGMA) method grouped the 27 accessions into two major clusters: cluster I, cultivated mulberry species (M. multicaulis Perr., M. alba Linn., M. atropurpurea oxb., M. bombycis Kiodz., M. australis Poir., M. rotundiloba Kiodz., M. alba var. pendula Dipp., M. alba var. macrophylla Loud., and M. alba var. venose Delile.); and cluster II, wild mulberry species (M. cathayana Hemsl., M. laevigata Wall., M. wittiorum Hand-Mazz., M. nigra Linn., and M. mongolica Schneid.). Our molecular analyses agree with the existing morphological classification of Morus and clarify the genetic relationships among mulberry species. Key words: Morus L., genetic diversity, inter-simple sequence repeat, relatedness

scholarly journals Molecular characterization of indigenous olive genotypes based on SSR analysis

Genetika ◽  
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.

scholarly journals Distinguishing Creeping Bluegrass (Poa annua var. reptans) Genotypes Using Inter-simple Sequence Repeat Markers

HortScience ◽  
2007 ◽  
Vol 42 (2) ◽  
pp. 373-377 ◽  
Author(s):  
Troy D. Carson ◽  
Donald B. White ◽  
Alan G. Smith
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relatedness ◽  
Inter Simple Sequence Repeat ◽  
Poa Annua ◽  
Golf Courses ◽  
Sequence Repeat ◽  
Marker Assisted Breeding ◽  
Issr Pcr ◽  
Simple Sequence ◽  
Issr Primers

Poa annua L. has long been a cultivated weed on golf courses. However, the recent development of improved cultivars of creeping bluegrass (Poa annua reptans Hausskn.) has generated an increasing interest in selection and breeding of this species. Inter-simple sequence repeat (ISSR) PCR is a relatively new method for genotype identification and measuring genetic diversity and was employed in this study for differentiating among creeping bluegrass genotypes. The objectives of this study were to test ISSR primers for production of polymorphic fragments and ascertain the applicability of ISSR PCR to distinguish closely related genotypes. Eight primers produced fragments, of which 77.3% were polymorphic, and primers UBC849, UBC850, and UMN001 produced over 75% of the total polymorphic fragments. These three primers had sufficient resolution to distinguish all but two of the diploid creeping bluegrass accessions. This method was a simple, fast, and relatively inexpensive method to produce useful DNA fragments in creeping bluegrass. It is a robust method for detecting polymorphic loci that can be used in the study of genetic relatedness, heritability, or linkage to important traits, development of linkage maps, and marker-assisted breeding.

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