scholarly journals Genetic diversity and population structure analysis in a large collection of white clover (Trifolium repens L.) germplasm worldwide

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11325
Author(s):  
Feifei Wu ◽  
Sainan Ma ◽  
Jie Zhou ◽  
Chongyang Han ◽  
Ruchang Hu ◽  
...  
Keyword(s):  
White Clover ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Large Collection ◽  
Weak Correlation ◽  
Breeding Programs ◽  
Population Structure Analysis ◽  
Trifolium Repens L ◽  
Amova Analysis ◽  
Simple Sequence

White clover is an important temperate legume forage with high nutrition. In the present study, 448 worldwide accessions were evaluated for the genetic variation and polymorphisms using 22 simple sequence repeat (SSR) markers. All the markers were highly informative, a total of 341 scored bands were amplified, out of which 337 (98.83%) were polymorphic. The PIC values ranged from 0.89 to 0.97 with an average of 0.95. For the AMOVA analysis, 98% of the variance was due to differences within the population and the remaining 2% was due to differences among populations. The white clover accessions were divided into different groups or subgroups based on PCoA, UPGMA, and STRUCTURE analyses. The existence of genetic differentiation between the originally natural and introduced areas according to the PCoA analysis of the global white clover accessions. There was a weak correlation between genetic relationships and geographic distribution according to UPGMA and STRUCTURE analyses. The results of the present study will provide the foundation for future breeding programs, genetic improvement, core germplasm collection establishment for white clover.

scholarly journals Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Qian You ◽  
Liping Xu ◽  
Yifeng Zheng ◽  
Youxiong Que
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Breeding Programs ◽  
Sugarcane Varieties ◽  
Breeding Station ◽  
The World ◽  
Breeding Programmes ◽  
Genetic Structures ◽  
Simple Sequence

Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use.

scholarly journals Genetic Relationships among 10 Prunus Rootstock Species from China, Based on Simple Sequence Repeat Markers

2016 ◽  
Vol 141 (5) ◽  
pp. 520-526 ◽  
Author(s):  
Qijing Zhang ◽  
Dajun Gu
Keyword(s):  
Phylogenetic Analysis ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Banding Patterns ◽  
Simple Sequence Repeat Markers ◽  
Ssr Primers ◽  
Relationship Of ◽  
Simple Sequence

To improve the efficiency of breeding programs for Prunus rootstock hybrids in China, we analyzed the subgenus status and relationship of 10 Chinese rootstock species, by using 24 sets of simple sequence repeat (SSR) primers. The SSR banding patterns and phylogenetic analysis indicated that subgenus Cerasus is more closely related to subgenus Prunophora than to subgenus Amygdalus, and that subgenus Lithocerasus is more closely related to subgenus Prunophora and subgenus Amygdalus than to subgenus Cerasus. In addition, Prunus triloba was more closely related to Prunus tomentosa than to the members of subgenus Amygdalus. Therefore, we suggest that P. tomentosa and P. triloba should be assigned to the same group, either to subgenus Lithocerasus or Prunophora, and we also propose potential parent combinations for future Prunus rootstock breeding.

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 variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

2018 ◽  
Vol 47 (4) ◽  
pp. 937-943
Author(s):  
Natalia Sukhikh ◽  
Valentina Malyarovskaya ◽  
Anastasiya Kamionskaya ◽  
Lidia Samarina ◽  
Svetlana Vinogradova
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Effective Number ◽  
Sequence Repeat ◽  
Base Pairs ◽  
Breeding Programs ◽  
Simple Sequence Repeat Markers ◽  
Hydrangea Macrophylla ◽  
High Level ◽  
Simple Sequence

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeats

2002 ◽  
Vol 121 (3) ◽  
pp. 259-262 ◽  
Author(s):  
D. H. KIM ◽  
G. ZUR ◽  
Y. DANIN-POLEG ◽  
S. W. LEE ◽  
K. B. SHIM ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

Assessment of genetic diversity in cultivars of white clover (Trifolium repens L.) detected by SSR polymorphisms

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 919-930 ◽  
Author(s):  
Julie George ◽  
Mark P Dobrowolski ◽  
Eline van Zijll de Jong ◽  
Noel O.I Cogan ◽  
Kevin F Smith ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Multidimensional Scaling ◽  
White Clover ◽  
Trifolium Repens ◽  
Simple Sequence Repeat ◽  
Nonmetric Multidimensional Scaling ◽  
Grass Species ◽  
Sequence Repeat ◽  
Trifolium Repens L ◽  
Simple Sequence

White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). Due to the outbreeding nature of white clover, cultivars are highly heterogeneous. Genetic diversity was assessed using 16 elite cultivars from Europe, North and South America, Australia, and New Zealand. Fifteen simple sequence repeat markers that detect single, codominant polymorphic genetic loci were selected for the study. The genetic relationships among individuals were compared using phenetic clustering, and those among cultivars were compared using nonmetric multidimensional scaling. Intrapopula tion variability exceeded interpopulation variability, with substantial overlap among populations and weak interpopula tion differentiation. No obvious or significant differentiation was observed on the basis of morphology or geographic origin of the cultivars. The number of parental genotypes used to derive each cultivar was not a major determinant of genome-wide genetic diversity. The outcomes of this assessment of genetic variation in elite white clover germplasm pools have important implications for the feasibility of molecular marker-based cultivar discrimination, and will be used to assist the design of linkage disequilibrium mapping strategies for marker-trait association.Key words: white clover, allotetraploid, genetic diversity, polymorphism, simple sequence repeat, cluster analysis, nonmetric multidimensional scaling.

scholarly journals Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

scholarly journals Genetic Variation and Structure of native and introduced Casuarina equisetifolia (L. Johnson) Provenances

2009 ◽  
Vol 58 (1-6) ◽  
pp. 79-85 ◽  
Author(s):  
G. H. Huang ◽  
C. L. Zhong ◽  
X. H. Su ◽  
Y. Zhang ◽  
K. Pinyopusarerk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Fragment Length Polymorphism ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Mantel Test ◽  
Casuarina Equisetifolia ◽  
Breeding Programs ◽  
The Pacific ◽  
The Mean ◽  
Amova Analysis

AbstractCasuarina equisetifolia is an important tree species in tropical/subtropical zones of Asia, the Pacific and Africa. In this study, 220 individuals from seven native provenances and eleven introduced provenances of C. equisetifolia were analyzed to assess the genetic variation and structure using amplified fragment length polymorphism (AFLP) markers. A total of 465 bands were obtained by eight primer pairs, among which 153 were polymorphic. The mean NEI’s gene diversity H = 0.2113 calculated for 18 provenances and the total gene diversity HT = 0.4065 calculated for native provenances suggested abundant variation within provenances and species. High genetic divergence coefficient (GST = 0.4737) and low gene flow (Nm = 0.5555) detected among native provenances suggesting high differentiation of C. equisetifolia. An AMOVA analysis for native provenances revealed a high proportion (46.07%) of the total genetic variation distributed among provenances. The UPGMA clustering (r = 0.8028) and the Mantel test (r = 0.0716) for native provenances showed there was no correlation among genetic relationships and geographical distribution. The genetic information provided important implications for the future conservation and breeding programs of C. equisetifolia.

scholarly journals Physic nut germplasm genetic diversity identified by internal simple sequence repeats (ISSR) markers

2017 ◽  
Vol 2 (2) ◽  
pp. 48
Author(s):  
Stella Maris Nucci ◽  
Maria Imaculada Zucchi ◽  
Glyn Mara Figueira ◽  
Renata Silva-Mann ◽  
José Baldin Pinheiro
Keyword(s):  
Genetic Diversity ◽  
Bayesian Analysis ◽  
Similarity Index ◽  
Production Capacity ◽  
Germplasm Collection ◽  
Issr Markers ◽  
Physic Nut ◽  
Jaccard Similarity ◽  
Breeding Programs ◽  
Simple Sequence

The physic nut has attracted great interest for their socioeconomic promising vegetable oil production capacity that can be used in biodiesel manufacturing. However, the species is still under a domestication process and many studies are still needed to start a breeding program. In this context, this study aimed to evaluate the genetic diversity in 29 physic nut accessions from two germplasm banks using 14 ISSR markers. Genetic characterization revealed that 86.64% of the genetic variation is present within the groups, whereas 13.36% corresponded to the variation between the groups. The total mean number of alleles per locus was 1.99 and the effective number of alleles corresponded to 1.42. The Bayesian analysis allocated the access into four clusters, showing that the clusters formed showed no relation to the origin of access. The Jaccard similarity index indicated that the extent of similarity between accessions ranged from 0.23 to 0.94. The dendrogram formed the same four access groups as those formed by the Bayesian analysis, and all groups were in agreement in both analyses. The study demonstrated the need and importance of a germplasm collection from several regions and countries in order to preserve the genetic diversity of the species and the development of Euphorbiaceae breeding programs

scholarly journals Simple Sequence Repeat Identification and Endocarp Characterization of Olive Tree Accessions in a Tunisian Germplasm Collection

HortScience ◽  
2010 ◽  
Vol 45 (10) ◽  
pp. 1429-1436 ◽  
Author(s):  
Mahdi Fendri ◽  
Isabel Trujillo ◽  
Ahmed Trigui ◽  
María Isabel Rodríguez-García ◽  
Juan de Dios Alché Ramírez
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Olive Tree ◽  
Sequence Repeat ◽  
Olive Cultivars ◽  
Correspondence Factor Analysis ◽  
Simple Sequence

Most traditional olive-producing countries possess a diversified genetic patrimony in Olea europaea L. Since the emergence of modern olive growing system, the identification, classification, and conservation of autochthonous olive cultivars is a priority for these countries. In this work, a total of 84 accessions belonging to the “Boughrara”-Sfax olive germplasm collection located in Tunisia have been screened using a powerful set of eight simple sequence repeat markers (SSRs). The study revealed a high genetic variability among the collection and detected a total of 64 alleles. For better management of the mentioned germplasm bank, an improved classification of the entries, including new denominations, has been proposed. In addition, several cases of mislabeling, synonymy, and homonymy have been clarified. Genetic relationships among cultivars have been analyzed showing four major clusters. Finally, a correspondence factor analysis demonstrated that cultivars tend to cluster depending on their main use as oil or table olives. No clear clustering tendencies were observed when the geographical origin of cultivars was used as the criteria for the analysis. All results obtained by SSR screening and classification were in accordance with classification based on morphological traits of fruit endocarps.

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