Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 938-945 ◽  
Author(s):  
Guohao He ◽  
C. S. Prakash ◽  
R. L. Jarret
Keyword(s):  
Genetic Diversity ◽  
Ipomoea Batatas ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Dna Amplification ◽  
Taq Polymerase ◽  
Plant Introductions ◽  
Vinyl Polymer ◽  
High Level ◽  
Selection Of

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.Key words: DNA fingerprinting, DNA markers, germplasm, genetic diversity, RAPD markers.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

scholarly journals Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

2020 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
Zhenqing Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Germplasm Characterization ◽  
2D Barcode ◽  
New Type ◽  
Generation Sequencing ◽  
Kasp Markers ◽  
Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 108-114 ◽  
Author(s):  
José Miguel Soriano ◽  
Carlos Romero ◽  
Santiago Vilanova ◽  
Gerardo Llácer ◽  
María Luisa Badenes
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Malus Domestica ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Mean Value ◽  
Eriobotrya Japonica ◽  
Fixation Index ◽  
Group Method ◽  
Malus Domestica Borkh

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus × domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (–0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus × domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.Key words: Eriobotrya japonica, SSR markers, microsatellites, genetic diversity.

Analysis of genetic diversity within Australian lucerne cultivars and implications for future genetic improvement

2002 ◽  
Vol 53 (6) ◽  
pp. 629 ◽  
Author(s):  
J. M. Musial ◽  
K. E. Basford ◽  
J. A. G. Irwin
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Random Amplified Polymorphic Dna ◽  
Population Diversity ◽  
Breeding Programs ◽  
Population Genetic Diversity ◽  
Medicago Sativa L ◽  
Components Analysis ◽  
High Level ◽  
Selection Of

Lucerne (Medicago sativa L.) is autotetraploid, and predominantly allogamous. This complex breeding structure maximises the genetic diversity within lucerne populations making it difficult to genetically discriminate between populations. The objective of this study was to evaluate the level of random genetic diversity within and between a selection of Australian-grown lucerne cultivars, with tetraploid M. falcata included as a possible divergent control source. This diversity was evaluated using random amplified polymorphic DNA (RAPDs). Nineteen plants from each of 10 cultivars were analysed. Using 11 RAPD primers, 96 polymorphic bands were scored as present or absent across the 190 individuals. Genetic similarity estimates (GSEs) of all pair-wise comparisons were calculated from these data. Mean GSEs within cultivars ranged from 0.43 to 0.51. Cultivar Venus (0.43) had the highest level of intra-population genetic diversity and cultivar Sequel HR (0.51) had the lowest level of intra-population genetic diversity. Mean GSEs between cultivars ranged from 0.31 to 0.49, which overlapped with values obtained for within-cultivar GSE, thus not allowing separation of the cultivars. The high level of intra- and inter-population diversity that was detected is most likely due to the breeding of synthetic cultivars using parents derived from a number of diverse sources. Cultivar-specific polymorphisms were only identified in the M. falcata source, which like M. sativa, is outcrossing and autotetraploid. From a cluster analysis and a principal components analysis, it was clear that M. falcata was distinct from the other cultivars. The results indicate that the M. falcata accession tested has not been widely used in Australian lucerne breeding programs, and offers a means of introducing new genetic diversity into the lucerne gene pool. This provides a means of maximising heterozygosity, which is essential to maximising productivity in lucerne.

Genetic diversity and relationships among Secale L. based on RAMP markers

2004 ◽  
Vol 1 (2) ◽  
pp. 73-78 ◽  
Author(s):  
Shang Hai-Ying ◽  
Zheng You-Liang ◽  
Wei Yu-Ming ◽  
Wu Wei ◽  
Yan Ze-Hong
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Group Method ◽  
Transitional Region ◽  
Arithmetic Average ◽  
Pair Group ◽  
Broad Leaf ◽  
Polymorphic Bands ◽  
High Level

AbstractGenetic diversity and relationships among 21 accessions of Secale L., including three species and 10 subspecies, were evaluated using RAMP markers. Forty-one out of 80 (50.5%) RAMP primers, which produced clear and polymorphic bands, were selected for PCR amplification of genomic DNA. A total of 446 bands were amplified from the 41 primers, and 428 of these bands (about 96%) were polymorphic. Three to 19 polymorphic bands could be amplified from each primer, with an average of 10.4 bands. The RAMP-based genetic similarity (GS) values among the 21 Secale accessions ranged from 0.266 to 0.658, with a mean of 0.449. A high level of genetic variation was found between or within the wild populations and the cultivars. Based on the GS matrix, a dendrogram was constructed using the unweighted pair group method with arithmetic average (UPGMA). All 21 accessions could be distinguished by RAMP markers. Clustering results showed that the genetic diversity of Secale based on RAMP markers was correlated with geographical distribution. Six rye cultivars, originating from Poland, Portugal, Mexico, Hungary, Armenia and Ukraine, were clustered into one group. The six countries are all located in the transitional region of broad-leaf forests between maritime and continental temperate zones, with narrow latitude span. In comparison, the other five cultivars from countries scattered over a region with large latitude span were distributed within different groups or subgroups. Genetic relationships based on RAMP markers had great deviation from the original taxonomy. Some subspecies of the same species were distributed within different groups, while some accessions of different species were closely clustered into one subgroup. These results suggest that RAMP markers could be an effective technique for detecting genetic diversity among Secale and give some useful information about its phylogenic relationships.

scholarly journals Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

2015 ◽  
Vol 71 (1) ◽  
pp. 81-95 ◽  
Author(s):  
Hoda Moradkhani ◽  
Ali Ashraf Mehrabi ◽  
Alireza Etminan ◽  
Alireza Pour-Aboughadareh
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Issr Marker ◽  
D Genome ◽  
Ploidy Levels ◽  
Marker Data ◽  
Geographical Regions ◽  
High Level

AbstractThe aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions ofAegilopsandTriticumspecies with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA) revealed that 81% (ISSR) and 84% (SSR) of variability was partitioned among individuals within populations. Comparing the genetic diversity ofAegilopsandTriticumaccessions, based on genetic parameters, shows that genetic variation ofAe. crassaandAe. tauschiispecies are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA) for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA), also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

scholarly journals DNA Sequence Analysis of Microsatellite Markers Enhances Their Efficiency for Germplasm Management in an Italian Olive Collection

2006 ◽  
Vol 131 (3) ◽  
pp. 352-359 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Nicola Lombardo ◽  
Aldo Musacchio ◽  
Maria Elena Noce ◽  
Giuseppe Pellegrino ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Microsatellite Markers ◽  
Dna Sequence ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Electrophoretic Analysis ◽  
Dna Sequence Analysis ◽  
Germplasm Management ◽  
Olive Cultivars ◽  
High Level

Genetic diversity studies using microsatelite analysis were carried out in a set of 39 accessions of Olea europaea L., corresponding to the majority of the regional autochthon germplasm in Apulia. Samples of olive leaves were harvested from plants growing in the olive germplasm collection of the Consiglio per la Ricerca e Sperimentazione in Agricoltura (C.R.A.) - Istituto Sperimentale per l'Olivicoltura at Rende in Cosenza Italy. Herein, we evaluated the extent to which microsatellite analysis using electrophoresis was capable of identifying traditional olive cultivars. In addition, the DNA sequence of all amplicons was determined and the number of repeat units was established for each sample. Using five loci, electrophoretic analysis identified 24 genotype profiles, while DNA sequence analysis detected 28 different genotype profiles, identifying 54% of cultivars. The remaining 46% were composed of seven different accession groups containing genetically indistinguishable cultivars, which are presumably synonyms. This study demonstrates the utility of microsatellite markers for management of olive germplasm and points out the high level of polymorphisms in microsatellite repeats when coupled with DNA sequence analysis. The establishment of genetic relationships among cultivars in the Apulian germplasm collection allows for the construction of a molecular database that can be used to establish the genetic relationships between known and unknown cultivars.

Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity and Relationships Among Cultivated Populations of Dendrobium officinale

2020 ◽  
Vol 14 (5) ◽  
pp. 624-631
Author(s):  
Bingzhong Ding ◽  
Benhou Zhang ◽  
Chao Li ◽  
Qingyun Xue ◽  
Wei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Dendrobium Officinale ◽  
Target Region ◽  
Target Region Amplification Polymorphism ◽  
Rare And Endangered Species ◽  
Upgma Dendrogram ◽  
Rare And Endangered ◽  
Cultivated Populations ◽  
High Level

Dendrobium officinale (Orchidacesae) is one of the rare and endangered species of herbs in China. Therefore, it will be beneficial to investigate the genetic diversity and relationships of cultivated populations of D. officinale for quality improvement. In this study, eight target region amplification polymorphism (TRAP) primer combinations were selected from fifty-four combinations, which were designed based on the related genes of the polysaccharides and alkaloids. A total of 148 fragments were scored in nine cultivated populations of D. officinale, including 130 (87.84%) polymorphic fragments. The analysis of genetic diversity revealed high level of genetic diversity in cultivated populations of D. officinale (H = 0.4125, I = 0.5985). Based on analysis of genetic structure, there was a moderate variation (Gst = 0.4706) and lower gene flow (Nm = 0.5625) among the cultivated populations due to some isolated measures, and domestication of excellent cultivars. Moreover, UPGMA dendrogram and Principal Coordinate Analysis (PCoA) indicated that nine cultivated populations were divided into four major groups. The results suggested that genetic relationships were associated with geographical germplasm sources instead of cultivation locations. Therefore, TRAP markers can be effectively employed to analyze genetic diversity and relationships among cultivated populations of D. officinale.

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

2007 ◽  
Vol 55 (3) ◽  
pp. 397-408 ◽  
Author(s):  
Abdelhameed Elameen ◽  
Siri Fjellheim ◽  
Arild Larsen ◽  
Odd Arne Rognli ◽  
Leif Sundheim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Germplasm Collection

scholarly journals Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

2012 ◽  
Vol 12 (2) ◽  
pp. 104-110 ◽  
Author(s):  
Ermis Yanes Paz ◽  
Katia Gil ◽  
Laureano Rebolledo ◽  
Andrés Rebolledo ◽  
Daniel Uriza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Morphological Characterization ◽  
Aflp Markers ◽  
Ananas Comosus ◽  
Morphological Descriptors ◽  
Low Level ◽  
Germplasm Collections

The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

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