scholarly journals Genetic diversity and population structure of sugarcane (Saccharum spp.) accessions by means of microsatellites markers

2020 ◽  
Vol 42 ◽  
pp. e45088
Author(s):  
Hugo Zeni Neto ◽  
Luiz Gustavo da Mata Borsuk ◽  
Luiz Renato Frederico dos Santos ◽  
Henrique Sanches Angeli ◽  
Guilherme Souza Berton ◽  
...  
Keyword(s):  
Population Structure ◽  
Probabilistic Models ◽  
Similarity Coefficient ◽  
Group Method ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Pair Group ◽  
Industrial Yield ◽  
Degree Of Similarity ◽  
Simple Sequence

The success of sugarcane (Saccharum spp.) breeding programs depends on the choice of productive parent lines that have a high industrial yield and are genetically divergent. This study assessed the genetic divergence and population structure of sugarcane accessions that are the parents of the RB05 Series of the Sugarcane Breeding Program of Brazil. The DNA of 82 accessions was evaluated using 36 simple sequence repeat markers. The Jaccard similarity coefficient and Unweighted Pair Group Method with Arithmetic Mean clustering method were used to generate a cluster that was divided into 17 distinct groups derived from probabilistic models. The similarity coefficient used in both cases showed that the degree of similarity varied from 0.4716 (RB971551 x RB965586) to 0.9526 (RB936001 x SP89-1115), with a mean of 0.8536. This result demonstrates a high similarity between the 82 accessions and confirms Wright’s F statistic (0.125), which indicates moderate genetic variability. The less-similar crosses suggest that breeders seek a higher number of crosses using cultivar RB965586, highlighting the RB971551 x RB965586 and RB965586 x RB855511 crosses. The results demonstrate that crosses such as RB936001 x SP89-1115 and RB945954 x RB896342 should be avoided because of their high genetic similarity.

Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers

2006 ◽  
Vol 3 (2) ◽  
pp. 119-126 ◽  
Author(s):  
Liu Yong ◽  
Liu De-Chun ◽  
Wu Bo ◽  
Sun Zhong-Hai
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Similarity Coefficient ◽  
Group Method ◽  
Allelic Polymorphism ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Arithmetic Average ◽  
Pair Group ◽  
Simple Sequence

AbstractGenetic diversity in 122 accessions of pummelo (Citrus grandis Osbeck) and its related varieties was assessed using simple sequence repeat (SSR) markers. Thirty-one pairs of SSR informative primers generated a total of 335 alleles. The average number of alleles per locus was 9.85. The value of allelic polymorphism information content (PIC) ranged from 0.1939 to 0.9073, with an average of 0.7085 per primer. The 122 accessions of pummelo and its related varieties could be clustered into seven groups by the unweighted pair-group method arithmetic average (UPGMA), in which the 110 pummelo accessions could be divided into 18 subgroups at similarity coefficient of 0.712. These subgroups were mainly composed of the Shatian pummelo variety group, the Wendan variety group and many of the hybrid pummelo groups. The classification method can be used in targeting many varieties in order to widen the genetic background of pummelo.

scholarly journals Genetic variability in sugarcane (Saccharum spp. hybrid) genotypes through inter simple sequence repeats (ISSR) markers

2016 ◽  
Vol 8 (3) ◽  
pp. 1404-1409 ◽  
Author(s):  
Vivekanand P. Rao ◽  
Sanjay Singh ◽  
R. Chaudhary ◽  
M. K. Sharma ◽  
R.S. Sengar ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Genomic Diversity ◽  
Group Method ◽  
Saccharum Spp ◽  
Arithmetic Average ◽  
Sugarcane Varieties ◽  
Pair Group ◽  
Simple Sequence

In the present study, 14 sugarcane (Saccharum spp. hybrid) genotypes were used for genomic diversity analysis based on nineteen inter simple sequence repeat (ISSR). These nineteen sets of ISSR markers generated a total of 164 discernible and reproducible bands including 109 polymorphic and 55 monomorphic bands. The unweighted pair group method with arithmetic average (UPGMA) analysis revealed three distinct clusters: I, II and III within the 14 genotypes. The polymorphic information content (PIC) value per locus ranged from 0.14 (UBC811) to 0.53 (ISSR1) locus with an average of 0.42 for all loci. The range of genetic distance or coefficient of similarity among sugarcane genotypes varied 0.14 - 0.78. The analysis of these similarities matrix revealed that greater similarity between CoS03234 and CoSe1424 (0.78), and lowest similarity between CoS03234 and Co0118 (0.14). The knowledge gained in this study would be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the increasing demand of sugarcane cultivation for sugar and bio energy uses.

scholarly journals Population Differentiation Within Anisogramma anomala in North America

2019 ◽  
Vol 109 (6) ◽  
pp. 1074-1082 ◽  
Author(s):  
Megan F. Muehlbauer ◽  
Janine Tobia ◽  
Joshua A. Honig ◽  
Ning Zhang ◽  
Bradley I. Hillman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Group Method ◽  
Summary Statistics ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Anisogramma Anomala ◽  
High Degree ◽  
Degree Of Similarity ◽  
Simple Sequence

Anisogramma anomala, a biotrophic ascomycete in the order Diaporthales, causes eastern filbert blight (EFB) of hazelnuts (Corylus spp.). Until recently, little has been documented on its genetic diversity and population structure. In this study, 18 simple sequence repeat markers were used to fingerprint 182 accessions of the fungus originating from across North America. Our results, based on summary statistics of the allelic data, a discriminant analysis of principal components (DAPC) scatterplot, an unweighted pair group method with arithmetic mean (UPGMA) dendrogram, and analysis of multilocus genotypes, show that A. anomala exhibits considerable genetic diversity across multiple populations. Eleven clusters were resolved from the DAPC scatterplot, five of which were validated by statistically supported clusters in the UPGMA dendrogram. The 11 DAPC clusters were statistically significant via an analysis of molecular variance. Dendrogram topology and DAPC scatterplot groups showed some correlation with collection origin; samples collected in proximity tended to cluster together and be genetically similar. However, some locations held populations that were diverse and some populations with a high degree of similarity had disparate origins, suggesting movement by humans. Overall, the results demonstrate the presence of multiple, genetically distinct populations of A. anomala in North America and serve as a reference to assist in understanding and managing EFB.

scholarly journals POPULATION STRUCTURE OF KAEMPFERIA GALANGA L. FROM EASTERN INDIA

2019 ◽  
pp. 62-65 ◽  
Author(s):  
REENA PARIDA ◽  
SUJATA MOHANTY ◽  
SANGHAMITRA NAYAK
Keyword(s):  
Population Structure ◽  
Random Amplified Polymorphic Dna ◽  
Crop Improvement ◽  
Germplasm Conservation ◽  
Similarity Coefficient ◽  
Genetic Identification ◽  
Group Method ◽  
Ammonium Bromide ◽  
Pair Group ◽  
Kaempferia Galanga

Objective: India has been a producer of a large number of aromatic medicinal plants which serves as a valuable genetic resource for future quality improvement to meet the ever-growing demand of human essential products. Thus, an urgent need arises for germplasm conservation of these high yielding varieties to help the pharmaceutical and other industries. For this understanding, the population structure is essential in order to explore their genetic identification by fingerprinting and molecular characterization. Methods: In the present study DNA was isolated using modified Cetyl Trimethyl Ammonium Bromide (CTAB) method and Polymerase Chain Reaction (PCR) was performed according to standardized method along with its data analysis. This study was undertaken to characterize the highly medicinal Kaempferia galanga collected from 4 different populations of Odisha using the molecular markers as Random Amplified Polymorphic DNA and Inter-Simple Sequence Repeats for the first time. Results: A dendrogram constructed through Sequential Agglomerative Hierarchical and Nested (SAHN) clustering and Unweighted Pair Group Method with Arithmetic mean (UPGMA) analysis showed an average similarity of 0.993 ranging between 0.967 to 1.000. Jaccard’s similarity coefficient of combined markers segregated the genotypes into two main clusters, 1 with six samples and the others at 0.98 similarity coefficient. Conclusion: Hence, the molecular analysis could be further used for the identification of important novel gene present in Kaempferia galanga which can be utilized for future crop improvement as well as pharmacological activities.

scholarly journals Characterization of 14 Microsatellite Markers for Genetic Analysis and Cultivar Identification of Walnut

2005 ◽  
Vol 130 (3) ◽  
pp. 348-354 ◽  
Author(s):  
Gerald S. Dangl ◽  
Keith Woeste ◽  
Mallikarjuna K. Aradhya ◽  
Anne Koehmstedt ◽  
Chuck Simon ◽  
...  
Keyword(s):  
Cultivar Identification ◽  
Paternity Analysis ◽  
Group Method ◽  
Breeding Programs ◽  
Persian Walnut ◽  
Germplasm Collections ◽  
Pair Group ◽  
Shared Alleles ◽  
Simple Sequence

One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 14 loci were selected to analyze a diverse group of 47 persian walnut accessions and one J. hindsii (Jepson) Jepson ex R.E. Sm × J. regia hybrid (Paradox) rootstock. Among the 48 accessions, there were 44 unique multi-locus profiles; the accessions with identical profiles appeared to be synonyms. The pairwise genetic distance based on proportion of shared alleles was calculated for all accessions and a UPGMA (unweighted pair group method with arithmetic mean) dendrogram constructed. The results agree well with what is known about the pedigree and/or origins of the genotypes. The SSR markers distinguished pairs of closely related cultivars and should be able to uniquely characterize all walnut cultivars with the exception of budsports. They provide a more powerful and reliable system for the molecular characterization of walnut germplasm than those previously tested. These markers have numerous applications for the walnut industry, including cultivar identification, verification of pedigrees for cultivar and rootstock breeding programs, paternity analysis, and understanding the genetic diversity of germplasm collections.

scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Evaluation of Olives Cultivated in Southern Italy by Simple Sequence Repeat Markers

HortScience ◽  
2009 ◽  
Vol 44 (3) ◽  
pp. 582-588 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Francesca Stefanizzi ◽  
Enzo Perri
Keyword(s):  
Mediterranean Basin ◽  
Clustering Algorithm ◽  
Southern Italy ◽  
Ex Situ ◽  
Group Method ◽  
Breeding Programs ◽  
Olive Cultivars ◽  
The Mediterranean ◽  
Simple Sequence ◽  
The Mediterranean Basin

Olive (Olea europaea L.) is a species of great economic importance in the Mediterranean basin. Italy is very important for the olive industry; in fact, olive's genetic patrimony is very rich and characterized by an abundance of cultivars. At present, the majority of ancient landraces are vegetatively propagated by farm. It is likely that the number of cultivars is underestimated because of inadequate information on minor local cultivars that are widespread in different olive-growing areas. The existence of many cultivars reinforces the need for a reliable identification method. It is important to improve the ex situ plant germplasm collection and fairly to characterize all cultivars for future breeding programs. In the present report, we used 11 loci microsatellites to characterize 211 olive cultivars of an olive collection cultivated in six regions of southern Italy. These regions represent the major area for olive cultivation in Italy and have a strategic geographical location in the Mediterranean basin. The dendrogram obtained, using the unweighted pair group method with arithmetic mean clustering algorithm, depicts the pattern of relationships between the studied cultivars. There is a clear structuring of the variability relative to the geographic origin of olive cultivars. This work, for the very high number of the Italian olive cultivars analyzed, highlights the degree and distribution of genetic diversity of this species for better exploitation of olive resources and for the design of plant breeding programs. Besides, the use of molecular markers, like simple sequence repeats, is imperative to build a database for cultivar analysis, for traceability of processed food, and for appropriate management of olive germplasm collections.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

scholarly journals SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Agronomy ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 449 ◽  
Author(s):  
Jiantao Wu ◽  
Qinnan Wang ◽  
Jing Xie ◽  
Yong-Bao Pan ◽  
Feng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Capillary Electrophoresis ◽  
Population Structure ◽  
Ssr Markers ◽  
High Performance ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Parental Lines ◽  
Assisted Management ◽  
High Performance Capillary Electrophoresis

Sugarcane (Saccharum spp. hybrids) is an important sugar and bioenergy crop with a high aneuploidy, complex genomes and extreme heterozygosity. A good understanding of genetic diversity and population structure among sugarcane parental lines is a prerequisite for sugarcane improvement through breeding. In order to understand genetic characteristics of parental lines used in sugarcane breeding programs in China, 150 of the most popular accessions were analyzed with 21 fluorescence-labeled simple sequence repeats (SSR) markers and high-performance capillary electrophoresis (HPCE). A total of 226 SSR alleles of high-resolution capacity were identified. Among the series obtained from different origins, the YC-series, which contained eight unique alleles, had the highest genetic diversity. Based on the population structure analysis, the principal coordinate analysis (PCoA) and phylogenetic analysis, the 150 accessions were clustered into two distinct sub-populations (Pop1 and Pop2). Pop1 contained the majority of clones introduced to China (including 28/29 CP-series accessions) while accessions native to China clustered in Pop2. The analysis of molecular variance (AMOVA), fixation index (Fst) value and gene flow (Nm) value all indicated the very low genetic differentiation between the two groups. This study illustrated that fluorescence-labeled SSR markers combined with high-performance capillary electrophoresis (HPCE) could be a very useful tool for genotyping of the polyploidy sugarcane. The results provided valuable information for sugarcane breeders to better manage the parental germplasm, choose the best parents to cross, and produce the best progeny to evaluate and select for new cultivar(s).

scholarly journals Molecular Characterization of 12 Mango Germplasm Using RAPD markers

2010 ◽  
Vol 20 (1) ◽  
pp. 91-99
Author(s):  
R. C. Jena ◽  
K. C. Samal ◽  
P. K. Chand ◽  
B. K. Das
Keyword(s):  
Molecular Characterization ◽  
Rapd Markers ◽  
Mangifera Indica ◽  
Pcr Amplification ◽  
Similarity Coefficient ◽  
Group Method ◽  
Base Pairs ◽  
Relationship Analysis ◽  
Pair Group

Randomly amplified polymorphic DNA (RAPD) markers were used for the genetic variation and relationship analysis among 12 Mango (Mangifera indica L.) germplasm. Five oligonucleotide primers were employed to amplify DNA from 12 cultivars. PCR amplification with five primers generated 45 reproducible, clear and distinct bands, out of which 41 bands are considered polymorphic and the remaining four fragments (8.88%)  monomorphic. The size of amplified product ranged from 200 (RPI-5) to 3000 base pairs (RPI-1) with an average of nine bands per primer. The average polymorphism in all the 12 cultivars using the five primers was found to be 91.91%. Among all the primers RPI-2 and RPI-4 have shown 100% polymorphism while RPI-5 was found to be least polymorphism (81.81%). One specific band, namely was found with RPI-5, in a particular variety, Chiratpuri. The UPGMA (Unweighted Pair Group Method of Arithmetic Mean) dendrogram based on Jaccard’s similarity coefficient segregated the 12 mango germplasm into two clusters. Langra, Chiratpuri, Pravasankar, Alphanso, Sindhu and Kesar formed one cluster and rest six mango germplasm grouped together into another cluster. Sindhu and Alphanso cultivar pair was very close to each other with highest similarity coefficient (0.78), which was comparatively higher than all other cultivar pairs. On the other hand, Pravasankar and Neelam cultivar pair was more distinct to each other with the lowest intervarietal similarity coefficient 0.38. This study showed clearly that cultivars from Orissa unveiled maximum diversity and indicated the potential of RAPD markers for the identification of management of mango germplasm for breeding purposes.  Key words: Molecular characterization, Mango germplasm, Dversity  D.O.I. 10.3329/ptcb.v20i1.5972 Plant Tissue Cult. & Biotech. 20(1): 91-99, 2010 (June)

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