scholarly journals Genetic Diversity and Population Structure of Plum Accessions from a Romanian Germplasm Collection Assessed by Simple Sequence Repeat (SSR) Markers

2018 ◽  
Vol 46 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Rodica POP ◽  
Monica HARTA ◽  
Katalin SZABO ◽  
Maria ZANESCU ◽  
Cristian Radu SISEA ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Three Dimensional ◽  
Germplasm Collection ◽  
Molecular Data ◽  
Conservation Strategies ◽  
Research Station ◽  
Correct Identification ◽  
International Reference ◽  
Breeding Programmes ◽  
Fruit Growing

In Romania, Prunus genetic resources are held in collections located mainly in research and development institutes or in fruit growing stations. A possible disadvantage of the utilization of these resources for genetic studies and also for breeding programmes is the lack of reliable data for correct identification and characterization of accessions. In this study, 27 plum accessions from Râmnicu-Vâlcea Fruit Research Station, Romania, were assessed using nine SSR markers generating a total of 134 distinct alleles, with an average of 14.89 alleles per locus. Differentiation between the Romanian plum cultivars and international reference cultivars was low, but significant, for all the nine loci (Fst = 0.012; P < 0.0001). Plum accessions were grouped in two clades, both including old and newly developed Romanian cultivars and also international reference cultivars, according to an UPGMA dendrogram. Bayesian analysis of genetic structure revealed significant admixture among examined accessions while principal coordinate analysis performed on the molecular data illustrated a substantial dispersion of old and newly developed Romanian plum accessions in the three-dimensional PCoA scatter plot. These results could make them attractive for future breeding programs and long-term conservation strategies based on identified genetic dissimilarities.

scholarly journals Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 656
Author(s):  
Evangelia Stavridou ◽  
Georgios Lagiotis ◽  
Parthena Kalaitzidou ◽  
Ioannis Grigoriadis ◽  
Irini Bosmali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Geographical Origin ◽  
Expressed Sequence Tag ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Dissimilarity Matrix ◽  
Heterotic Groups ◽  
Hrm Analysis ◽  
Sesame Genotypes

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

2005 ◽  
Vol 3 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Sally L. Dillon ◽  
Peter K. Lawrence ◽  
Robert J. Henry
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Diversity Indices ◽  
Basic Knowledge ◽  
Apparent Lack ◽  
Breeding Programmes ◽  
Diversity Studies ◽  
Potential Use ◽  
Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

scholarly journals Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)

2016 ◽  
Vol 7 (2) ◽  
pp. 76
Author(s):  
Dwinita Wikan Utami ◽  
Sutoro Sutoro ◽  
Nurul Hidayatun ◽  
Andari Risliawati ◽  
Ida Hanarida
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Heading Date ◽  
Germplasm Collection ◽  
Dna Fingerprint ◽  
Early Maturity ◽  
Plant Variety ◽  
Variety Protection ◽  
Genetic Analyzer

<p>Genetic Diversity of 96 Accession of Rice Germplasm<br />Using 30 SSR Markers Linked to Heading Date Genes (HD<br />Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun,<br />Andari Risliawati, and Ida Hanarida. Rice with early<br />maturity is one of an important genetic resources in rice<br />germplasm collection. Characterization and identification of<br />genetic diversity is an important issue for plant variety protection.<br />Molecular identification by microsatellite markers<br />using Genetic Analyzer enables resolve of this issue. The<br />objective of this research is to identify the genetic diversity of<br />96 rice accessions based on their specific DNA fingerprint<br />using microsatellite markers. A total of 96 accessions consisting<br />of a diverse variety of maturity classification were<br />genotyped with 30 SSR markers linked to HD genes which<br />spread out in 12 chromosomes of rice geneome. The total<br />297 alleles were detected indicated the level of marker<br />informativeness. RM5607 generated 7 allele with the size<br />range from 103 to 197 and the highest PIC at 0.90. RM3571<br />(linked to HD12 gene) has a significant value associated with<br />varieties which have early maturity trait. Clustering analysis<br />showed the cluster based on Sub Species genome background<br />and on early maturity trait.</p>

scholarly journals Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

2021 ◽  
Author(s):  
S. P. Jeevan Kumar ◽  
C. Susmita ◽  
K. V. Sripathy ◽  
Dinesh K. Agarwal ◽  
Govind Pal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Crop Yield ◽  
Gene Pool ◽  
Stress Factors ◽  
Soybean Cultivars ◽  
Genetic Base ◽  
Purity Analysis ◽  
Breeding Programmes

Abstract Background The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers. Methods and results A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean. Conclusion In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

scholarly journals Pigeonpea composite collection and identification of germplasm for use in crop improvement programmes

2011 ◽  
Vol 9 (01) ◽  
pp. 97-108 ◽  
Author(s):  
H. D. Upadhyaya ◽  
K. N. Reddy ◽  
Shivali Sharma ◽  
R. K. Varshney ◽  
R. Bhattacharjee ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Crop Improvement ◽  
Germplasm Collection ◽  
Sources Of Resistance ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Mini Core Collection ◽  
Breeding Programmes ◽  
Simple Sequence ◽  
High Seed Yield

Pigeonpea (Cajanus cajan(L.) Millsp. is one of the most important legume crops as major source for proteins, minerals and vitamins, in addition to its multiple uses as food, feed, fuel, soil enricher, or soil binder, and in fencing, roofing and basket making. ICRISAT's genebank conserves 13,632 accessions of pigeonpea. The extensive use of few parents in crop improvement is contrary to the purpose of collecting a large number of germplasm accessions and has resulted in a narrow base of cultivars. ICRISAT, in collaboration with the Generation Challenge Program, has developed a composite collection of pigeonpea consisting of 1000 accessions representing the diversity of the entire germplasm collection. This included 146 accessions of mini core collection and other materials. Genotyping of the composite collection using 20 microsatellite or simple sequence repeat (SSR) markers separated wild and cultivated types in two broad groups. A reference set comprising 300 most diverse accessions has been selected based on SSR genotyping data. Phenotyping of the composite collection for 16 quantitative and 16 qualitative traits resulted in the identification of promising diverse accessions for the four important agronomic traits: early flowering (96 accessions), high number of pods (28), high 100-seed weight (88) and high seed yield/plant (49). These accessions hold potential for their utilization in pigeonpea breeding programmes to develop improved cultivars with a broad genetic base. Pigeonpea germplasm has provided sources of resistance to abiotic and biotic stresses and cytoplasmic-male sterility for utilization in breeding programmes.

Relationships of walnut cultivars in a germplasm collection: Comparative analysis of phenotypic and molecular data

2013 ◽  
Vol 153 ◽  
pp. 124-135 ◽  
Author(s):  
Iulia Francesca Pop ◽  
Adina Cristina Vicol ◽  
Mihai Botu ◽  
Paul Andrei Raica ◽  
Kourosh Vahdati ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Germplasm Collection ◽  
Molecular Data

scholarly journals Identification and multi-environment validation of resistance to rust (Uromyces viciae-fabae) in Vicia faba

2017 ◽  
Vol 68 (11) ◽  
pp. 1013 ◽  
Author(s):  
Josefina C. Sillero ◽  
María M. Rojas-Molina ◽  
Amero A. Emeran ◽  
Mohamed Kharrat ◽  
Johanna Winkler ◽  
...  
Keyword(s):  
Vicia Faba ◽  
Phenotypic Expression ◽  
Germplasm Collection ◽  
Environment Interaction ◽  
Genotype Environment Interaction ◽  
Complete Resistance ◽  
Stability Of Resistance ◽  
Breeding Programmes ◽  
The Mediterranean ◽  
Efficiency Of Selection

A germplasm collection of 484 accessions of Vicia faba was screened for resistance to rust (Uromyces viciae-fabae) under field conditions. Accessions varied in the levels of rust infection, although no complete resistance was identified. Stability of resistance of the 39 most-resistant accessions was tested in a multi-location experiment in Austria, Egypt, Tunisia, United Kingdom and Spain over three additional field seasons. Genotype × environment interaction accounted for 43% of the sum of squares of the multi-environment evaluation, revealing instability of the phenotypic expression across environments. This might hamper the efficiency of selection suggesting the need for selection in different environments. Three possible mega-environments were discerned in the studied area, Mediterranean (Spain, Tunisia and Egypt), Oceanic (UK) and Continental (Austria). Córdoba (Spain) and Kafr El-Sheik (Egypt) showed as ideal environments for rust resistance screenings within Mediterranean environment. Several accessions (300, 303, 311, 313, 720, 1196 and 1271) were grouped as moderately to highly resistant in the three defined mega-environments. These accessions showed clear differences both in terms of reduced disease severity and high stability, which make them good candidates for international faba bean breeding programmes. Concerning each mega-environment, accessions 300 and 311 were the most resistant and stable ones across the Mediterranean one, followed by accessions 720, 1022, 1272, 1320 and BPL261. On the contrary other accessions (313, 452, 481 and 1196) were the most resistant in Oceanic and Continental environments. However, 452 and 481 were susceptible in the Mediterranean mega-environment. This contrasting performance across the environments was also supported by contradictory performance of the checks BPL261 and Baraca in Oceanic and Continental environments, suggesting differential virulence in rust populations, which deserves further attention.

scholarly journals Evidence of apple blotch resistance in wild apple germplasm (Malus spp.) accessions

2020 ◽  
Author(s):  
Thomas Wöhner ◽  
Ofere Francis Emeriewen ◽  
Monika Höfer
Keyword(s):  
Gene Pool ◽  
Field Survey ◽  
Recent Literature ◽  
Germplasm Collection ◽  
Economic Losses ◽  
Apple Breeding ◽  
High Interest ◽  
Breeding Programmes ◽  
Apple Cultivars ◽  
Inoculation Assay

AbstractDiplocarpon coronariae causes apple blotch, which results in significant economic losses. Resistance to apple blotch in commercial apple cultivars has not been reported in recent literature. The Malus germplasm collection from the Fruit Genebank of the Julius Kühn-Institut that is maintained in Dresden, Germany consists of 516 accessions of about 49 Malus species. This apple gene pool was evaluated for resistance to Diplocarpon coronariae. A four-year field survey was subsequently followed by artificial inoculation of field-selected accessions. Fifteen accessions that represent nine different species and hybrids were confirmed to be highly resistant following a repeated inoculation assay in the laboratory. The results from this investigation is of high interest to breeders for future apple breeding programmes and investigations of resistance to Diplocarpon coronariae.

scholarly journals Quantification of Extent, Density, and Status of Aquatic Reed Beds Using Point Clouds Derived from UAV–RGB Imagery

2018 ◽  
Vol 10 (12) ◽  
pp. 1869 ◽  
Author(s):  
Nicolás Corti Meneses ◽  
Florian Brunner ◽  
Simon Baier ◽  
Juergen Geist ◽  
Thomas Schneider
Keyword(s):  
Cross Sections ◽  
Vegetation Index ◽  
Low Cost ◽  
Three Dimensional ◽  
Field Measurements ◽  
Point Clouds ◽  
Conservation Strategies ◽  
Reed Beds ◽  
Combining Data ◽  
Reed Bed

Quantification of reed coverage and vegetation status is fundamental for monitoring and developing lake conservation strategies. The applicability of Unmanned Aerial Vehicles (UAV) three-dimensional data (point clouds) for status evaluation was investigated. This study focused on mapping extent, density, and vegetation status of aquatic reed beds. Point clouds were calculated with Structure from Motion (SfM) algorithms in aerial imagery recorded with Rotary Wing (RW) and Fixed Wing (FW) UAV. Extent was quantified by measuring the surface between frontline and shoreline. Density classification was based on point geometry (height and height variance) in point clouds. Spectral information per point was used for calculating a vegetation index and was used as indicator for vegetation vitality. Status was achieved by combining data on density, vitality, and frontline shape outputs. Field observations in areas of interest (AOI) and optical imagery were used for reference and validation purposes. A root mean square error (RMSE) of 1.58 m to 3.62 m for cross sections from field measurements and classification was achieved for extent map. The overall accuracy (OA) acquired for density classification was 88.6% (Kappa = 0.8). The OA for status classification of 83.3% (Kappa = 0.7) was reached by comparison with field measurements complemented by secondary Red, Green, Blue (RGB) data visual assessments. The research shows that complex transitional zones (water–vegetation–land) can be assessed and support the suitability of the applied method providing new strategies for monitoring aquatic reed bed using low-cost UAV imagery.

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