scholarly journals Low level of genetic variation within Melica transsilvanica populations from the Kraków-Częstochowa Upland and the Pieniny Mts revealed by AFLPs analysis

2011 ◽  
Vol 76 (4) ◽  
pp. 321-331 ◽  
Author(s):  
Magdalena Szczepaniak ◽  
Elżbieta Cieślak
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Breeding System ◽  
Genetic Relationships ◽  
Gene Pools ◽  
Closely Related Species ◽  
Low Level ◽  
Fragmented Distribution ◽  
Hierarchical Amova ◽  
Continuous Range

Fragmented distribution, the breeding system and effects of genetic drift in small-size populations occurring at edge of the species range play an important role in shaping genetic diversity of such a species. <em>Melica transsilvanica</em> is a plant rare in the flora of Poland, where it reaches the northern limit of its continuous range. Amplified Fragment Length Polymorphism (AFLP) DNA profiling method was applied to measure genetic diversity among and within populations of <em>M. transsilvanica</em>. Additionally, genetic relationships between M. transsilvanica and Melica ciliata, two closely related species, were explored. A total of 68 plants from 7 populations of <em>M. transsilvanica</em> and 24 plants from 2 populations of <em>M. ciliata</em>, collected in Poland and outside it, were analyzed. Using 294 AFLP fragments from 3 primer combinations, accessions were grouped into two major clusters associating with <em>M. ciliata</em> and <em>M. transsilvanica</em>, respectively. Further, two subclusters, corresponding to the samples collected from the Pieniny Mts and from the Kraków - Częstochowa Upland were clearly distinguished within the <em>M. transsilvanica</em> group. The hierarchical AMOVA exhibited significant genetic distinction between these geographic regions (60.89%, p &lt; 0.001). The obtained results showed that the most genetic diversity resided between the populations of <em>M. transsilvanica</em> (86.03%) while considerably lower genetic variation was found within the populations (13.97%), which is consistent with the results reported for self-plants. The low level of AFLP genetic variation of <em>M. transsilvanica</em> can be caused by the geographic isolation of populations, which preserves the dominant self-mating breeding system of the species. Individual populations of <em>M. transsilvanica</em> are characterized by isolated gene pools differing by a small number of loci.

Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey

2021 ◽  
Vol 34 ◽  
pp. 3
Author(s):  
Yılmaz Çiftci ◽  
Oğuzhan Eroğlu ◽  
Şirin Firidin ◽  
Hacı Savaş ◽  
Yusuf Bektaş
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Relationships ◽  
Significance Test ◽  
Management Plan ◽  
Lake Van ◽  
Essential Information ◽  
Low Level ◽  
Lake Van Basin ◽  
Sustainable Fishery

In this study, the genetic relationships of 804 tarek (Alburnus tarichi) samples from a total of 18 populations, including the potamodromus and resident individuals from Lake Van basin in eastern Turkey, were studied by using nine microsatellite loci. A total of 93 alleles was detected, and the average number of alleles per locus was 10.3 ± 3.39. The mean estimated observed and expected heterozygosity were 0.340 ± 0.016 and 0.362 ± 0.015, respectively, which indicated a low level of polymorphism. After Bonferroni correction (P < 0.0027), the multi-locus test applied to each population revealed that 12 out of 18 populations were in Hardy-Weinberg equilibrium (HWE) (P = 0.0120–0.9981). Analysis of molecular variance (AMOVA) showed more than 76% genetic variability within individuals and 19% among populations, which was significantly higher than zero (FST = 0.19), and furthermore, a low level of genetic variation was observed among individuals within populations (4.84%: FIS = 0.06). Bayesian clustering analysis indicated that the total genetic variation grouped into 3 clusters. Additionally, the significance test results revealed that 11 of the 18 populations are threatened with extinction due to recent bottleneck events.We conclude that the tarek populations from the Lake Van basin can be classified into distinct genetic groups, based on microsatellite information. In addition, our results provide essential information for the development of a management plan that conserves the tarek's genetic diversity and achieves a sustainable fishery.

scholarly journals Genetic diversity of Carica papaya as revealed by AFLP markers

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 503-512 ◽  
Author(s):  
M S Kim ◽  
P H Moore ◽  
F Zee ◽  
M MM Fitch ◽  
D L Steiger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Related Species ◽  
Genetic Similarity ◽  
Carica Papaya ◽  
Genetic Relationships ◽  
Aflp Markers ◽  
Gene Pools ◽  
Breeding Lines ◽  
Similar Gene

Genetic relationships among Carica papaya cultivars, breeding lines, unimproved germplasm, and related species were established using amplified fragment length polymorphism (AFLP) markers. Seventy-one papaya accessions and related species were analyzed with nine EcoRI–MseI primer combinations. A total of 186 informative AFLP markers was generated and analyzed. Cluster analysis suggested limited genetic variation in papaya, with an average genetic similarity among 63 papaya accessions of 0.880. Genetic diversity among cultivars derived from the same or similar gene pools was smaller, such as Hawaiian Solo hermaphrodite cultivars and Australian dioecious cultivars with genetic similarity at 0.921 and 0.912, respectively. The results indicated that self-pollinated hermaphrodite cultivars were as variable as open-pollinated dioecious cultivars. Genetic diversity between C. papaya and six other Carica species was also evaluated. Carica papaya shared the least genetic similarity with these species, with an average genetic similarity of 0.432; the average genetic similarity among the six other species was 0.729. The results from AFLP markers provided detailed estimates of the genetic variation within and among papaya cultivars, and supported the notion that C. papaya diverged from the rest of Carica species early in the evolution of this genus.Key words: DNA fingerprinting, germplasm, genetic relationship, molecular phylogeny, polymorphism.

scholarly journals Genetic diversity in sugar apple (Annona squamosa L.) by using RAPD markers

Revista CERES ◽  
2013 ◽  
Vol 60 (3) ◽  
pp. 428-431 ◽  
Author(s):  
João Filipi Rodrigues Guimarães ◽  
Silvia Nietsche ◽  
Márcia Regina Costa ◽  
Glaucia Bethania Rocha Moreira ◽  
Marlon Cristian Toledo Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Rapd Markers ◽  
Geographical Origin ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Annona Squamosa ◽  
Low Level ◽  
Molecular Grouping

Genetic diversity in a collection of 64 sugar apple accessions collected from different municipalities in northern Minas Gerais was assessed by RAPD analysis. Using 20 selected RAPD primers 167 fragments were generated, of which 48 were polymorphic (28.7%) producing an average of 2.4 polymorphic fragments per primer. Low percentage of polymorphism (< 29%) was observed by using the set of primers indicating low level of genetic variation among the 64 accessions evaluated. Genetic relationships were estimated using Jaccard's coefficient of similarity. Accessions from different municipalities clustered together indicating no correlation between molecular grouping and geographical origin. The dendrogram revealed five clusters. The first cluster grouped C19 and G29 accessions collected from the municipalities of Verdelândia and Monte Azul, respectively. The second cluster grouped G16 and B11 accessions collected from the municipalities of Monte Azul and Coração de Jesus, respectively. The remaining accessions were grouped in three clusters, with 8, 15 and 37 accessions, respectively. In summary, RAPD showed a low percentage of polymorphism in the germplasm collection.

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals The Impact of Genetic Changes during Crop Domestication

Agronomy ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 119 ◽  
Author(s):  
Petr Smýkal ◽  
Matthew Nelson ◽  
Jens Berger ◽  
Eric Von Wettberg
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Pools ◽  
Human Society ◽  
Selective Sweeps ◽  
Crop Domestication ◽  
Effective Population ◽  
Evolutionary Trajectory ◽  
Nutrient Levels ◽  
The Impact

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Genetic diversity and morphological characteristics of native seashore paspalum in Indonesia

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Rahayu Rahayu ◽  
Fatimah Suwardjo ◽  
Ji Bae Eun ◽  
Geun Mo Yang ◽  
Soo Choi Joon
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Relationships ◽  
Morphological Characteristics ◽  
Warm Season ◽  
Morphological Characters ◽  
Seashore Paspalum ◽  
Turf Quality ◽  
Marker Cluster

Abstract. Rahayu, Fatimah, Bae EJ, Mo YG, Choi JS. 2020. Genetic diversity and morphological characteristics of native seashore paspalum in Indonesia. Biodiversitas 21: 4981-4989. Seashore paspalum (Paspalum vaginatum) is a warm-season turfgrass indigenous to tropical and coastal areas worldwide. The objectives of this study were to measure the genetic diversity and genetic variation of Indonesian seashore paspalum germplasm. Three turf quality, six morphological characters, and ten SSR (microsatellite) markers were used to assess genetic relationships and genetic variation among 22 germplasm resources from Indonesia and one commercial variety (Salam) from United States of America. The results showed significant variation for five morphological characters among 23 tested seashore paspalum accessions. The cluster analysis of morphological characters of 23 seashore paspalum accessions using 0,6 cut off divided into three morphological types: tall high-density, intermediate, and dwarf low-density ecotype. The genetic variation revealed 22 alleles with average number of alleles per locus was 2 and polymorphism information content (PIC) values average was 0.33. The microsatellite marker cluster analysis showed that 23 seashore paspalum accessions were grouped into two major groups, with a genetic similarity coefficient was 0,72. The low level of genetic diversity occurred among Indonesia natural grass germplasm and the genetic distance was relatively low between Indonesian germplasm and Salam variety. The genetic diversity and morphological characteristics will be useful for further study and utilization of Indonesian seashore paspalum germplasm.

scholarly journals Genetic diversity of three European Veratrum species revealed by Amplified Fragment Length Polymorphism

2017 ◽  
Vol 47 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Magdalena Szeliga ◽  
Joanna Ciura ◽  
Mirosław Tyrka
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Veratrum Album ◽  
Metabolic Properties

Abstract Chemical and genetic characterization of Veratrum species deposited in European collections is important for genepool preservation and identification of populations with desired metabolic properties. Veratrum album, V. lobelianum and V. nigrum are native to Europe, and in Poland are ranked as rare or threatened. Genetic variation of European Veratrum species was characterized by Amplified Fragment Length Polymorphism (AFLP) markers. The accumulation of jervine as a representative of steroidal alkaloids was measured in seeds. Distribution of 380 markers generated from eight primer combinations was useful for studying genetic relationships among and within species in the Veratrum genus and the most divergent populations were identified. Genetic variation between 12 populations of Veratrum species supports the classification of V. lobelianum as a subspecies of V. album. However, the results need further validation on extended material. A higher genetic diversity (22.3%) was observed between populations of V. nigrum as compared to V. album (14.5%). Contents of jervine allowed for discrimination of the studied Veratrum species and can be used as a potential chemotaxonomic marker. The highest jervine levels were found in V. album. V. nigrum seeds had only trace amounts and no jervine was detected in seeds of V. lobelianum.

scholarly journals Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243238
Author(s):  
Wilson Nkhata ◽  
Hussein Shimelis ◽  
Rob Melis ◽  
Rowland Chirwa ◽  
Tenyson Mzengeza ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Common Bean ◽  
Southern Africa ◽  
Crop Improvement ◽  
Phenotypic Expression ◽  
Snp Markers ◽  
High Yield ◽  
Gene Pools

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

scholarly journals Classification of Genus Acanthopanax in Korea and Genetic Diversity Using Allozymes

2005 ◽  
Vol 54 (1-6) ◽  
pp. 206-210 ◽  
Author(s):  
M. K. Huh ◽  
H. W. Huh
Keyword(s):  
Genetic Diversity ◽  
Representative Sample ◽  
Genetic Relationships ◽  
Woody Species ◽  
Small Population ◽  
Geographic Ranges ◽  
Low Level ◽  
Low Genetic Diversity ◽  
Population Sizes

Abstract Genus Acanthopanax is a long-lived woody species that is primarily distributed throughout Asia. Many species of this genus are regarded as medically and ecologically important. We evaluated a representative sample of the nine taxa with allozymes to estimate genetic relationships within the genus. As some Korean populations were isolated and patchily distributed, they exhibited a low level of genetic diversity. The narrow geographic ranges, artificial distribution of habitats, and small population sizes are proposed as factors contributing to low genetic diversity. Acanthopanax seoulense was similar to A. sessiliflorus, while a cluster of the A. rufinerve population is distant from any other species. A. senticosus is closely related to A. seoulense and A. sessiliflorus, whereas other species (A. koreanum) are more distinct from the Korean populations. Korean species are clustered together and clearly differentiated from the Chinese and Russian Acanthopanax taxa, genus Acanthopanax

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