Population structure of two ecologically distinct forms of ninespine stickleback, Pungitius pungitius: gene flow regimes and genetic diversity based on mtDNA sequence variations

2003 ◽  
Vol 60 (4) ◽  
pp. 421-432 ◽  
Author(s):  
Hiroshi Takahashi ◽  
Tetsuya Tsuruta ◽  
Akira Goto
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brackish Water ◽  
Gene Pools ◽  
Water Type ◽  
Pungitius Pungitius ◽  
Ninespine Stickleback ◽  
Sequence Variations ◽  
Mtdna Sequence ◽  
Mtdna Lineages

The population structure and its effect on genetic diversity were investigated in two ecologically distinct forms (fresh- and brackish-water types) of ninespine stickleback (Pungitius pungitius L.), which coexist on the coast of eastern Hokkaido, Japan. Obvious population subdivision (φST = 0.102 to 0.668) between freshwater systems in the freshwater type compared with that in the brackish-water type (φST = <0 to 0.078) was revealed on the basis of mitochondrial DNA (mtDNA) control region sequence variations. Results of the nested clade analysis suggested that the geographic distribution patterns of mtDNA lineages were mainly due to the contemporary population structure, rather than population histories. Although local populations were sampled from a similar geographic range for the two types, gene and nucleotide diversities of the freshwater type were significantly greater (0.94 and 0.016) than those of the brackish-water type (0.55 and 0.003). The increment of genetic diversity should be attributable to the obvious population structure and existence of divergent mtDNA lineages in the former, which clearly increased the effective population size of a subdivided population. Although these two forms maintain distinct gene pools, small sequence differences among mtDNA haplotypes obtained from each type suggested that mtDNA introgression has occurred between them.

Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites

2011 ◽  
Vol 9 (01) ◽  
pp. 86-96 ◽  
Author(s):  
Lucy M. Díaz ◽  
Héctor F. Buendía ◽  
Myriam C. Duque ◽  
Matthew W. Blair
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Common Bean ◽  
Gene Pool ◽  
Major Gene ◽  
Gene Pools ◽  
Silver Stain ◽  
Fluorescent Marker ◽  
Fluorescent Markers

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgarisL.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescentversusnon-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

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 On genetic diversity in caraway: Genotyping of a large germplasm collection

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244666
Author(s):  
Daniel von Maydell ◽  
Heike Lehnert ◽  
Thomas Berner ◽  
Evelyn Klocke ◽  
Wolfram Junghanns ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Size ◽  
Phylogenetic Trees ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
History Of ◽  
Winter Annual ◽  
Neighbor Network

Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted material are necessary. Analysis of genetic diversity can accompany this process, for instance, by revealing untapped gene pools. Here, we analyzed 137 accessions using genotyping by sequencing (GBS). Hence, we can report a broad overview of population structure and genetic diversity of caraway. Population structure was determined using a principal coordinate analysis, a Bayesian clustering analysis, phylogenetic trees and a neighbor network based on 13,155 SNPs. Genotypic data indicate a clear separation of accessions into two subpopulations, which correlates with the flowering type (annual vs. biennial). Four winter-annual accessions were closer related to biennial accessions. In an analysis of molecular variance, genetic variation between the two subpopulations was 7.84%. In addition, we estimated the genome size for 35 accessions by flow cytometry. An average genome size of 4.282 pg/2C (± 0.0096 S.E.) was estimated. Therefore, we suggest a significantly smaller genome size than stated in literature.

scholarly journals The Genetic Structure of WildOrobanche cumanaWallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Rocío Pineda-Martos ◽  
Antonio J. Pujadas-Salvà ◽  
José M. Fernández-Martínez ◽  
Kiril Stoyanov ◽  
Leonardo Velasco ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Wild Species ◽  
Resistance Mechanisms ◽  
Wild Plants ◽  
Gene Pools ◽  
Wild Populations ◽  
Fresh Tissue ◽  
Main Gene ◽  
South Eastern Europe

Orobanche cumanais a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower ofO. cumanapopulations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eightO. cumanapopulations and mature seeds of four of them were collectedin situon wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed thatO. cumanapopulations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

scholarly journals Genetic diversity and population structure of breeds of Askanian sheep by analysing polymorphisms in qualitative trait loci

2020 ◽  
Vol 7 (1) ◽  
pp. 3-13
Author(s):  
V. Iovenko ◽  
Yu. Vdovychenko ◽  
N. Pysarenko ◽  
K. Skrepets ◽  
I. Hladii
Keyword(s):  
Genetic Diversity ◽  
Growth Hormone ◽  
Population Structure ◽  
Genetic Structure ◽  
The Body ◽  
Gene Pools ◽  
Qualitative Trait ◽  
Homozygous Genotype ◽  
Meat Productivity ◽  
Genotype A

Aim. To determine the level of polymorphism of some genes, pertaining to the quantitative traits of sheep and to study the genetic diversity and population structure of breeds of Askanian sheep and one of its hybrids. Methods. Molecular–genetic, population–statistical, biometric methods. Results. The genetic structure of populations of the Askanian Fine-Fleeced (AFF, n = 33), Askanian Meat-and-Wool (AMW, n = 22) and Askanian Karakul (AK, n = 46) breeds and a hybrid of Askanian Fine-Fleeced × Texel (AFFT, n = 40) has been studied for the fi rst time in terms of the polymorphisms of the following qualitative trait genes (loci) : meat productivity genes: ovine growth hormone (GH), calpastatin (CAST) and myostatin (MSTN); prolifi cacy genes: Booroola (fecundity gene FecB) and bone morphogenetic protein (BMP15). The sheep in all studied breeds and the hybrid mentioned above are characterized by the polymorphism of two loci, GH and CAST. The other three loci studied did not show polymorphism for the markers studied. GH is present as two genotypes (A/A, A/B), and CAST as three genotypes (A/A, A/B, B/B). The remaining genes were found to be in the monomorphic state. The frequencies of certain genotypes and alleles change in the direction from fi ne–fl eeced to meat animals. For instance, the concentration of heterozygous growth hormone (GH) genotype A/B increases from 0.0 % (AFFB) to 38.2 % (AMWB), and the concentration of allele A – from 0.083 to 0.191. The live bodyweight of fi ne–fl eeced lambs with GH genotype A/B at birth equaled 4.5 kg, and those with homozygous genotype A/A – 4.9 kg (P < 0.001). Therefore, homozygous genotype А/А determined the increased level of meat productivity of sheep. A similar dependence was established at birth for the Askanian Karakul breed. Conclusions. The specifi city of genetic structure of Askanian breeds and hybrid is polymorphism of the GH and CAST and absence of polymorphism of BMP15 and FecB genes, determining the prolifi cacy (reproduction) trait. According to the distribution of polymorphic loci variants, the gene pools of Askanian Meat-and-Wool breed and the local Askanian-Texel hybrid are closely related and therefore explains the same direction of their productivity. At the same time, all populations are in a state of genetic equilibrium according to Hardy-Weinberg, which indicates a high level of their consolidation. Sheep which have the A/A homozygote of the gene growth hormone are characterized by an increased level of the body weight development.

scholarly journals Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1054
Author(s):  
Charles Nelimor ◽  
Baffour Badu-Apraku ◽  
Ana Luísa Garcia-Oliveira ◽  
Antonia Tetteh ◽  
Agre Paterne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Pool ◽  
Allelic Variation ◽  
Sub Saharan Africa ◽  
Genetic Enhancement ◽  
Gene Pools ◽  
International Institute ◽  
Improvement Program ◽  
Wide Range

Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

scholarly journals Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jessica Delfini ◽  
Vânia Moda-Cirino ◽  
José dos Santos Neto ◽  
Paulo Maurício Ruas ◽  
Gustavo César Sant’Ana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Pool ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Gene Pools ◽  
Genome Wide Association Studies ◽  
Mesoamerican Gene Pool ◽  
Diversity Panel

AbstractBrazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

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