scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

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 Genetic Diversity and Population Structure Analysis of Dalbergia Odorifera Germplasm and Development of a Core Collection Using Microsatellite Markers

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 281 ◽  
Author(s):  
Fu-Mei Liu ◽  
Ning-Nan Zhang ◽  
Xiao-Jin Liu ◽  
Zeng-Jiang Yang ◽  
Hong-Yan Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Genetic Resources ◽  
Tree Species ◽  
Core Collection ◽  
Southern China ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Dalbergia Odorifera

Dalbergia odorifera T. Chen (Fabaceae) is a woody tree species indigenous to Hainan Island in China. Due to its high medicinal and commercial value, this tree species has been planted over 3500 ha2 in southern China. There is an urgent need for improvement of the D. odorifera germplasm, however, limited information on germplasm collection, conservation, and assessment of genetic resources is available. Therefore, we have built a database of 251 individuals collected across the whole of southern China, which included 42 wild trees and 210 cultivated trees, with the following objectives. (1) Evaluate genetic diversity and population structure of the database using 19 microsatellite markers and (2) develop a core collection for improvement and breeding programs. Totally, the 19 microsatellite markers harbored 77 alleles across the database with the polymorphic information content (PIC) ranging from 0.03 to 0.66. Medium genetic diversity level was inferred by Nei’s gene diversity (0.38), Shannon’s information index (0.65), and observed (0.33) and expected heterozygosity (0.38). Structure analysis showed that four was the optimum cluster size using the model-based Bayesian procedure, and the 251 D. odorifera individuals were grouped into five populations including four pure ones (RP1-4) and one mixed one (MIX) based on their maximum membership coefficients. Among these populations, the expected heterozygosity varied from 0.30 (RP3) to 0.38 (RP4). Analysis of molecular variance (AMOVA) showed 11% genetic variation existed among populations, and moderate population differentiation was inferred by the matrix of pairwise Fst (genetic differentiation among populations), which was in the range of 0.031 to 0.095. Moreover, a core collection of 31 D. odorifera individuals including six wild and 25 cultivated trees was developed, which was only 12.4% of the database but conserved the whole genetic diversity. The results of this study provided additional insight into the genetic structure of the large D. odorifera germplasm, and the core collection will be useful for the efficient and sustainable utilization of genetic resources, as well as efficient improvement in breeding programs.

scholarly journals Genetic Diversity and Population Structure of Chionanthus virginicus

2022 ◽  
Vol 147 (1) ◽  
pp. 62-69
Author(s):  
Phillip A. Wadl ◽  
Timothy A. Rinehart ◽  
Richard T. Olsen ◽  
Benjamin D. Waldo ◽  
Joseph H. Kirkbride
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Germplasm Collection ◽  
Eastern United States ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Tree Form ◽  
Wide Range

The genus Chionanthus, known as fringetrees, is a member of the olive family (Oleaceae). Chionanthus virginicus is an understory tree or shrub with a wide range in forests of the eastern United States and is used as an ornamental tree that is known to be free of insects and disease in the wild. The species is tolerant of a wide range of environmental conditions, and there is interest in developing new cultivars with improved horticultural traits, such as tree form or upright growth habit and superior flowering display that are widely adapted. To identify genepools in the native range of C. virginicus for use in breeding programs, the genetic diversity and population structure were assessed for 274 individuals from 12 locations in four states (Florida, Maryland, North Carolina, and Texas) using 26 simple sequence repeats (SSRs). An average of 12.54 alleles/locus were detected, allelic richness averaged 2.80. Genetic differentiation was 0.11, indicating moderate differentiation among subpopulations. Despite the high genetic diversity and low population differentiation, Bayesian clustering analysis identified six genetic groups that match the geographic distribution of collection sites. Analysis of molecular variance indicated that most (82%) of the variation is explained within individuals, and 11% and 7% of the variation is due to differences among individuals within populations and among populations. Analysis of isolation by distance across all samples showed a weak positive relationship between geographic distance and genetic distance. The C. virginicus samples analyzed in this study indicate there is sufficient diversity for germplasm collection for use in breeding programs. Given the relatively moderate genetic differentiation, there are not likely to be unique islands of genetic diversity that may be missed when gathering parental materials for a breeding program

scholarly journals Structure and genetic diversity of Theobroma speciosum (Malvaceae) and implications for Brazilian Amazon conservation

Rodriguésia ◽  
2021 ◽  
Vol 72 ◽  
Author(s):  
Juliana de Freitas Encinas Dardengo ◽  
Ana Aparecida Bandini Rossi ◽  
Luiz Orlando de Oliveira ◽  
Guilherme Ferreira Pena ◽  
Luiz Henrique Rivas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Molecular Genetic ◽  
Economic Value ◽  
Natural Populations ◽  
Brazilian Amazon ◽  
Fixation Index ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Refuge Area

Abstract The genetic diversity of Theobroma speciosum is important because its use in breeding programs, once the species is closely related to species of great economic value such as Theobroma cacao (cocoa) and Theobroma grandiflorum (cupuaçu). Thus, the objective of this work is to characterize the intra and interpopulational genetic diversity of Theobroma speciosum in natural populations in the Brazilian Amazon. Ninety individuals of T. speciosum from four populations localized in different states of legal Amazon were selected and genotyped. The data were obtained by fluorescence microsatellite analysis and the number of alleles, number of private alleles, fixation index, observed and expected heterozygosity were analyzed. Bayesian analysis, AMOVA and PCOa were used to reveal the molecular genetic structure of the populations, using the programs Structure and GenAIEx 6.5, respectively. All populations studied present great levels of gene diversity, although, there was a greater similarity among the AUR, API and MAC populations, while RBC population presented higher heterozygosity and less inbreeding than the others, becoming a possible refuge area in the Amazon, and the most important population for T. speciosum conservation.

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

2021 ◽  
Vol 12 ◽  
Author(s):  
◽  
Aline Fugeray-Scarbel ◽  
Catherine Bastien ◽  
Mathilde Dupont-Nivet ◽  
Stéphane Lemarié
Keyword(s):  
Genetic Diversity ◽  
Genomic Selection ◽  
Plant Species ◽  
Animal Species ◽  
Animal Breeding ◽  
Breeding Cycle ◽  
Breeding Programs ◽  
The Third ◽  
Wide Range ◽  
Selection For

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

scholarly journals Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

scholarly journals Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

2021 ◽  
Author(s):  
Kyle M Lewald ◽  
Antoine Abrieux ◽  
Derek A Wilson ◽  
Yoosook Lee ◽  
William R Conner ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Weather Conditions ◽  
The United States ◽  
Future Research ◽  
Drosophila Suzukii ◽  
Significant Damage ◽  
Wide Range ◽  
Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

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).

Patterns of allozyme variation within and among Douglas-fir breeding zones in southwest Oregon

1987 ◽  
Vol 17 (5) ◽  
pp. 402-407 ◽  
Author(s):  
S. A. Merkle ◽  
W. T. Adams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Frequency ◽  
Quantitative Traits ◽  
Allozyme Variation ◽  
Douglas Fir ◽  
Expected Heterozygosity ◽  
Breeding Zone ◽  
Southwest Oregon ◽  
Environmental Distance

Gametophytes from wind-pollinated seeds of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco var. menziesii) parent trees (mean 56) in each of 22 breeding zones in southwest Oregon were analyzed electrophoretically for gene frequency patterns at 27 loci. Allozyme variability levels were high, as shown by breeding-zone averages for the percentage of polymorphic loci (71.7%, 0.99 criterion), mean number of alleles per locus (2.46), and expected heterozygosity (0.178). Differences among zones in allele frequency were significant (p < 0.05) for only 2 of the 27 loci surveyed, and analysis of hierarchical population structure showed that less than 1% of genetic diversity was attributable to differences among breeding zones. Genetic distance between zones was small [Formula: see text] and, in general, bore no relation to geographical or environmental distance. The limited allozyme differentiation among zones contrasts strikingly with the environment-related variation in seedling quantitative traits previously reported for southwest Oregon Douglas-fir. Allozymes do not appear to be useful for mapping patterns of adaptive variation or for certifying Douglas-fir seed in this region.

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