scholarly journals Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kassa Semagn ◽  
Muhammad Iqbal ◽  
Nikolaos Alachiotis ◽  
Amidou N’Diaye ◽  
Curtis Pozniak ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Spring Wheat ◽  
Snp Array ◽  
Categorical Variables ◽  
Selective Sweeps ◽  
Wheat Cultivars ◽  
Breeding Programs ◽  
The Impact

AbstractPrevious molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future 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 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 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 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 Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

scholarly journals Dynamic genetic diversity and population structure of Coreius guichenoti

ZooKeys ◽  
2021 ◽  
Vol 1055 ◽  
pp. 135-148
Author(s):  
Dongqi Liu ◽  
Feng Lan ◽  
Sicai Xie ◽  
Yi Diao ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Yangtze River ◽  
Fish Passage ◽  
The Yangtze River ◽  
Artificial Breeding ◽  
Significant Difference ◽  
High Elevations

To investigate the genetic effects on the population of Coreius guichenoti of dam constructions in the upper reaches of the Yangtze River, we analyzed the genetic diversity and population structure of 12 populations collected in 2009 and 2019 using mitochondrial DNA (mtDNA) control regions. There was no significant difference in genetic diversity between 2009 and 2019 (P &gt; 0.05), but the population structure tended to become stronger. Genetic differentiation (FST) among five populations (LX, BB, YB, SF and JA) collected in 2009 was not significant (P &gt; 0.05). However, some populations collected in 2019 were significantly differentiated (P &lt; 0.05), indicating that the population structure has undergone change. A correlation analysis showed that the genetic diversity of the seven populations collected in 2019 was significantly negatively correlated with geographical height (r = −0.808, P = 0.028), indicating that the populations at high elevations were more vulnerable than those at low elevations. In order to prevent the further decrease of genetic diversity and population resources, some conservation and restoration suggestions, such as fish passage and artificial breeding, are put forward.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

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).

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