Population structure and genetic diversity in sweet cassava accessions from South of Brazil

Cassava (Manihot esculenta Crantz) is a crop of high socioeconomic importance for several tropical and subtropical regions of the world. It is mainly present in small cultivated areas that unintentionally guard a large part of the species' germplasm. The present work aimed to evaluate the population structure and genetic diversity of 156 traditional sweet cassava accessions from the Western of Paraná and Midwestern regions of Santa Catarina using 29 microsatellite molecular markers. All loci included were considered polymorphic, ranging from 3.00 to 7.00, with an average of 3.93 alleles per locus, and the average value of heterozygosity (Ho) was 0.6185. The polymorphism information content (PIC) presented an amplitude that varied from 0.4887 (GA134) to 0.7041 (GA131), with an average of 0.6130, while the genetic diversity ranged from 0.5688 (GA134) to 0.7424 (GA131), with an average of 0.6751. Analysis of the population structure based on the 29 microsatellite loci demonstrate that the accessions can be separated into two distinct subpopulations - in Santa Catarina and Paraná - with some mixtures observed according to Delta K = 2 groups. The ideal number of groups was found at K = 3, a level in which accessions from Santa Catarina were divided into two subpopulations and accessions from Paraná were grouped into a unique subpopulation. The genetic variability found among the traditional sweet cassava cultivars evaluated was considered wide, and the most dissimilar groups were mostly the accessions from Toledo and Santa Catarina states, constituting a source of genes for the sweet cassava breeding programs and for the development of new sweet cassava cultivars.

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Population Structure and Genetic Diversity in Sweet Cassava Accessions in Paraná and Santa Catarina, Brazil

Plant Molecular Biology Reporter ◽

10.1007/s11105-019-01175-0 ◽

2019 ◽

Vol 38 (1) ◽

pp. 25-38 ◽

Cited By ~ 1

Author(s):

Vanesca Priscila Camargo Rocha ◽

Maria Celeste Gonçalves-Vidigal ◽

Alex Henrique Tiene Ortiz ◽

Giseli Valentini ◽

Rebecca Caroline Ulbricht Ferreira ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Santa Catarina ◽

Sweet Cassava

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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

Scientific Reports ◽

10.1038/s41598-021-94802-4 ◽

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.

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

Brazilian Journal of Biology ◽

10.1590/1519-6984.226889 ◽

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.

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

BMC Genomics ◽

10.1186/s12864-021-08127-7 ◽

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.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids) Breeding Programs

Agronomy ◽

10.3390/agronomy9080449 ◽

2019 ◽

Vol 9 (8) ◽

pp. 449 ◽

Cited By ~ 3

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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Genetic diversity and population structure of Algerian chickpea (Cicer arietinum) genotypes: use of agro-morphological traits and molecular markers linked or not linked to the gene or QTL of interest

Crop and Pasture Science ◽

10.1071/cp19255 ◽

2020 ◽

Vol 71 (2) ◽

pp. 155

Author(s):

Djihad Bellemou ◽

Teresa Millàn ◽

Juan Gil ◽

Aissa Abdelguerfi ◽

Meriem Laouar

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Cicer Arietinum ◽

Morphological Traits ◽

Ascochyta Blight ◽

Principal Component ◽

Breeding Programs ◽

Average Value ◽

Conservation Of Genetic Resources ◽

Resistant Genotypes

Assessment of genetic diversity among chickpea (Cicer arietinum L.) germplasm at the morphological and molecular levels is fundamental for chickpea breeding and conservation of genetic resources. Genetic variability of 46 chickpea genotypes including 42 Algerian genotypes and four control varieties was evaluated by using 15 agro-morphological traits. Eleven molecular markers including nine simple sequence repeats, one sequence characterised amplified region (SCY17) and one gene-specific (CaETR4) were used to characterise the 46 genotypes and eight references varieties added for disease resistance or susceptibility. Genotypes resistant to ascochyta blight were identified by the markers SCY17 and CaETR4 present together. High diversity was observed for all measured morphological traits between genotypes. Yield components, plant height, phenological traits and growth habit were the traits most involved in variation among genotypes and were partitioned into four groups by using principal component analysis. All molecular markers were polymorphic. In total, 91 alleles were obtained ranging from 2 to 21 per locus with average of 8.27 alleles per marker. Polymorphism information content ranged from 0.58 to 0.99 with an average value of 0.87. UPGMA clustering and Bayesian-based model structure analysis grouped genotypes into two clusters, but the distribution of the genotypes by cluster was not the same for the two analyses. According to the presence of markers indicating resistance to ascochyta blight (SCY17 and CaETR4), three resistant genotypes (FLIP 82-C92, ILC 6909, ILC 7241) were selected and should be tested in controlled conditions for confirmation. Considering the narrow diversity of cultivated chickpea, the Algerian genotypes can be considered as interesting for future breeding programs.

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Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

Acta Agrobotanica ◽

10.5586/aa.7343 ◽

2020 ◽

Vol 73 (4) ◽

Author(s):

Salem Marzougui ◽

Mohamed Kharrat ◽

Mongi Ben Younes

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Hordeum Vulgare L ◽

Software Analysis ◽

Average Value ◽

Allele Number ◽

Cultivar Development ◽

Principal Coordinates ◽

Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (Hordeum vulgare L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

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Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes ◽

10.3390/genes10090676 ◽

2019 ◽

Vol 10 (9) ◽

pp. 676 ◽

Cited By ~ 3

Author(s):

Farahani ◽

Maleki ◽

Mehrabi ◽

Kanouni ◽

Scheben ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Large Scale ◽

Principal Component ◽

Snp Markers ◽

Genome Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Population Structure Analysis

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

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Repeatability of agronomic and morphological characteristics in ornamental pepper

Horticultura Brasileira ◽

10.1590/s0102-053620150000300012 ◽

2015 ◽

Vol 33 (3) ◽

pp. 352-355 ◽

Cited By ~ 1

Author(s):

Wellington S Ribeiro ◽

Lucas C Costa ◽

Fabíola S Dias ◽

Francisco CS Silva ◽

Cleide MF Pinto ◽

...

Keyword(s):

Significant Influence ◽

Calculation Method ◽

Morphological Characteristics ◽

Success Factor ◽

Repeatability Coefficient ◽

Breeding Programs ◽

Selection Processes ◽

Ideal Number ◽

Commercially Important ◽

The Ideal

Breeding programs seek to reduce the time spent assessing characteristics more times than necessary. However, this reduction should in no way undermine the representativeness and reliability of the information. Thus, an important success factor in breeding programs is the knowledge of the ideal number of assessments needed to evaluate commercially important characteristics in each species or population. In this context, this study aimed to determine the repeatability coefficient of eight biometric traits in four populations of ornamental pepper, seeking to increase the efficiency of evaluation and selection processes. There was no significant influence of the calculation method used over the estimate of the repeatability coefficient. The results indicated that five plants are necessary to assess plant height; leaf number, length and width; and fruit number, length and width in the ornamental pepper material we used with a determination coefficient of 90%.

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