Genetic diversity, population structure and linkage disequilibrium analysis in the endangered TunisianPancratium maritimumLinnaeus (Amaryllidaceae) populations

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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Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

Plant Disease ◽

10.1094/pdis-12-20-2679-re ◽

2021 ◽

Author(s):

Yeirme Jaimes ◽

Carolina Gonzalez ◽

Jairo Rojas ◽

Jessica Johana Rivera ◽

Christian Cilas ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Geographic Origin ◽

Genetic Change ◽

Linkage Disequilibrium Analysis ◽

Host Genotype ◽

Dispersal Patterns ◽

Moniliophthora Perniciosa ◽

Analysis Of Molecular Variance ◽

Molecular Variance

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

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Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing

OMICS A Journal of Integrative Biology ◽

10.1089/omi.2021.0159 ◽

2021 ◽

Author(s):

Muliyar Krishna Rajesh ◽

Sunil Shivaji Gangurde ◽

Manish Kumar Pandey ◽

Vittal Niral ◽

Raju Sudha ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Genotyping By Sequencing

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Genetic Diversity, Linkage Disequilibrium and Population Structure of Bulgarian Bread Wheat Assessed by Genome-Wide Distributed SNP Markers: From Old Germplasm to Semi-Dwarf Cultivars

Plants ◽

10.3390/plants10061116 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1116

Author(s):

Vladimir Aleksandrov ◽

Tania Kartseva ◽

Ahmad M. Alqudah ◽

Konstantina Kocheva ◽

Krasimira Tasheva ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Bread Wheat ◽

Clustering Algorithm ◽

Agronomic Traits ◽

Gene Diversity ◽

Geographic Region ◽

Snp Markers ◽

Genetic Diversity And Structure

Genetic diversity and population structure are key resources for breeding purposes and genetic studies of important agronomic traits in crops. In this study, we described SNP-based genetic diversity, linkage disequilibrium and population structure in a panel of 179 bread wheat advanced cultivars and old accessions from Bulgaria, using an optimized wheat 25K Infinium iSelect array. Out of 19,019 polymorphic SNPs, 17,968 had а known chromosome position on the A (41%), B (42%) and D (11%) genome, and 6% were not assigned to any chromosome. Homoeologous group 4, in particular chromosome 4D, was the least polymorphic. In the total population, the Nei’s gene diversity was within the range 0.1-0.5, and the polymorphism information content ranged from 0.1 to 0.4. Significant differences between the old and modern collections were revealed with respect to the linkage disequilibrium (LD): the average values for LD (r2), the percentage of the locus pairs in LD and the LD decay were 0.64, 16% and 3.3 for the old germplasm, and 0.43, 30% and 4.1 for the modern releases, respectively. Structure and k-means clustering algorithm divided the panel into three groups. The old accessions formed a distinct subpopulation. The cluster analysis further distinguished the modern releases according to the geographic region and genealogy. Gene exchange was evidenced mainly between the subpopulations of contemporary cultivars. The achieved understanding of the genetic diversity and structure of the Bulgarian wheat population and distinctiveness of the old germplasm could be of interest for breeders developing cultivars with improved characteristics. The obtained knowledge about SNP informativeness and the LD estimation are worthwhile for selecting markers and for considering the composition of a population in association mapping studies of traits of interest.

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