scholarly journals Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Efficient Manner ◽  
Lilium Species ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

scholarly journals Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1233
Author(s):  
Alemayehu Teressa Negawo ◽  
Meki S. Muktar ◽  
Yilikal Assefa ◽  
Jean Hanson ◽  
Alieu M. Sartie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Snp Markers ◽  
Correction Coefficient ◽  
Rhodes Grass ◽  
Representative Subset ◽  
Population Structure Analysis ◽  
Chloris Gayana ◽  
Molecular Information

Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future.

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

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 676 ◽  
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.

scholarly journals Genetic diversity and population structure of sweet orange [Citrus sinensis (L.) Osbeck] germplasm of India revealed by SSR and InDel markers

2022 ◽  
Author(s):  
Prasanth Tej Kumar Jagannadham ◽  
Thirugnanavel Anbalagan ◽  
Devendra Y Upadhyay ◽  
Snehal A. Kamde ◽  
Prafulla R. Jalamkar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Citrus Sinensis ◽  
Sweet Orange ◽  
Polymorphic Information Content ◽  
Citrus Fruit ◽  
Molecular Data ◽  
Expected Heterozygosity ◽  
Indel Markers ◽  
Population Structure Analysis

Sweet orange (Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers, SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of a total number of alleles, a number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He), and the polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In both the cases, they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed the presence of two distinct subpopulations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through the intensive collection in the northeastern region. These results of intraspecific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

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

2019 ◽  
Author(s):  
Somayeh Farahani ◽  
Mojdeh Maleki ◽  
Rahim Mehrabi ◽  
Homayoun Kanouni ◽  
Reza Talebi
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 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 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 covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed 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. Un-weighted 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 suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated 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.

scholarly journals RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Karim Sorkheh ◽  
Mehrana Koohi Dehkordi ◽  
Sezai Ercisli ◽  
Attila Hegedus ◽  
Júlia Halász
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Inter Simple Sequence Repeat ◽  
High Genetic Diversity ◽  
Hrm Analysis ◽  
And Performance ◽  
Wild Almond ◽  
Simple Sequence

Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.

scholarly journals Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jedidah Wangari Mwangi ◽  
Oduor Richard Okoth ◽  
Muchemi Peterson Kariuki ◽  
Ngugi Mathew Piero
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Mung Bean ◽  
Phenotypic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Breeding Programs ◽  
Population Structure Analysis

Abstract Background Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. Results Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). Conclusion These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

scholarly journals Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1324
Author(s):  
Alimatu Sadia Osuman ◽  
Baffour Badu-Apraku ◽  
Beatrice E. Ifie ◽  
Pangirayi Tongoona ◽  
Ebenezer Obeng-Bio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Central Africa ◽  
Inbred Lines ◽  
Heterotic Groups ◽  
Maize Inbred Lines ◽  
Wide Range ◽  
Early Maturing ◽  
West And Central Africa

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa.

scholarly journals Genetic diversity and population structure of cowpea [Vigna unguiculata (L.) Walp.] accessions from Togo using SSR Markers

2021 ◽  
Author(s):  
Yao Dodzi Dagnon ◽  
Koffi Kibalou Palanga ◽  
Damigou Bammite ◽  
Ghislain Comlan AKABASSI ◽  
Koffi Tozo
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Vigna Unguiculata ◽  
Polymorphic Information Content ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Conservation Program ◽  
Population Structure Analysis

Cowpea [ Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional potential. I is very appreciate by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. Twenty-eight out of the thirty-two (32) primer pairs screened for polymorphism were polymorphic, and a total of 164 alleles were detected for the 28 loci with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.18 to 0.895, with an average value of 0.67. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 85% of genetic variation existed among individuals within regions. The fixation index (Fst) value, which was 0.018, was low, indicating relatively low population differentiation. The Togolese cowpea germplasm collection was grouped into four groups independently of theirs origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.

scholarly journals Plant parasitic nematodes occurrence and genetic diversity of banana cultivars grown in Tanzania

Plant Omics ◽  
2020 ◽  
pp. 21-29
Author(s):  
Doreen M. Mgonja ◽  
Gladness E. Temu ◽  
Sylvester L. Lyantagaye ◽  
Abdalah Makaranga ◽  
Joseph C. Ndunguru ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Nematode Species ◽  
High Yield ◽  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Ecological Zones ◽  
Population Structure Analysis ◽  
Plant Parasitic

The genetic diversity of bananas (Musa spp.), one of the most economically important crops in Tanzania, is underestimated with scarce reports available. In addition, cultivation of banana is severely constrained by plant parasitic nematodes (PPN). We assessed genetic diversity and population structure of 159 banana varieties from four agro-ecological zones (Northern, Southern highlands, Lake and Zanzibar islands) of Tanzania using 20 SSR markers analysed with UPGMA method. We also, assessed the PPN occurrence through isolation and counting of PPN from each banana genotype where leaf samples were collected. SSR primer pairs were polymorphic; and generated 63 distinct reproducible bands. The polymorphic information content values of each SSR marker ranged from 0.50 to 0.75 indicating high level of genetic diversity among banana varieties. The 159 banana varieties were grouped into two clusters: A and B, based on UPGMA cluster and population structure analysis. A total of 128 independent and 31 overlapping genotypes were identified. Higher kinship among genotypes was observed in cluster A compared with cluster B. Some of the clusters in A and B genotypes showed high genetic distance. The most prevalent and abundant nematode species was Pratylenchus goodeyi with a mean count of 63%, followed by Radopholus similis (31%) and P. coffeae (6%). The results from this study provides a foundation for understanding genetic variability of bananas existing in Tanzania and PPN occurrence that will be valuable information for breeding disease and pest-resistant bananas with high yield traits.

scholarly journals Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 88
Author(s):  
Alemayehu Teressa Negawo ◽  
Yilikal Assefa ◽  
Jean Hanson ◽  
Asebe Abdena ◽  
Meki S. Muktar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Core Collection ◽  
Reference Genome ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Soil Conditions ◽  
Cenchrus Ciliaris ◽  
Population Structure Analysis ◽  
Wide Range

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.

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