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

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.

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

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00168-5 ◽

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.

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

Scientific Reports ◽

10.1038/s41598-020-75553-0 ◽

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.

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Microsatellite analysis to rationalize grape germplasm in India and development of a molecular database

Plant Genetic Resources ◽

10.1017/s1479262113000117 ◽

2013 ◽

Vol 11 (3) ◽

pp. 225-233 ◽

Cited By ~ 2

Author(s):

Anuradha Upadhyay ◽

Lalitkumar B. Aher ◽

Manisha P. Shinde ◽

Kavita Y. Mundankar ◽

Anuj Datre ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Data ◽

Computer Application ◽

Parental Genotype ◽

Application Software ◽

Microsatellite Data ◽

Population Structure Analysis ◽

Varietal Improvement ◽

User Friendly

Three hundred and seventeen grape accessions from the National Active Grape Germplasm Site in India were analysed with 25 microsatellite markers. A total of 411 alleles were detected, of which 42% were rare alleles. Unique alleles for 56 genotypes were also identified. The analysis of microsatellite data identified 63 duplicate accessions and only 254 accessions were unique genotypes. Several cases of misnomers, synonymy and homonymy were identified. Parental genotype for a few clonal selections was ascertained. Population structure analysis grouped 254 unique genotypes into four major clusters. The analysis also revealed the presence of admixtures with only 79% of pure ancestry. A core collection comprising 80 genotypes was identified, which represented all the alleles and genetic diversity. A user-friendly and interactive computer application software was developed for storage and the retrieval of molecular data. A molecular database for the 254 genotypes was created. This analysis will help in the rationalization and better management of germplasm. Information on genetic diversity and population structure will form the basis for varietal improvement programmes.

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

Genes ◽

10.3390/genes12081233 ◽

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.

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Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽

10.3390/agronomy11061121 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1121

Author(s):

Hela Chikh-Rouhou ◽

Najla Mezghani ◽

Sameh Mnasri ◽

Neila Mezghani ◽

Ana Garcés-Claver

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phenotypic Diversity ◽

Diversity Index ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Molecular Data ◽

Mantel Test ◽

Phenotypic Traits ◽

Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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Genetic diversity and population structure in caprifigs (Ficus carica var. caprificus) using SSR markers

Spanish Journal of Agricultural Research ◽

10.5424/sjar/2018163-11662 ◽

2018 ◽

Vol 16 (3) ◽

pp. e0703

Author(s):

Oguzhan Caliskan ◽

Safder Bayazit ◽

Muruvvet Ilgin ◽

Nesrin Karatas ◽

Ali Ergul

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Reference Group ◽

Molecular Data ◽

Ficus Carica ◽

Factorial Correspondence Analysis ◽

Breeding Programs ◽

Germplasm Resource ◽

Population Structure Analysis ◽

Great Genetic Diversity

Abundant wild and cultivated fig germplasm can be found in Turkey, a center of diversity for figs; however, many of these valuable genetic resources have not yet been identified or characterized using molecular markers. In the present study, microsatellite markers were used to characterize a set of 96 caprifig (Ficus carica var. caprificus) accessions from Turkey. The caprifig accessions showed considerable polymorphism with an average of 8.3 alleles per locus. The number of alleles per locus varied from three for the loci LMFC18 and LMFC23, to 14 for the loci FCUPO38-6 and FCUPO08. Genetic distance values and cluster analyses revealed high genetic similarities, except for the reference group, among the caprifig groups. Factorial correspondence analysis also separated the caprifig groups, suggesting that caprifig populations from Turkey were unmixed, probably because of low gene flow, likely because germplasm has not yet been moved among geographical areas and because many caprifig populations arose from propagation by seed. In our population structure analysis, the caprifig accessions could be grouped according to the regions from where they were sampled. Our molecular data revealed great genetic diversity within this caprifig germplasm. This genetically rich caprifig germplasm resource will be useful for both fig breeding programs and analysis of the complex genetic structure of figs that reproduce using various pollination strategies.

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

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00245-9 ◽

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.

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

10.1101/2021.05.17.444438 ◽

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.

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

Plant Omics ◽

10.21475/poj.13.01.20.p2085 ◽

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.

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