Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

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Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

Asian Fisheries Science ◽

10.33997/j.afs.2021.34.2.007 ◽

2021 ◽

Vol 34 (2) ◽

Author(s):

MUHAMMAD FORHAD ALI ◽

◽

MD. RAFIQUL ISLAM SARDER ◽

MOHAMMAD MATIUR RAHMAN ◽

MD. FAZLUL AWAL MOLLAH ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Genetic Difference ◽

Information Index ◽

Hardy Weinberg Equilibrium ◽

High Gene ◽

High Level ◽

Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

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Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

Legume Research - An International Journal ◽

10.18805/lr-358 ◽

2017 ◽

Cited By ~ 1

Author(s):

Shuying Yin ◽

Yanrong Wang ◽

Zhibiao Nan

Keyword(s):

United States ◽

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Polymorphic Information Content ◽

The United States ◽

Microsatellite Analysis ◽

Information Index ◽

Diversity Studies ◽

Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

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Genetic associations in the detection of QTLs for wheat spike-related traits

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000200007 ◽

2015 ◽

Vol 50 (2) ◽

pp. 149-159 ◽

Cited By ~ 1

Author(s):

Ljiljana Brbaklić ◽

Dragana Trkulja ◽

Ankica Kondić-Špika ◽

Nikola Hristov ◽

Srbislav Denčić ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linear Model ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Association Studies ◽

Mixed Linear Model ◽

General Linear ◽

Genetic Associations ◽

Trait Associations

The objective of this work was to assess the genetic diversity and population structure of wheat genotypes, to detect significant and stable genetic associations, as well as to evaluate the efficiency of statistical models to identify chromosome regions responsible for the expression of spike-related traits. Eight important spike characteristics were measured during five growing seasons in Serbia. A set of 30 microsatellite markers positioned near important agronomic loci was used to evaluate genetic diversity, resulting in a total of 349 alleles. The marker-trait associations were analyzed using the general linear and mixed linear models. The results obtained for number of allelic variants per locus (11.5), average polymorphic information content value (0.68), and average gene diversity (0.722) showed that the exceptional level of polymorphism in the genotypes is the main requirement for association studies. The population structure estimated by model-based clustering distributed the genotypes into six subpopulations according to log probability of data. Significant and stable associations were detected on chromosomes 1B, 2A, 2B, 2D, and 6D, which explained from 4.7 to 40.7% of total phenotypic variations. The general linear model identified a significantly larger number of marker-trait associations (192) than the mixed linear model (76). The mixed linear model identified nine markers associated to six traits.

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

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221036 ◽

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.

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Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-487 ◽

2019 ◽

Author(s):

Bouri Amina ◽

Mediouni Mohammed Rida ◽

Ameur Ameur Abdelkader ◽

Udupa Sripada ◽

Gaouar Souheil Bechir Semir

Keyword(s):

Genetic Diversity ◽

Information Content ◽

Cicer Arietinum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Geographic Origin ◽

Diversity Analysis ◽

Factorial Correspondence Analysis ◽

Genetic Diversity Analysis ◽

Cicer Arietinum L

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P less than 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

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Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China

Frontiers in Plant Science ◽

10.3389/fpls.2021.655254 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yusen Shen ◽

Jiansheng Wang ◽

Ranjan K. Shaw ◽

Huifang Yu ◽

Xiaoguang Sheng ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Brassica Oleracea ◽

Structure Analysis ◽

Genetic Relatedness ◽

Gene Diversity ◽

Principal Component ◽

Resolving Power ◽

Limited Information ◽

Large Collection

Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.

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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 within local and introduced cultivars of wheat (Triticum aestivum L.) grown under Mediterranean environment as revealed by AFLP markers

Acta Biologica Szegediensis ◽

10.14232/abs.2019.1.25-30 ◽

2019 ◽

Vol 63 (1) ◽

pp. 25-30

Author(s):

Mohammed Imad Eddin Arabi ◽

Amina Shoaib ◽

Eyad Al-Shehadah ◽

Mohammed Jawhar

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Principal Component ◽

Triticum Aestivum L ◽

Wheat Breeding ◽

Aflp Markers ◽

Group Method ◽

Wheat Cultivars ◽

Arithmetic Means

Information on genetic diversity among cultivars is critical in wheat improvement. In this work, heterogeneity within local and introduced cultivars of bread wheat grown in Syria was investigated using amplified fragment length polymorphism (AFLP) markers. The eight primer pairs were used to detect 177 polymorphic bands among the 21 cultivars resulting in an average of 22.13 (57.3%) polymorphic loci per primer pair. Major allelic frequency ranged from 0.50 to 0.75 with a mean 0.64, and estimated gene diversity was 0.45. Values of average polymorphic information content (PIC) for these markers were estimated to be 0.34. This low value might be attributed to the rigorous selection pressure aimed at cultivar purity and associated breeding practices. Dissimilarity values ranged from 0.32 to 0.66 with an average of 0.54, indicating that such techniques sample distinct genome regions. Three major subgroups of wheat cultivars were identified using the unweighted pair-group method with arithmetic means analysis (UPGMA), with all local cultivars falling into one cluster, which was confirmed by a principal component analysis (PCA). The narrow genetic diversity observed among Syrian wheat cultivars suggests the need of broadening the genetic base of wheat breeding materials, including local landraces.

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Genetic diversity in sorghum (Sorghum bicolor L. Moench) accessions using SNP based Kompetitive allele-specific (KASP) markers

Australian Journal of Crop Science ◽

10.21475/ajcs.21.15.06.p3088 ◽

2021 ◽

pp. 890-898

Author(s):

Thulo Sejake ◽

Nemera Shargie ◽

Riann Christian ◽

Assefa B. Amelework ◽

Toi J. Tsilo

Keyword(s):

Genetic Diversity ◽

Agricultural Research ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Population Analysis ◽

Geographic Origin ◽

Snp Analysis ◽

Germplasm Bank ◽

Allele Specific ◽

Kasp Markers

Genetic diversity analysis is an important component in conventional and marker-assisted breeding. The objective of this study was to assess the level of genetic diversity among 100 sorghum accessions, which were selected randomly from the Sorghum National Germplasm Bank maintained at Agricultural Research Council, South Africa. A total of 136 Kompetitive Allele-Specific PCR (KASP) markers were used in this study. The KASP markers were previously derived from single-nucleotide polymorphic (SNP) analysis of the world-wide sorghum accessions by other research groups. A total of 110 KASP markers were polymorphic and recorded an average polymorphic information content (PIC) value of 0.3, which indicated high level of discrimination of the markers. The markers had an average gene diversity and observed heterozygosity of 0.3 and 0.10, respectively. Analysis of molecular variance revealed a significantly high variation among accessions (83% and 89%) than within accessions (10% and 11%) based on breeding status and geographic origin, respectively. Genetic distance varied from 0.0 between SA0672 and SA0673, SA1282 and SA0670 to 0.57 between Hakika and SA1442 with an average mean of 0.30. The dendrogram and model-based population analysis identified three and four distinct groups in 95 sorghum accessions, respectively. These results imply the presence of genetic diversity and lack of genetic bottleneck within the National Sorghum Germplasm Bank, which could be highly relevant for sorghum breeding and germplasm maintenance

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Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank

Frontiers in Plant Science ◽

10.3389/fpls.2021.692463 ◽

2021 ◽

Vol 12 ◽

Author(s):

C. Backiyalakshmi ◽

Mani Vetriventhan ◽

Santosh Deshpande ◽

C. Babu ◽

V. Allan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Finger Millet ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Shannon Index ◽

Snp Markers ◽

Full Potential ◽

Average Genetic Distance

Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.

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