Genetic Diversity and Differentiation of Eleven Medicago Species from Campania Region Revealed by Nuclear and Chloroplast Microsatellites Markers

The species belonging to the genus Medicago are considered a very important genetic resource at global level both for planet’s food security and for sustainable rangelands management. The checklist of the Italian flora (2021) includes a total number of 40 Medicago species for Italy, and 27 for Campania region, with a number of doubtful records or related to species no more found in the wild. In this study, 10 Medicago species native to Campania region, and one archaeophyte (M. sativa), identified by means of morphological diagnostic characters, were analyzed in a blind test to assay the efficacy of nine microsatellite markers (five cp-SSRs and four n-SSRs). A total number of 33 individuals from 6 locations were sampled and genotyped. All markers were polymorphic, 40 alleles were obtained with n-SSRs ranging from 8–12 alleles per locus with an average of 10 alleles per marker, PIC values ranged from 0.672 to 0.847, and the most polymorphic SSR was MTIC 564. The cp-SSRs markers were highly polymorphic too; PIC values ranged from 0.644 to 0.891 with an average of 0.776, the most polymorphic cp-SSR was CCMP10. 56 alleles were obtained with cp-SSRs ranging from 7 to 17 alleles per locus with an average of 11. AMOVA analysis with n-SSR markers highlighted a great level of genetic differentiation among the 11 species, with a statistically significant fixation index (FST). UPGMA clustering and Bayesian-based population structure analysis assigned these 11 species to two main clusters, but the distribution of species within clusters was not the same for the two analyses. In conclusion, our results demonstrated that the combination of the used SSRs well distinguished the 11 Medicago species. Moreover, our results demonstrated that the use of a limited number of SSRs might be considered for further genetic studies on other Medicago species.

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Variance additivity of genetic populational parameter estimates obtained through bootstrapping

Scientia Agricola ◽

10.1590/s0103-90162003000100015 ◽

2003 ◽

Vol 60 (1) ◽

pp. 97-103 ◽

Cited By ~ 1

Author(s):

Luciana Aparecida Carlini-Garcia ◽

Roland Vencovsky ◽

Alexandre Siqueira Guedes Coelho

Keyword(s):

Bootstrap Method ◽

Natural Populations ◽

Molecular Data ◽

Fixation Index ◽

Parameter Estimates ◽

Genetic Population ◽

Relative Contribution ◽

Population Structure Analysis ◽

Resampling Procedure ◽

Variance Estimates

Studying the genetic structure of natural populations is very important for conservation and use of the genetic variability available in nature. This research is related to genetic population structure analysis using real and simulated molecular data. To obtain variance estimates of pertinent parameters, the bootstrap resampling procedure was applied over different sampling units, namely: individuals within populations (I), populations (P), and individuals and populations simultaneously (I, P). The considered parameters were: the total fixation index (F or F IT), the fixation index within populations (f or F IS) and the divergence among populations or intrapopulation coancestry (theta or F ST). The aim of this research was to verify if the variance estimates of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">, found through the resampling over individuals and populations simultaneously (I, P), correspond to the sum of the respective variance estimates obtained from separated resampling over individuals and populations (I+P). This equivalence was verified in all cases, showing that the total variance estimate of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">can be obtained summing up the variances estimated for each source of variation separately. Results also showed that this facilitates the use of the bootstrap method on data with hierarchical structure and opens the possibility of obtaining the relative contribution of each source of variation to the total variation of estimated parameters.

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The Genetic Diversity and Structure of Tomato Landraces from the Campania Region (Southern Italy) Uncovers a Distinct Population Identity

Agronomy ◽

10.3390/agronomy11030564 ◽

2021 ◽

Vol 11 (3) ◽

pp. 564

Author(s):

Martina Caramante ◽

Youssef Rouphael ◽

Giandomenico Corrado

Keyword(s):

Genetic Diversity ◽

Southern Italy ◽

Molecular Profile ◽

Campania Region ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Conservation Actions ◽

Regional Population ◽

Regional Brand ◽

The Individual

Italy is one of the main producers and processors of tomato and it is considered a secondary center of diversity. In some areas, such as the Campania region (Southern Italy), a range of traditional tomato landraces is still cultivated. The distinction of this heritage germplasm is often based only on folk taxonomy and a more comprehensive definition and understanding of its genetic identity is needed. In this work, we compared a set of 15 local landraces (representative of traditional fruit types) to 15 widely used contemporary varieties, using 14 fluorescent Simple Sequence Repeat (SSR) markers. Each of the accessions possessed a unique molecular profile and overall landraces had a genetic diversity comparable to that of the contemporary varieties. The genetic diversity, multivariate, and population structure analysis separated all the genotypes according to the pre-defined groups, indicating a very reduced admixture and the presence of a differentiated (regional) population of landraces. Our work provides solid evidence for implementing conservation actions and paves the way for the creation of a premium regional brand that goes beyond the individual landrace names of the Campania region known throughout the world.

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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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Phylogeography and Antioxidant Activity of Proso Millet (Panicum miliaceum L.)

Plants ◽

10.3390/plants10102112 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2112

Author(s):

Xiaohan Wang ◽

Myung Chul Lee ◽

Yu-Mi Choi ◽

Seong-Hoon Kim ◽

Seahee Han ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Association Analysis ◽

Agronomic Traits ◽

Fixation Index ◽

Total Phenolic ◽

Panicum Miliaceum ◽

Proso Millet ◽

Population Structure Analysis

Proso millet (Panicum miliaceum L.) or broomcorn millet is among the most important food crops to be domesticated by humans; it is widely distributed in America, Europe, and Asia. In this study, we genotyped 578 accessions of P. miliaceum using 37 single-sequence repeat (SSR) markers, to study the genetic diversity and population structure of each accession. We also investigated total phenolic content (TPC) and superoxide dismutase (SOD) activity and performed association analysis using SSR markers. The results showed that genetic diversity and genetic distance were related to geographic location and the fixation index (Fst). Population structure analysis divided the population into three subpopulations. Based on 3 subpopulations, the population is divided into six clusters in consideration of geographical distribution characteristics and agronomic traits. Based on the genetic diversity, population structure, pairwise Fst, and gene flow analyses, we described the topological structure of the six proso millet subpopulations, and the geographic distribution and migration of each cluster. Comparison of the published cluster (cluster 1) with unique germplasms in Japan and South Korea suggested Turkey as a possible secondary center of origin and domestication (cluster 3) for the cluster. We also discovered a cluster domesticated in Nepal (cluster 6) that is adapted to high-latitude and high-altitude cultivation conditions. Differences in phenotypic characteristics, such as TPC, were observed between the clusters. The association analysis showed that TPC was associated with SSR-31, which explained 7.1% of the total variance, respectively. The development of markers associated with TPC and SOD will provide breeders with new tools to improve the quality of proso millet through marker-assisted selection.

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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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Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽

10.3390/plants9121643 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1643

Author(s):

Didas Kimaro ◽

Rob Melis ◽

Julia Sibiya ◽

Hussein Shimelis ◽

Admire Shayanowako

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Improvement ◽

Polymorphic Information Content ◽

Geographic Origin ◽

Germplasm Collection ◽

Fixation Index ◽

Population Structure Analysis ◽

The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

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Prevalence of Infection with Porcine Circovirus Types 2 and 3 in the Wild Boar Population in the Campania Region (Southern Italy)

Animals ◽

10.3390/ani11113215 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3215

Author(s):

Maria Grazia Amoroso ◽

Francesco Serra ◽

Claudia Esposito ◽

Nicola D’Alessio ◽

Gianmarco Ferrara ◽

...

Keyword(s):

Southern Italy ◽

Health Concern ◽

Porcine Circovirus ◽

Wild Boar Population ◽

Quantitative Real Time Pcr ◽

Hunting Season ◽

Campania Region ◽

Wild Boars ◽

In The Wild

In recent years, porcine circovirus (PCV) infection has been documented as an important and emerging health concern for livestock and wildlife worldwide. The purpose of the present study was to assess the molecular prevalence of PCV-2 and PCV-3 and to clarify the epidemiological role of wild boars in the circulation of this virus in Campania, Southern Italy. For this purpose, samples from several organs were collected during the hunting season 2017–2018 from 148 wild boars in the Campania region. Quantitative real-time PCR was used for the detection and quantification of PCV-2 and PCV-3 genomes. The combined prevalence of PCV-2 and PCV-3 was 74.32% in the wild boars tested. The proportions of wild boars positive for PCV-2 or PCV-3, or coinfected, were 47.30%, 49.32%, and 22.30%, respectively. No link was detected between PCV positivity and location, but gender was a risk factor for the disease (female; p < 0.0001; OR 0.29). Furthermore, our study provides a snapshot of PCV-2 and PCV-3 circulation in wild boars in the Campania region: our findings can help us to better understand the role of wildlife in PCV circulation.

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Freeze-substituted fungal cells of Nectria haematococca: A comparison of the macroconidial walls of the adhesion-competent wild type with an adhesion-reduced mutant

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100160996 ◽

1990 ◽

Vol 48 (3) ◽

pp. 688-689

Author(s):

Thecan Caesar-Ton That ◽

Lynn Epstein

Keyword(s):

Freeze Substitution ◽

Uranyl Acetate ◽

Wild Type ◽

Nectria Haematococca ◽

Fruit Extract ◽

Dialysis Tubing ◽

Tube Emergence ◽

Contrast Microscopy ◽

In The Wild ◽

Freeze Damage

Nectria haematococca mating population I (anamorph, Fusarium solani) macroconidia attach to its host (squash) and non-host surfaces prior to germ tube emergence. The macroconidia become adhesive after a brief period of protein synthesis. Recently, Hickman et al. (1989) isolated N. haematococca adhesion-reduced mutants. Using freeze substitution, we compared the development of the macroconidial wall in the wild type in comparison to one of the mutants, LEI.Macroconidia were harvested at 1C, washed by centrifugation, resuspended in a dilute zucchini fruit extract and incubated from 0 - 5 h. During the incubation period, wild type macroconidia attached to uncoated dialysis tubing. Mutant macroconidia did not attach and were collected on poly-L-lysine coated dialysis tubing just prior to freezing. Conidia on the tubing were frozen in liquid propane at 191 - 193C, substituted in acetone with 2% OsO4 and 0.05% uranyl acetate, washed with acetone, and flat-embedded in Epon-Araldite. Using phase contrast microscopy at 1000X, cells without freeze damage were selected, remounted, sectioned and post-stained sequentially with 1% Ba(MnO4)2 2% uranyl acetate and Reynold’s lead citrate. At least 30 cells/treatment were examined.

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