Assessing Genetic Variability and Population Structure of Ziziphus Nummularia as Characterized by Phenotypic Traits and SSR Markers with Climatic Distribution

Abstract Genus of Ziziphus (family Rhamnaceae), approximately 170 species of prodigious economic and ecological importance. Studies on the genetic diversity within Pakistani Ziziphus species are limited, and to date, no single report on the application of DNA barcoding attempt for identification of Ziziphus species is available in the literature. Therefore, the current study was designed to biogeographic distribution, to assess diversity based on phenotypic traits, SSRs markers, and relationships among Ziziphus nummularia (Burm.f.) Wight & Arn. genotypes. For the first time we use ArcGIS modeling, and their cartographic function for the identification of diversity in climatic variables such as temperature, mean diurnal, humidity, precipitation, and precipitation seasonality and the using of these techniques to determine the important variable which is responsible for the recent distribution of the Ziziphus species. A total of 11 phenotypic traits were noted and have significant phenotypic variation among the traits. The study has used 40 simple sequence repeats (SSR) markers for gaining insights into the genetic diversity within 180 genotypes of Z. nummularia. Successful amplification was achieved with 27 SSRs and was applied for understanding the population structure and relationships among the genotypes. A total of 120 alleles were amplified from Z. nummularia genotypes collected from three districts of the Malakand division, alleles per locus ranged from 2 to 6, averaging 4.4286. whereas polymorphism information content (PIC) from 0.332 to 0.794 in locus JSSR-490 and JSSR-97, within mean value was 0.671 per locus, expected heterozygosity (He), was 0.575, observed heterozygosity (Ho), 0.6618 and average gene diversity 0.494. Flow estimates (6.415) indicated frequent gene flow within Z. nummularia genotypes. Analysis of molecular variance (AMOVA) revealed high genetic variability (80%). The genetic relationship inferred from the neighbor-joining (NJ) phylogeny separate genotypes into three clusters and Bayesian model-based STRUCTURE analyses and PCoA analysis resolved all genotypes and indicted that the KP, populations, Swat and Buner, represent excesses of two different migration routes, with one designated from Swat and Dir (L). The overall results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries has retained unique alleles and this may facilitate the development of agronomically desirable and genetically improved Ziziphus cultivars and collections that can help achieve efficient conservation.

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Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

The Scientific World JOURNAL ◽

10.1100/2012/648427 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 11

Author(s):

Salvatore Bordonaro ◽

Anna Maria Guastella ◽

Andrea Criscione ◽

Antonio Zuccaro ◽

Donata Marletta

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Genetic Information ◽

Gene Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Population Structure Analysis ◽

The Mean ◽

Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

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Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽

10.21273/hortsci.44.7.1820 ◽

2009 ◽

Vol 44 (7) ◽

pp. 1820-1824 ◽

Cited By ~ 13

Author(s):

Emmanouil N. Tzitzikas ◽

Antonio J. Monforte ◽

Abdelhak Fatihi ◽

Zacharias Kypriotakis ◽

Tefkros A. Iacovides ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Ssr Markers ◽

Structure Analysis ◽

Simple Sequence Repeat ◽

Cucumis Melo ◽

Sequence Repeat ◽

Population Structure Analysis ◽

Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

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Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽

10.3390/agronomy10010068 ◽

2020 ◽

Vol 10 (1) ◽

pp. 68 ◽

Cited By ~ 2

Author(s):

Kyung Jun Lee ◽

Jung-Ro Lee ◽

Raveendar Sebastin ◽

Gyu-Taek Cho ◽

Do Yoon Hyun

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Gene Diversity ◽

Research Effort ◽

Molecular Genetic ◽

Allelic Diversity ◽

Perennial Herb ◽

Molecular Evidence ◽

Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

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Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-018-0709-3 ◽

2018 ◽

Vol 66 (1) ◽

pp. 243-257 ◽

Cited By ~ 1

Author(s):

Nawel Belalia ◽

Antonio Lupini ◽

Abderrahmane Djemel ◽

Abdelkader Morsli ◽

Antonio Mauceri ◽

...

Keyword(s):

Genetic Diversity ◽

Zea Mays ◽

Population Structure ◽

Ssr Markers ◽

Zea Mays L ◽

Phenotypic Traits

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Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China by 3 Types of Genetic Markers

10.21203/rs.3.rs-1050153/v1 ◽

2021 ◽

Author(s):

Yu Zhang ◽

Yewen Wang ◽

Peijiang Li ◽

Yuexing Wang ◽

Shimao Zheng ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Markers ◽

Ssr Markers ◽

Diversity Index ◽

Indica Rice ◽

Mantel Test ◽

Phenotypic Traits ◽

Phenotypic Analysis

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

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Population structure and impact of recurrent selection on popcorn using EST-SSR markers

Acta Scientiarum Agronomy ◽

10.4025/actasciagron.v40i1.35218 ◽

2018 ◽

Vol 40 (1) ◽

pp. 35218 ◽

Cited By ~ 3

Author(s):

Amanda Gonçalves Guimarães ◽

Antônio Teixeira do Amaral Júnior ◽

Janeo Eustáquio de Almeida Filho ◽

Guilherme Ferreira Pena ◽

Cássio Vittorazzi ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Microsatellite Markers ◽

Ssr Markers ◽

Genomic Dna ◽

Recurrent Selection ◽

Genetic Diversity And Structure ◽

Young Leaves ◽

The Impact

The success of any recurrent selection program depends on the genetic variability of the evaluated population, which is used to refer to the diversity of existing alleles at many genetic loci. Thus, the goal of the present study was to investigate the impact of recurrent selection across nine cycles of a UENF-14 popcorn population through the analysis of genetic diversity and structure using microsatellite markers (EST-SSRs). Genomic DNA was extracted from young leaves of 25 individuals from each cycle (C0, C1 C2, C3, C4, C5, C6, C7, and C8), totaling 225 samples from the UENF-14 population. Fifty EST-SSR markers were used for the analysis of genetic diversity across the recurrent selection cycles, 16 of which were polymorphic. Thirty-four alleles were detected, with an average of 2.13 alleles per locus. Throughout all the recurrent selection cycles, there was a reduction in heterozygosity and an increase in inbreeding. The population structure showed a sharing of alleles, inferring that some may be directly related to the main selection characteristics.

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Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China By 3 Types of Genetic Markers

10.21203/rs.3.rs-1050153/v2 ◽

2022 ◽

Author(s):

Yu Zhang ◽

Qiaoqiao He ◽

Xixi Zhou ◽

Yewen Wang ◽

Peijiang Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Markers ◽

Ssr Markers ◽

Diversity Index ◽

Indica Rice ◽

Mantel Test ◽

Phenotypic Traits ◽

Phenotypic Analysis

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Assessment of Genetic Diversity and Population Structure in Pea (Pisum sativum L.) Germplasm based on Morphological Traits and SSR Markers

Legume Research - An International Journal ◽

10.18805/lr-4751 ◽

2021 ◽

Author(s):

Shalini Singh ◽

B. Singh ◽

V.R. Sharma ◽

M. Kumar ◽

U. Sirohi

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Morphological Traits ◽

Phenotypic Traits ◽

Pisum Sativum L ◽

New Varieties ◽

Components Analysis ◽

Structure Result ◽

Diversity Estimates

Background: The study was undertaken to assess the genetic diversity and genetic structure among fifty-five pea accessions using morphological traits and SSR markers. Methods: A total of 55 pea accessions were analyzed using eleven phenotypic traits and twenty SSR markers. The data obtained by morphological and molecular profiling was used for the analysis of genetic diversity and for the estimation of genetic diversity estimates, correlation, principal components analysis and population structure. Result: This study reveals that majority of genetic variation was due to variation within population and were clustered into two distinct groups, which reveals a high admixture within individuals. Accessions viz., VRP-82, VRP-320, VRP-194, VRP-375, EC-97280 and EC-8724, showed great diversity as compared to the other accessions based on both morphological and molecular markers. These accessions may assist in developing and planning breeding strategies aimed to produce new varieties in the future.

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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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The roles of marginal lagoons in the maintenance of genetic diversity in the Brazilian migratory fishes Prochilodus argenteus and P. costatus

Neotropical Ichthyology ◽

10.1590/s1679-62252013000300016 ◽

2013 ◽

Vol 11 (3) ◽

pp. 625-636 ◽

Cited By ~ 11

Author(s):

Bruno F. Melo ◽

Yoshimi Sato ◽

Fausto Foresti ◽

Claudio Oliveira

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Genetic Variability ◽

Reproductive Season ◽

Migration Routes ◽

Single Population ◽

Genetic Studies ◽

Fish Resources ◽

Adequate Management

The rio São Francisco basin contains many endemic species, such as Prochilodus argenteus and P. costatus, which have great commercial importance. However, information about the main recruitment sites and genetic studies containing extensive sampling of these species are scarce. To investigate the roles of the marginal lagoons in the maintenance of genetic variability and in the population structure, we analyzed six microsatellite loci in nine sampling groups of P. argenteusand five sampling groups of P. costatus. Our results showed high levels of genetic variability and low values of genetic differentiation for P. argenteus (FST =0.008, P< 0.05) and for P. costatus(FST =0.031, P < 0.05). In addition, high values of gene flow combined with a small genetic distance suggest the presence of a single population for each species in the middle rio São Francisco basin. Moreover, putative migration routes involving marginal lagoons during the reproductive season could be detected, confirming the importance of these nurseries in the lifecycle of these species. Our results also indicate the necessity of adequate management of the fish resources and the conservation of the floodplains in the rio São Francisco basin.

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