Universal Rice Primer (URP) and Start Codon Target (SCoT) Markers in Studying Population Structures and Genetic Variation in Ferula AssafoetidaL. Accessions

Abstract Ferula assafoetidais an herbaceous, annual and monocarpic genus of the Apiaceae family. So far, there has been common usage of Ferula oleo resinous gum in food and herbal medicines.The origin of F.assafoetidais can be traced back into the steppes of Iran and some reigns of Afghanistan with an extended distribution. Despite the economic value and therapeutic importance of F.assafoetida, only a few studies have reported on the genetic capacity of this herb.The present study was carried out on a set of 90 individual plants belonging to different populations of Ferula assafoetida L. via the start codon target marker (SCoT) and the universal rice primer (URP) markers. Twelve SCoT and twelve URP primers generated 192 and 149 polymorphic fragments, while having 16 and 12.41 fragments respectively on average per primer. The Polymorphism information content (PIC) for URP primers and ScoT ranged from 0.31 to 0.43 and 0.34 to 0.44 respectively, which indicated a good efficiency forboth markers. The diversity indices including heterozygosity (He), percentage of polymorphic bands (PPB), Shannon’s information index (I) and marker index (MI) were calculated based on the SCoT and URP data.The results revealed that SCoT primers were more efficient than URP primers in identifying genetic diversity within populations. Neighbor joining (Nj), as a base for clustering, classified 90 accessions into 5 and 6 groups using SCoT and URP data respectively. Moreover, the combined data (SCoT+URP) succeeded in classifying all accessions into 6 groups, although this did not correspond with the geographical distribution of accessions. Structure analysis divided 90 genotypesinto 5 subpopulations using SCoT and URP markers, whereas the combined data (SCoT+URP) divided the accessions into 6 subpopulations, which confirmed the classification achieved by the Nj method. Principal coordinate analysis (PCoA) corroborated these conclusions. According to the analysis of molecular variance) AMOVA(, a high percentage of genetic diversity was found within the species, suggesting a rich diversity of germplasm for breeding plans. The assessment of population structure demonstrated a high rate of gene flow and the mixture of populations. Taken together, our findings suggest SCoT markers are more efficient than URP markers in assessing genetic diversity among F.assafoetida genotypes. All in all, genetic diversity could help the selection of appropriate markers and special genotypes for breeding plans.

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Gene-Targeted markers to assess genetic diversity and population structure within Tunisian Phoenix dactylifera L. cultivars

Silvae Genetica ◽

10.2478/sg-2020-0005 ◽

2020 ◽

Vol 69 (1) ◽

pp. 29-35

Author(s):

Rhouma-Chatti Soumaya ◽

Choulak Sarra ◽

Moussa Maha ◽

Chatti Khaled ◽

Chatti Noureddine

Keyword(s):

Genetic Diversity ◽

Date Palm ◽

Gene Diversity ◽

Phoenix Dactylifera ◽

Start Codon ◽

Marker System ◽

Average Value ◽

Information Index ◽

Scot Marker ◽

Phoenix Dactylifera L

AbstractGenetic variability in date palm genotypes collected from different regions of southern Tunisia was analyzed using a Start Codon Targeted (SCoT) marker system. Thirty-one accessions collected from three locations were investigated. One hundred and nine amplicons were produced among which 84 % were polymorphic. The PIC value and the Rp values testified of the efficiency of used primers. The percentage of polymorphic loci (Pp) varied from 44.57 to 83.70 %, Nei‘s gene diversity (H) from 0.175 to 0.273 with a mean of 0.228, and Shannon‘s information index (I) values ranging from 0.257 to 0.409 with an average value of 0.338 were illustrated. The Tunisian date palm populations exhibited high genetic differentiation (GST = 0.319) and gene flow (Nm = 1.063). The AMOVA analysis presented 70 % of the variation within the population and 30 % of the variation between them. Phylogenetic analysis and the Bayesian clustering approach also revealed high genetic variation among genetic variants with a net divergence of the wild insular population of Kerkennah from other cultivars. The present investigation suggests the effectiveness of the SCoT marker system to estimate the genetic diversity of Phoenix dactylifera genotypes.

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Genetic diversity and SSR markers development of ancient Camellia sinensis in Sandu County of Guizhou Province

10.21203/rs.3.rs-208220/v1 ◽

2021 ◽

Author(s):

Yichen Zhao ◽

Runying Wang ◽

Qing Liu ◽

Xuan Dong ◽

De-Gang Zhao

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Molecular Genetic ◽

Diversity Indices ◽

Guizhou Province ◽

Information Index ◽

Molecular Genetic Diversity ◽

Qualitative Characters ◽

Breed Selection

Abstract Background: The genetic abundance of ancient tea germplasm has been preserved in the long evolution process, which provides valuable resources for the protection and breed selection of ancient tea germplasm. However, the limited studies related to the genetic diversity of ancient tea germplasm restrict protection and breed selection. Therefore, the genetic diversity of ancient tea germplasm in Sandu county of Guizhou Province was explored in this study. II.Methods and Results: The genetic diversity was analyzed using phenotypes and SSR markers. The ranges for the variation coefficients of the six quantitative and seven qualitative characters were 17.76%-60.37% and 18.58%-50.64%, respectively. The ranges of diversity indices of the six quantitative and seven qualitative characters were 1.72-2.74 and 0.55-0.84, respectively. Ninety-six bands were amplified using 15 pairs of SSR primers from the 145 samples, and the average polymorphism information index was 0.66. The analysis revealed that the average values of Nei’s genetic diversity index (H) and the Shannon information index (I) are 0.26 and 0.41, respectively. Further, a genetic similarity coefficient of 0.734 shown by UPGMA dendrogram classified the 145 samples decreased into four groups. III.Conclusions: This study revealed the rich phenotypic variation and high molecular genetic diversity and the genetic diversity of the arbor is higher than that of the shrub of the ancient tea germplasm in Sandu of Guizhou province. Thus, this study not only provides a theoretical basis for the protection and breed selection but also promotes further research of ancient tea germplasm.

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Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Agronomy ◽

10.3390/agronomy9100647 ◽

2019 ◽

Vol 9 (10) ◽

pp. 647 ◽

Cited By ~ 3

Author(s):

Ünal Karık ◽

Muhammad Azhar Nadeem ◽

Ephrem Habyarimana ◽

Sezai Ercişli ◽

Mehtap Yildiz ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Diversity ◽

Diversity Indices ◽

Primer Binding Site ◽

Neighbor Joining ◽

Marker System ◽

Information Index ◽

Geographical Regions ◽

The World

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.

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Assessment of genetic diversity of Musa species accessions with variable genomes using ISSR and SCoT markers

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01202-8 ◽

2021 ◽

Author(s):

David Okeh Igwe ◽

Onyinye Constance Ihearahu ◽

Anne Adhiambo Osano ◽

George Acquaah ◽

George Nkem Ude

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Allelic Richness ◽

Crop Improvement ◽

Inter Simple Sequence Repeat ◽

Start Codon ◽

Information Index ◽

Cluster Resolution ◽

Musa Species ◽

Simple Sequence

AbstractAssessing the effectiveness of different molecular markers is essential for identification of appropriate ones for crop improvement and conservation, hence, inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers were used for this study. Sixty-six accessions with different genomes obtained from International Transit Center, Belgium, were used for DNA extraction, amplification with ISSR and SCoT markers and agarose gel electrophoresis. The reproducible bands were scored for analyses. We identified high allelic richness of 299 (ISSR) and 326 (SCoT). Polymorphic information contents (ISSR: 0.9225; SCoT: 0.9421) were high but SCoT exhibited higher level of informativeness. The two markers demonstrated high percentage polymorphic loci (ISSR: 91.21–100%; SCoT: 96.97–100%). Other genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon information index were higher in SCoT and further elucidated the usefulness of the markers. Intraspecific genetic diversity, interspecific genetic diversity, coefficient of gene differentiation and level of gene flow revealed extensive gene flow and larger variability within the accessions. Both ISSR and SCoT grouped the accessions via dendrogram, biplot and structure analyses. Though the two marker systems varied in their informativeness, they demonstrated high effectiveness in resolving genetic diversity (GD) of the different accessions, with higher efficiency in SCoT markers. Due to higher GD indices exhibited by SCoT, AS is the most genetically endowed one. Our study showed that SCoT markers are more informative than ISSR for GD exploration, assessment and cluster resolution of Musa species, thereby revealing the potential of SCoT markers for improved breeding and conservation.

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Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers

Scientia Agriculturae Bohemica ◽

10.1515/sab-2015-0029 ◽

2015 ◽

Vol 46 (4) ◽

pp. 145-153 ◽

Cited By ~ 3

Author(s):

M. Ocelák ◽

P. Hlásná Čepková ◽

I. Viehmannová ◽

Z. Dvořáková ◽

D.C. Huansi ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Genetic Relationships ◽

Diversity Indices ◽

Issr Markers ◽

Information Index ◽

Geographical Distances ◽

Plukenetia Volubilis ◽

Polymorphic Bands

Abstract The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%), gene diversity (0.103), and Shannon’s information index (0.15) were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%), and the Santa Cruz population the highest Nei’s gene diversity index (0.238) and Shannon’s information index (0.357). The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

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Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections

Microorganisms ◽

10.3390/microorganisms9010051 ◽

2020 ◽

Vol 9 (1) ◽

pp. 51

Author(s):

Min Yi Wong ◽

Yuan-Hsi Tseng ◽

Tsung-Yu Huang ◽

Bor-Shyh Lin ◽

Chun-Wu Tung ◽

...

Keyword(s):

Genetic Diversity ◽

Vascular Access ◽

Burkholderia Cepacia ◽

Bacterial Species ◽

Diversity Indices ◽

Burkholderia Cepacia Complex ◽

Reca Gene ◽

Clinical Effects ◽

Environmental Distribution ◽

Microbiological Characteristics

Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.

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On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Genetics Selection Evolution ◽

10.1186/s12711-021-00639-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Gabriele Senczuk ◽

Salvatore Mastrangelo ◽

Paolo Ajmone-Marsan ◽

Zsolt Becskei ◽

Paolo Colangelo ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Melting Pot ◽

Cattle Breeds ◽

Snp Data ◽

Early Migration ◽

Genome Wide ◽

European Colonization ◽

Approximate Bayesian ◽

European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

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Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians

Scientific Reports ◽

10.1038/s41598-021-96135-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Agnieszka Sutkowska ◽

Józef Mitka ◽

Tomasz Warzecha ◽

Jakub Bunk ◽

Julia Rutkowska ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Western Carpathians ◽

Genetic Structuring ◽

Long Distance ◽

Plant Populations ◽

Genetic Stock ◽

Melting Pot ◽

Mountain Ranges ◽

Eastern Carpathians

AbstractThe genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.

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Molecular diversity analysis in hexaploid wheat (Triticum aestivum L.) and two Aegilops species (Aegilops crassa and Aegilops cylindrica) using CBDP and SCoT markers

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00157-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Ghazal Ghobadi ◽

Alireza Etminan ◽

Ali Mehras Mehrabi ◽

Lia Shooshtari

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Crop Improvement ◽

Wild Relatives ◽

Resolving Power ◽

Start Codon ◽

Aegilops Cylindrica ◽

Aegilops Crassa

Abstract Background Evaluation of genetic diversity and relationships among crop wild relatives is an important task in crop improvement. The main objective of the current study was to estimate molecular variability within the set of 91 samples from Triticum aestivum, Aegilops cylindrica, and Aegilops crassa species using 30 CAAT box–derived polymorphism (CBDP) and start codon targeted (SCoT) markers. Results Fifteen SCoT and Fifteen CBDP primers produced 262 and 298 fragments which all of them were polymorphic, respectively. The number of polymorphic bands (NPB), polymorphic information content (PIC), resolving power (Rp), and marker index (MI) for SCoT primers ranged from 14 to 23, 0.31 to 0.39, 2.55 to 7.49, and 7.56 to 14.46 with an average of 17.47, 0.34, 10.44, and 5.69, respectively, whereas these values for CBDP primers were 15 to 26, 0.28 to 0.36, 3.82 to 6.94, and 4.74 to 7.96 with a mean of 19.87, 0.31, 5.35, and 6.24, respectively. Based on both marker systems, analysis of molecular variance (AMOVA) indicated that the portion of genetic diversity within species was more than among them. In both analyses, the highest values of the number of observed (Na) and effective alleles (Ne), Nei’s gene diversity (He), and Shannon’s information index (I) were estimated for Ae. cylindrica species. Conclusion The results of cluster analysis and population structure showed that SCoT and CBDP markers grouped all samples based on their genomic constitutions. In conclusion, the used markers are very effective techniques for the evaluation of the genetic diversity in wild relatives of wheat.

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Mitochondrial Genetic Diversity among Farmed Stocks of Oreochromis spp. (Perciformes, Cichlidae) in Madagascar

Diversity ◽

10.3390/d13070281 ◽

2021 ◽

Vol 13 (7) ◽

pp. 281

Author(s):

Nicolas Hubert ◽

Elodie Pepey ◽

Jean-Michel Mortillaro ◽

Dirk Steinke ◽

Diana Edithe Andria-Mananjara ◽

...

Keyword(s):

Genetic Diversity ◽

Low Income ◽

Food System ◽

Production Systems ◽

Dna Barcode ◽

Diversity Indices ◽

Low Income Countries ◽

Wild Populations ◽

Fast Development ◽

Well Differentiated

The fast development of aquaculture over the past decades has made it the main source of fish protein and led to its integration into the global food system. Mostly originating from inland production systems, aquaculture has emerged as strategy to decrease malnutrition in low-income countries. The Nile tilapia (Oreochromis niloticus) was introduced to Madagascar in the 1950s, and is now produced nationally at various scales. Aquaculture mostly relies on fry harvested from wild populations and grow-out in ponds for decades. It has recently been diversified by the introduction of several fast-growing strains. Little is known how local genetic diversity compares to recently introduced strains, although high and comparable levels of genetic diversity have previously been observed for both wild populations and local stocks. Our study compares DNA barcode genetic diversity among eight farms and several strains belonging to three species sampled. DNA-based lineage delimitation methods were applied and resulted in the detection of six well differentiated and highly divergent lineages. A comparison of DNA barcode records to sequences on the Barcode of Life Data System (BOLD) helped to trace the origin of several of them. Both haplotype and nucleotide diversity indices highlight high levels of mitochondrial genetic diversity, with several local strains displaying higher diversity than recently introduced strains. This allows for multiple options to maintain high levels of genetic diversity in broodstock and provides more options for selective breeding programs.

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