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Diversity
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Use of Molecular Markers in Genetic Diversity Research
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Use of Molecular Markers in Genetic Diversity Research

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (31 January 2014) | Viewed by 97289

Special Issue Editor

Dr. Mario A. Pagnotta

E-Mail Website
Guest Editor
Department of Agricultural and Forest Sciences, Tuscia University, Via S. C. de Lellis, snc, 01100 Viterbo, Italy
Interests: plant population genetics; plant evolution and domestication; in situ and ex situ conservation of plant germplasm; molecular characterization; molecular markers; molecular evolution; plant breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

A molecular marker can be defined as a genomic locus, detected through probe or specific starters (primer) which, in virtue of its presence, distinguishes unequivocally the chromosomic trait which it represents as well as the flanking regions at the 3’ and 5’ extremity. Thus, these markers, generally have no reference to the activity of specific genes, but are directly based on highlighting differences (polymorphisms) within a nucleic sequence in different individuals, as a result of insertion, deletions, translocations, duplications, point mutations, etc. Molecular marker is probably the more powerful tool developed at the end of last century. Thousands of them are now known, thus enabling the study of a much larger number of genes that code for plant expression, as well as for other non-coding segments of the chromosome. Thanks to them genetic maps have been developed and their position in the genome is known. They are widely used in several aspects from variety identification, to gene detection passing from the assessing of genetic diversity and its partition within and among populations. More and more, molecular marker studies are being used to identify diversity “hotspots” for in situ conservation.
Several molecular markers typologies are developed and each typology has its own property with advantages and disadvantages.
The aim of this special issues is to bring together researches addressed to assess by molecular markers the genetic diversity present in the germplasm. But also addressed to evaluate and develop the most suitable marker(s) to be use as well as the statistical analysis which their use imply.

Prof. Dr. Mario A. Pagnotta
Guest Editor

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Keywords

  • genetic diversity
  • polymorphism
  • markers developing
  • population genetics
  • molecular evolution
  • maps
  • phylogeny
  • molecular marker
  • SNP
  • microsatellite
  • statistical analysis

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Published Papers (8 papers)

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Research

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583 KiB  
Article
Maintenance of Genetic Diversity in Natural Spawning of Captively-Reared Endangered Sockeye Salmon, Oncorhynchus nerka
by Ruth E. Withler, David S. O'Brien, Nicolette M. Watson and K. Janine Supernault
Diversity 2014, 6(2), 354-379; https://doi.org/10.3390/d6020354 - 19 Jun 2014
Cited by 4 | Viewed by 6657
Abstract
Captive propagation of Pacific salmon is routine, but few captive breeding programs have been conducted to successfully re-establish extirpated wild populations. A captive breeding program for endangered Sakinaw Lake sockeye salmon was established from 84 adults between 2002 and 2005, just prior to [...] Read more.
Captive propagation of Pacific salmon is routine, but few captive breeding programs have been conducted to successfully re-establish extirpated wild populations. A captive breeding program for endangered Sakinaw Lake sockeye salmon was established from 84 adults between 2002 and 2005, just prior to extirpation of the wild population. After several years of absence, sockeye salmon released from captivity returned to spawn in Sakinaw Lake in 2010 and in all years thereafter. Freshwater survival rates of released hatchery fry and naturally produced progeny of reintroduced sockeye salmon have not limited abundance of the reintroduced population. In contrast, marine survival rates for Sakinaw sockeye salmon have been <1%, a level that precludes population restoration in the absence of supplementation. Genetic diversity commensurate with the number of parental founders has been maintained in captivity. The 517 adult second-generation captive fish that spawned in Sakinaw Lake in 2011 produced a smolt emigration of almost 28,000 juvenile fish with an effective population size of 132. Allelic richness and gene diversity levels in the smolts were similar to those observed in captivity. This indicates genetic contributions from all or most founding parents have been retained both in captivity and in the nascent reintroduced natural population. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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342 KiB  
Communication
Meta-Analysis of Mitochondrial DNA Reveals Several Population Bottlenecks during Worldwide Migrations of Cattle
by Johannes A. Lenstra, Paolo Ajmone-Marsan, Albano Beja-Pereira, Ruth Bollongino, Daniel G. Bradley, Licia Colli, Anna De Gaetano, Ceiridwen J. Edwards, Marleen Felius, Luca Ferretti, Catarina Ginja, Peter Hristov, Juha Kantanen, Juan Pedro Lirón, David A. Magee, Riccardo Negrini and Georgi A. Radoslavov
Diversity 2014, 6(1), 178-187; https://doi.org/10.3390/d6010178 - 14 Mar 2014
Cited by 46 | Viewed by 20535
Abstract
Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of [...] Read more.
Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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1271 KiB  
Article
Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism
by Sukhjiwan Kaur, Noel O. I. Cogan, John W. Forster and Jeffrey G. Paull
Diversity 2014, 6(1), 88-101; https://doi.org/10.3390/d6010088 - 24 Jan 2014
Cited by 37 | Viewed by 10139
Abstract
Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population [...] Read more.
Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP) markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC) values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ) dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA), deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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1073 KiB  
Article
Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) Marker Resources for Diversity Analysis of Mango (Mangifera indica L.)
by Natalie L. Dillon, David J. Innes, Ian S. E. Bally, Carole L. Wright, Luke C. Devitt and Ralf G. Dietzgen
Diversity 2014, 6(1), 72-87; https://doi.org/10.3390/d6010072 - 20 Jan 2014
Cited by 35 | Viewed by 12760
Abstract
In this study, a collection of 24,840 expressed sequence tags (ESTs) generated from five mango (Mangifera indica L.) cDNA libraries was mined for EST-based simple sequence repeat (SSR) markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST [...] Read more.
In this study, a collection of 24,840 expressed sequence tags (ESTs) generated from five mango (Mangifera indica L.) cDNA libraries was mined for EST-based simple sequence repeat (SSR) markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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769 KiB  
Article
Genetic Diversity and Seed Quality of the “Badda” Common Bean from Sicily (Italy)
by Lucia Lioi and Angela Rosa Piergiovanni
Diversity 2013, 5(4), 843-855; https://doi.org/10.3390/d5040843 - 6 Dec 2013
Cited by 4 | Viewed by 6241
Abstract
The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats [...] Read more.
The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats (SSR) (or microsatellite) molecular markers provided useful information on genetic variation and relationships between “Badda bianco” and “Badda nero” morphotypes. Based on SSR data, the nine accessions examined were grouped in three sub-clusters. The first sub-cluster included all the accessions belonging to the “Badda bianco”. Conversely, “Badda nero” was constituted by two well-distinguished sub-clusters, one of them forming a well-separated branch. This result suggests that two constitutive nuclei contributed to the genetic background of “Badda nero”. Moreover, technological and nutritional data evidenced a good seed protein content (mean value 240.7 g kg−1) and differences in seed hydration rate among accessions. Knowledge of genetic structure appear to be fundamental in planning safeguard strategies of an appreciate landrace such as the “Badda” bean. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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Review

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240 KiB  
Review
DNA Markers for Food Products Authentication
by Daria Scarano and Rosa Rao
Diversity 2014, 6(3), 579-596; https://doi.org/10.3390/d6030579 - 5 Sep 2014
Cited by 77 | Viewed by 10018
Abstract
Media constantly refer of unscrupulous producers that adulterate, alter or replace premium products in food chains with the goal to maximize illegally profits. Food traceability is a central issue for the identification of improper labeling of processed food and feed and there are [...] Read more.
Media constantly refer of unscrupulous producers that adulterate, alter or replace premium products in food chains with the goal to maximize illegally profits. Food traceability is a central issue for the identification of improper labeling of processed food and feed and there are rules aimed to protect consumers and producers against fraudulent substitution of quality products in food chain, but the tools available are not always appropriate. DNA-based markers proved very effective for fresh and processed food molecular authentication. In this review, we illustrate potential and limits of different DNA markers focusing on low, medium and high-throughput markers, in order to monitor the genetic identity of food components in meat, fish and plants net-chains. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
927 KiB  
Review
Planarian (Platyhelminthes, Tricladida) Diversity and Molecular Markers: A New View of an Old Group
by Marta Álvarez-Presas and Marta Riutort
Diversity 2014, 6(2), 323-338; https://doi.org/10.3390/d6020323 - 15 Apr 2014
Cited by 31 | Viewed by 14129
Abstract
Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many [...] Read more.
Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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486 KiB  
Review
Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers
by Ilga Porth and Yousry A. El-Kassaby
Diversity 2014, 6(2), 283-295; https://doi.org/10.3390/d6020283 - 4 Apr 2014
Cited by 91 | Viewed by 14236
Abstract
Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of [...] Read more.
Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes. Full article
(This article belongs to the Special Issue Use of Molecular Markers in Genetic Diversity Research)
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