Group Of Molecular Markers Research Articles

Applications of Microsatellites and Single Nucleotide Polymorphisms for the Genetic Characterization of Cattle and Small Ruminants: An Overview

The status of genetic diversity, adaptation to climate change or the identification of genes associated with traits of interest in livestock populations has been a major concern for scientists in the last decades. Biotechnology has evolved continuously, offering new tools and methodologies to analyse the genomes of livestock species. Biochemical markers or protein polymorphisms were the tools used for population studies many years ago, but over the last three decades the methodologies available to analyse livestock genomes have changed notably. The development of DNA molecular markers, especially microsatellites and Single Nucleotide Polymorphisms, opened new possibilities for a better understanding of livestock genomes, unthinkable until recently. However, Whole-Genome Sequencing technologies or genome editing techniques are changing the way to analyse or interact with the genomes, even before full advantage can be taken of all the possibilities open by the last group of molecular markers. The aim of this review is to summarize the opportunities available through livestock genome analysis in cattle and small ruminant populations, namely through the molecular markers most widely used over the last few years, including microsatellites and Single Nucleotide Polymorphisms.

Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

Temporal Trends of Variation in Italian Rice Germplasm over the Past Two Centuries Revealed by AFLP and SSR Markers

The aim of this study was to characterize the Italian rice (Oryza sativa L.) gene pool, paying particular attention to its variation over time, to determine whether human activity can reduce genetic variability, and whether such a reduction actually occurred in Italian rice varieties. We analyzed 135 Italian rice accessions, representing genotypes either introduced from abroad or developed in Italy from 1880 to 2001, using two groups of molecular markers, amplified fragment length polymorphisms and simple sequence repeats. These accessions were divided into four groups for which different statistical analyses were performed. The levels of gene diversity, from 0.1023 to 0.1921, and genetic richness, from 0.1579 to 0.3064, increased over time. Genetic structure, as estimated by analysis of molecular variance, revealed that the within‐component was overwhelmingly dominant (92%) compared with the among‐component. These results show that the level of genetic diversity in Italian rice accessions has remained high since 1850 and continues to increase. This is most likely the result of Italian breeding programs that developed new cultivars and introduced others from abroad, without substituting previous accessions. Our results show that the management and improvement of rice germplasm in Italy have been successful in maintaining sufficient genetic diversity.

Molecular characterization of the progeny of Solanum etuberosum identifies a genomic region associated with resistance to potato leafroll virus

Potato leafroll virus (PLRV; Genus Polerovirus; Family Luteoviridae) is one of the most important virus pathogens of potato worldwide and breeders are looking for new sources of resistance. Solanum etuberosum Lindl., a wild potato species native to Chile, was identified as having resistances to PLRV, potato virus Y, potato virus X, and green peach aphid. Barriers to sexual hybridization between S. etuberosum and cultivated potato were overcome through somatic hybridization. Resistance to PLRV has been identified in the BC1, BC2 and BC3 progeny of the somatic hybrids of S. etuberosum (+) S. tuberosum haploid × S. berthaultii Hawkes. In this study, RFLP markers previously mapped in potato, tomato or populations derived from S. palustre (syn S. brevidens) × S. etuberosum and simple sequence repeat (SSR) markers developed from tomato and potato EST sequences were used to characterize S. etuberosum genomic regions associated with resistance to PLRV. The RFLP marker TG443 from tomato linkage group 4 was found to segregate with PLRV resistance. This chromosome region has not previously been associated with PLRV resistance and therefore suggests a unique source of resistance. Synteny groups of molecular markers were constructed using information from published genetic linkage maps of potato, tomato and S. palustre (syn. S. brevidens) × S. etuberosum. Analysis of synteny group transmission over generations confirmed the sequential loss of S. etuberosum chromosomes with each backcross to potato. Marker analyses provided evidence of recombination between the potato and S. etuberosum genomes and/or fragmentation of the S. etuberosum chromosomes.

The Use of Microsatellite DNA Loci for Genetic Monitoring of Atlantic Salmon Populations

This work addresses the application of a new group of molecular markers, microsatellite loci, to monitor genetic diversity in stocks used in fish enhancement programs. To illustrate the potential use of these markers, we examined the genetic variation associated with the Connecticut River and Penobscot River populations of Atlantic salmon Salmo salar in the United States. Both rivers are stocked annually with fry from captive or cultured stocks that are one generation removed from sea-run adults. We analyzed microsatellite loci variation among sea-run adults and the derived cultured stock for the Connecticut River in a given year, along with two consecutive cohorts of cultured age-0 juveniles for the Penobscot River. Our results reveal subtle differences in allele frequencies between the two samples for each stock and some potential increases of homozygotes. These results demonstrate the potential value of microsatellite loci for routine genetic monitoring of cultured Atlantic salmon populations associated with restoration programs in the eastern United States.