Markers For Genetic Diversity Research Articles

Identification and genetic diversity analysis of four rainbow trout strains using microsatellites

We evaluated the genetic diversity among four rainbow trout strains at 30 microsatellite loci.In addition,we compared the genetic diversity in these strains with that of samples collected in 2005 to evaluate the genetic differentiation attributable to selection pressure.All 30 microsatellite loci are suitable markers of genetic diversity in the four rainbow trout strains.The mean number of alleles in the four strains varied from 3.77 to 5.80;the mean number of effective alleles varied from 2.746 1 to 3.630 3;the mean expected heterozygosity ranged from 0.590 6 to 0.722 1,the mean observed heterozygosity ranged from 0.587 5 to 0.786 1,and the mean polymorphism information content ranged from 0.535 0 to 0.647 0.All four rainbow trout strains exhibited a high level in genetic diversity.Analysis of the genetic distance revealed that Finland rainbow trout and Norway rainbow trout cluster together and the two Golden trout cluster together.When compared with the samples acquired in 2005,Norway rainbow trout and American golden trout have significantly lower allele numbers,effective allele numbers,and polymorphism information content(P0.01),but there was no difference for Finland rainbow trout.

Molecular markers for genetic diversity and phylogeny research of Brazilian sheep breeds

Brazilian sheep descended from several breeds brought to the New World by Portuguese and Spanish colonists, and they have evolved and adapted to local climatic variations and acquired tolerance or resistance to many diseases. Molecular markers are widely used in analyzing genetic variability, and markers such as amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), microsatellite, mtDNA and single nucleotide polymorphism (SNP) have facilitated the characterization of genetic diversity and population structure, and in the investigation of the natural history, behavior, and evolution of several sheep breeds. In this context, we present here a review of the uses of molecular markers in ecological and conservation research of Brazilian sheep breeds. Key words: DNA polymorphism, genetic conservation, Ovis aries .

Exploitation of random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) markers for genetic diversity of saffron collection

Saffron is the most expensive spice in the world. Considering the importance of germplasm characterization and evaluation particularly in saffron, the present study was formulated with an objective to access the structure of genetic diversity among the accession of saffron at molecular levels. Twenty six primers from Operon Technologies were used in random amplified polymorphic DNA (RAPD) analysis, thirty primers were screened using sequence-related amplified polymorphism (SRAP) method were assayed in six clone ofCrocus sativus from six center of production of saffron in Iran. The RAPD primers developed 95 robust loci, which revealed 56% polymorphism and 75 SRAP markers generated 43% polymorphism. Genetic diversity parameters for RAPD and SRAP along with Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering based on Jaccard coefficient were estimated with a view to assess efficiency of the marker system in saffron. Accessions were classified into four clusters using both methods, which supplied molecular evidences for the exploit of this rich source in Iran. RAPD markers were almost as efficient as SRAP markers with regards to detection of polymorphism, number of loci scored and polymorphism information content (PIC) values. Therefore saffron is not monomorphic and we can find diversity for breeding purposes. Key words: Crocus sativus, genetic differentiation, molecular marker.

Development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.] and their transferability to other Vigna species

Expressed sequence tag (EST) sequences available in the public databases provide a cost-effective and valuable genomic resource for the development of molecular markers. Introns which are non-coding DNA sequences of the gene could be used as potential molecular markers as they are highly variable compared to the coding sequences. This study reports the development of intron length polymorphism markers in cowpea [Vigna unguiculata (L.) Walp.]. The ESTs of cowpea were aligned with genomic sequences of Arabidopsis and soybean to predict the position and number of introns in cowpea. Of the 110 PCR primer pairs designed to amplify the intronic regions, 98 primer pairs resulted in successful amplification and were identified as cowpea intron length polymorphism (CILP) markers. Out of the 45 randomly selected CILP markers, 36 % markers produced length variation in the ten cowpea genotypes, collectively yielding 33 alleles with an average of 2.0 alleles/locus. The polymorphism information content of the CILP markers ranged from 0.18 to 0.64 with an average of 0.34. Of the 98 CILP markers, 93 markers (95 %) showed transferability to other Vigna species. Dendrograms based on CILP markers clearly distinguished the cowpea genotypes as well as other Vigna species, demonstrating the utility of CILP markers in genetic diversity and phylogenetic studies. These CILP markers will be very useful in the genome analysis and marker-assisted breeding of cowpea and other Vigna species.

Short communication: Development of a new polymorphic genetic marker in Araucaria araucana (Mol) K. Koch

Seed storage proteins have been used as genetic marker in forest species to evaluate genetic variability, demonstrating its effectiveness both in conifers and broad-leaved. In conifers, megagametophyte storage proteins are particularly useful because of their haploid nature. The aim of this study was to determine whether these proteins could be used as a new marker of genetic diversity in Araucaria araucana, one of the oldest conifers of South America and a representative symbol of Chilean forest biodiversity. For this, megagametophytes from two A. araucana populations were assessed to identify polymorphic bands and to obtain a preliminary estimation of the genetic diversity. The results revealed that globulin is the best fraction for measuring the variability in the species, due to their high level of variation (20 identified bands, eleven of them polymorphic). Both populations showed high genetic diversity, with more than 92% of the variation within populations. The study highlighted that these proteins can be used to measure the genetic diversity in A. araucana, providing good information to ensure the preservation of the species genetic resources.

Morphological and molecular characterisation of Lasiodiplodia theobromae from various banana cultivars causing crown rot disease in fruits

Twelve isolates of Lasiodiplodia theobromae were collected from 12 different commercial banana cultivars belonging to various banana growing regions of Tamil Nadu, India. The results revealed that most of the L. theobromae isolates exhibited significant differences in morphology, colour and spore size. However, all 12 isolates took 3–4 days invariably to cover the 90 mm Petri plates. Among the 12 isolates, the isolates LT3a from Robusta and LT10c from dwarf Cavendish produced abundant pycnidia. These isolates were also analysed through Random amplified polymorphic DNA (RAPD) markers for genetic diversity. Polymerase chain reaction amplification of total genomic DNA of the 12 isolates of L. theobromae with 14 random primers generated numerous polymorphisms among the isolates, while many of the intense bands were shared among majority of the isolates. Cluster analysis also indicated a high degree of genetic variability within L. theobromae isolates from different banana cultivars. The 12 isolates were separated into three clusters namely A, B and C. The maximum similarity index of 80% was recorded between the isolates LT7d from Karpuravalli and LT10c from dwarf Cavendish. The least similarity index of 29.41% was recorded with the isolates LT1f isolated from Poovan and LT5a isolated from Virupakshi. Within the species of L. theobromae the genetic variability was high and it underlines and validates existence of significant intra-specific diversity in isolates of L. theobromae infecting different banana cultivars.

Mitochondrial DNA as a Marker for Genetic Diversity and Evolution

Mitochondrial DNA as a Marker for Genetic Diversity and Evolution The formulation of the modern breed concept during mid-1800s has caused remarkable changes in the livestock sector: largescale production expanded and its application to breeding and husbandry practices led to the formation of well-defined breeds, exposed to intense anthropogenic selection. As a consequence, farmers progressively substituted the less productive, locally adapted, native breeds with highly productive cosmopolitan breeds and progressively abandoned marginal areas.

Developmental stability covaries with genome-wide and single-locus heterozygosity in house sparrows.

Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed.

Comparative analysis of genetic diversity in Citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers

In this study we evaluate the informativeness and efficiency of Amplified Fragment Length Polymorphism (AFLP), Sequence-Specific Amplified Polymorphism (S-SAP), Selectively Amplified Microsatellite Polymorphic Loci (SAMPL) and Simple Sequence Repeat (SSR) markers for genetic diversity, phylogenetic relationship among the Citrus species and mapping ability of the marker system. The SSR exhibited relatively higher level of polymorphism information content in terms of the expected heterozygosity, than that of the AFLPs, SSAPs and SAMPLs. For each marker system, average level of the discriminating potential was very close to the actual discriminating potential. Similarity matrices showed weak, yet significant correlations when Mantel's test was applied. The highest positive (0.72) correlation was found between the AFLP and SSAP markers. The SSR and SAMPL markers were poorly correlated. The dendrogram topology among the four marker systems had high similarity. Taken together, the SSAP and SAMPL were highly efficient in detecting genetic similarity in Citrus, while the SSR may be more useful for segregation studies and genome mapping in Citrus. The SSAP and SAMPL markers could be useful for Citrus genome mapping in combination with AFLP and SSR markers. To our knowledge, this was the first detail report of a comparison of performances among AFLP, SSR and retrotrasposon based molecular marker technique on a set of samples of Citrus. Our result provides guidance for future efficient use of these molecular methods in genetic analysis of Citrus sp. and its relatives.

Use of ribosomal introns as new markers of genetic diversity in Exophiala dermatitidis

Exophiala dermatitidis is one of the prevalent black yeasts found as opportunistic pathogens or colonizers in humans. In the tropics its natural habitat is thought to be fruit surfaces and it is also found in the digestive system of fruit-eating animals. However, it has recently been abundantly isolated from human-made environments (steam baths, railway ties, dishwashers) in tropical and temperate climates. Two genotypes have been distinguished within this species: genotype A, mostly corresponding to strains isolated from patients, and genotype B, to strains isolated from the natural environment. In human-made environments, both genotypes A and B occur. A previous study suggested that one genotype had been selected for in the human host. In our study, the distribution of ribosomal insertions agrees with an ecological specialization of E. dermatitidis genotypes by showing a significantly higher frequency of ribosomal insertions in clinical strains in comparison to environmental ones. The characterization of these insertions shows that they correspond to introns of group IC or IE, the most frequent types within the fungal kingdom. These ribosomal group I introns could be used as new markers for populations of E. dermatitidis.

Cultural and genetic variability in Macrophomina phaseolina (Tassi.) Goid. and incidence of mulberry root rot

Five isolates of Macrophomina phaseolina (Tassi.) Goid. were collected from different mulberry growing districts of Tamil Nadu. Among the five isolates, Coimbatore isolate took five days to cover the entire plate. The same isolate also produced a maximum number of sclerotia on solid and liquid medium when compared to other isolates. These isolates were also analysed through RAPD markers for genetic diversity. A similarity matrix and Jacard's similarity coefficient between isolates indicated that these five isolates showed 66–80% similarity coefficient. The five isolates were separated into two clusters, namely A and B. Again cluster A is divided into two clusters, namely A1 and A2. The cluster A1 contains isolates of Erode and Dindigul. These two exhibit 72.5% similarity coefficient. The cluster A2 represents isolate Coimbatore and Salem isolate which exhibited a similarity coefficient of 80%. Cluster B contains Dharmapuri isolate which differed from other isolates of Erode, Dindigul, Coimbatore and Salem.

Comparison of genetic detection efficiency of different markers under the same genetic background

Chinese native sheep populations, Hu sheep, Tong sheep, Small-tailed Han sheep and Tan sheep were used to study the efficiency of genetic markers. The genetic markers used in this study include morphological and ecological indices, blood protein enzyme, microsatellite DNA and the combination of three markers. The results showed that the morphological and ecological indices are not accurate tools to determine the relationships among populations. In contrast, blood protein enzyme and microsatellite DNA were the best markers for genetic diversity among sheep populations. Therefore, selection of markers depends on the aim of research; for instance neutral markers are selected to study the origin of breeds, trait indices for economical or ecological classification, and multi-combined genetic markers for the relations among populations.

Genetic diversity of Dianthus accessions as assessed using two molecular marker systems (SRAPs and ISSRs) and morphological traits

Dianthus chinensis, Dianthus barbatus and Dianthus superbus are members of the Caryophyllaceae and are grown widely as ornamental plants. Information about relative genetic relationships can facilitate breeding programs. Here, we have compared two polymerase chain reaction (PCR)-based systems (sequence-related amplified polymorphisms (SRAPs) and inter-simple sequence repeats (ISSRs)) and morpological trait measurements for their relative effectiveness in estimating the genetic diversity found between 22 Chinese pink ( D. chinensis) inbred-lines, one accession of D. barbatus and one accession of D. superbus. Interspecific differences were readily detected but the markers were less reliable in distinguishing the accessions according to their region of origin or in separating the wild species from the cultivars. Morphological traits were found to be the least effective genetic markers. The relative effectiveness of the three systems as markers for genetic diversity was concluded to be SRAP > ISSR > morphological traits, but the combined data from ISSR + SRAP analyses was superior to all three. The information generated by the SRAP marker system correlated more closely with morphological variability than did the ISSR marker system. The morphological markers of plant height/crown size ratio, lower leaf length, ovary shape index and calyx length showed strong correlations with the genetic diversity index (GD ij, PPB(II) and PSB) as generated by the percentage of polymorphic bands and percentage of special bands of the PCR-based markers.

Representing key phytoplankton functional groups in ocean carbon cycle models: Coccolithophorids

Carbonates are the largest reservoirs of carbon on Earth. From mid‐Mesozoic time, the biologically catalyzed precipitation of calcium carbonates by pelagic phytoplankton has been primarily due to the production of calcite by coccolithophorids. In this paper we address the physical and chemical processes that select for coccolithophorid blooms detected in Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) ocean color imagery. Our primary goal is to develop both diagnostic and prognostic models that represent the spatial and temporal dynamics of coccolithophorid blooms in order to improve our knowledge of the role of these organisms in mediating fluxes of carbon between the ocean, the atmosphere, and the lithosphere. On the basis of monthly composite images of classified coccolithophorid blooms and global climatological maps of physical variables and nutrient fields, we developed a probability density function that accounts for the physical chemical variables that predict the spatiotemporal distribution of coccolithophorids in the world oceans. Our analysis revealed that areas with sea surface temperatures (SST) between 3° and 15°C, a critical irradiance between 25 and 150 μmol quanta m−2 s−1, and decreasing nitrate concentrations (ΔN/Δt < 0) are selective for upper ocean large‐scale coccolithophorid blooms. While these conditions favor both Northern and Southern Hemisphere blooms of the most abundant coccolithophorid in the modern oceans, Emiliania huxleyi, the Northern and Southern Hemisphere populations of this organism are genetically distinct. Applying amplified fragment length polymorphism as a marker of genetic diversity, we identified two major taxonomic clades of E. huxleyi; one is associated with the Northern Hemisphere blooms, while the other is found in the Southern Hemisphere. We suggest a rule of “universal distribution and local selection”: that is, coccolithophorids can be considered cosmopolitan taxa, but their genetic plasticity provides physiological accommodation to local environmental selection pressure. Sea surface temperature, critical irradiance, and ΔN/Δt were predicted for the years 2060–2070 using the NCAR Community Climate System Model to generate future monthly probability distributions of coccolithophorids based upon the relationships observed between the environmental variables and coccolithophorid blooms in modern oceans. Our projected probability distribution analysis suggests that in the North Atlantic, the largest habitat for coccolithophorids on Earth, the areal extent of blooms will decrease by up to 50% by the middle of this century. We discuss how the magnitude of carbon fluxes may be affected by the evolutionary success of coccolithophorids in future climate scenarios.

Genetic Diversity of phlD from 2,4-Diacetylphloroglucinol-Producing Fluorescent Pseudomonas spp.

ABSTRACT Fluorescent Pseudomonas spp. that produce 2,4-diacetylphloroglucinol (2,4-DAPG) have biocontrol activity against damping-off, root rot, and wilt diseases caused by soilborne fungal pathogens, and play a key role in the natural suppression of Gaeumannomyces graminis var. tritici, known as take-all decline. Diversity within phlD, an essential gene in the biosynthesis of 2,4-DAPG, was studied by restriction fragment length polymorphism (RFLP) analysis of 123 2,4-DAPG-producing isolates from six states in the United States and six other locations worldwide. Clusters defined by RFLP analysis of phlD correlated closely with clusters defined previously by BOX-polymerase chain reaction (PCR) genomic fingerprinting, indicating the usefulness of phlD as a marker of genetic diversity and population structure among 2,4-DAPG producers. Genotypes defined by RFLP analysis of phlD were conserved among isolates from the same site and cropping history. Random amplified polymorphic DNA analyses of genomic DNA revealed a higher degree of polymorphism than RFLP and BOX-PCR analyses. Genotypic diversity in a subset of 30 strains representing all the phlD RFLP groups did not correlate with production in vitro of monoacetylphloroglucinol, 2,4-DAPG, or total phloroglucinol compounds. Twenty-seven of the 30 representative strains lacked pyrrolnitrin and pyoluteorin biosynthetic genes as determined by the use of specific primers and probes.

Sequence variation of the tRNA(Leu) intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens.

We examined the genetic diversity of Nostoc symbionts in some lichens by using the tRNA(Leu) (UAA) intron as a genetic marker. The nucleotide sequence was analyzed in the context of the secondary structure of the transcribed intron. Cyanobacterial tRNA(Leu) (UAA) introns were specifically amplified from freshly collected lichen samples without previous DNA extraction. The lichen species used in the present study were Nephroma arcticum, Peltigera aphthosa, P. membranacea, and P. canina. Introns with different sizes around 300 bp were consistently obtained. Multiple clones from single PCRs were screened by using their single-stranded conformational polymorphism pattern, and the nucleotide sequence was determined. No evidence for sample heterogenity was found. This implies that the symbiont in situ is not a diverse community of cyanobionts but, rather, one Nostoc strain. Furthermore, each lichen thallus contained only one intron type, indicating that each thallus is colonized only once or that there is a high degree of specificity. The same cyanobacterial intron sequence was also found in samples of one lichen species from different localities. In a phylogenetic analysis, the cyanobacterial lichen sequences grouped together with the sequences from two free-living Nostoc strains. The size differences in the intron were due to insertions and deletions in highly variable regions. The sequence data were used in discussions concerning specificity and biology of the lichen symbiosis. It is concluded that the tRNA(Leu) (UAA) intron can be of great value when examining cyanobacterial diversity.

Nuclear Ribosomal DNA Unit Lenght Variation: A Putative Marker of Genetic Diversity in Jojoba

Jojoba (Simmondsia chinensis [Link] Schneider) is a crop of high economic interest that is grown for the exceptional quality of its seed oil. We have taken advantage of the large variation commonly shown by ribosomal DNA (rDNA) in many plant species to assess the genetic diversity between clones and among individuals in jojoba. The variation of rDNA was analyzed with the use of a homologous 1.7-kbp probe generated by PCR and a 20-mer oligonucleotide probe targeting, respectively, the 17S and 25S coding regions. The multiple-step ladder obtained with the BamH I-EcoR I restriction fragment containing the intergenic spacer (IGS) was the best indicator of variation in length of rDNA unit. In addition to variations observed among selected clones, significant differences in the relative proportion of length variants were seen among individuals grown from seeds of unknown origin.

Codominant isoenzymic alleles as markers of genetic diversity correlated with heterosis in maize (Zea mays)

The average F1 yields were found to be significantly correlated with the genetic diversity of the parental strains calculated from the zymogram patterns of five enzyme systems in a sample of eight strains and their diallelic crosses.Despite the relatively small number of loci (eight) studied, there is evidence that these codominant alleles are good markers for genetic heterogeneity that is a source of heterosis.