Differences In Allelic Composition Research Articles

Determination of Genetic Stability in Cacao Plants (Theobroma Cacao L.) Derived from Somatic Embryogenesis Using Microsatellite Molecular Markers (SSR)

ABSTRACT The clonal propagation of T. cacao by somatic embryogenesis (SE) is a promising approach to multiply elite genotypes. Assessing clonal fidelity in plants regenerated from somatic embryos is the first step toward ensuring genetic uniformity in the mass production of planting material. This study assessed the genetic stability of cacao plantlets propagated by SE and conventional grafting for genotypes CCN51 and TSH565 using 13 SSR. The leaves of in vitro plantlets (IVL) were collected from 6-month-old plants and leaves of field plants (FPL) were selected from 3-year-old trees. The 13 analyzed loci revealed 25 alleles in genotype CCN51 and 24 alleles in genotype TSH565. The highest PIC value was observed for all SSR, only mTcCIR8 and mTcUNICAMP09 were intermediate, with PIC values of less than 0.250. IVL and FPL populations were genetically equal. According to the results, no differences in allelic composition were observed between FPL and IVL in each genotype. This indicates that plants propagated by SE did not show perceptible detriment to their genome with the used SSR. In addition, Jaccard’s coefficient showed more than a 91% similarity for TSH565 and 92% for CCN51. The UPGMA and PCA showed that the populations tended to group within two genotypes. The SSR results obtained do not exclude the occurrence of other changes in the nuclear genome. However, considering the morphological stability of in vitro propagated plants, the results indicate that the protocol used is suitable and efficient for large scale, true-to-type propagation of genotypes CCN51 and TSH565 for commercial purposes.

Positive selection in coding regions and motif duplication in regulatory regions of bottlenose dolphin MHC class II genes.

The vertebrate immune response is mediated through highly adaptive, quickly evolving cell surface receptors, the major histocompatibility complex (MHC). MHC molecules bind and present a diverse array of pathogenic molecules and trigger a cascade of defenses. Use of MHC variation as a marker for population health has also evolved quickly following advances in sequencing methods. We applied a combination of traditional and next generation sequencing methodology to characterize coding (peptide binding region) and regulatory (proximal promoter) sequence variation in MHC Class II DQA and DQB genes between estuarine and coastal populations of the bottlenose dolphin, Tursiops truncatus, an apex predator whose health status is indicative of anthropogenic impacts on the ecosystem. The coding regions had 10 alleles each at DQA and DQB; the promoters had 6 and 7 alleles at DQA and DQB, respectively with variation within key regulatory motifs. Positive selection was observed for the coding regions of both genes while both coding and promoter regions exhibited geographic differences in allele composition that likely indicates diversifying selection across habitats. Most notable was the discovery of a complete duplication of a 14-bp T-box motif in the DQA promoter. Four class II promoter regions (DQA, DQB, DRA, DRB) were characterized in species from four cetacean families (Delphinidae, Monodontidae, Lipotidae, and Physeteridae) and revealed substantial promoter structural diversity across this order. Peptide binding regions may not be the only source of adaptive potential within cetacean MHC for responding to pathogenic threats. These findings are the first analysis of cetacean MHC regulatory motifs, which may divulge unique immunogenetic strategies among cetaceans and reveal how MHC transcriptional control continues to evolve. The combined MHC regulatory and coding data provide new genetic context for distinct vulnerability profiles between coastal and estuarine populations, which are key concerns for health and risk management.

Analysis of the genetic diversity and structure of the Spanish apple genetic resources suggests the existence of an Iberian genepool

AbstractThe nature and structure of genetic diversity in the Spanish apple germplasm preserved at the national level was widely unknown, since studies performed to date on this topic have been exclusively carried out at the regional scale. Here, 1453 accessions from Spanish collections of Malus × domestica were evaluated with a common set of 13 SSR (Simple Sequence Repeats) markers in order to estimate genetic diversity, to identify the underlying genetic structure and to unravel the relationships among them and among a wide set of international cultivars for reference. In total, 737 unique genotypes were identified, 581 diploids and 156 triploids. Using a model‐based Bayesian clustering procedure, two reconstructed populations were obtained for diploid genotypes; one retaining only Spanish cultivars (42% of genotypes), and a second containing all foreign cultivars the latter exhibiting evidence supporting the existence of a secondary sub‐structure. Similarly, analysis performed on the 156 triploid genotypes also revealed two reconstructed populations; one exclusively associated with local Spanish genotypes (44%). The Jaccard coefficient allowed clustering by UPGMA (Unweighted Pair Group Method) diploid and triploid genotypes, and remarkable differences in allelic composition among the different partitioning levels were found. AMOVA analyses showed moderate but significant differentiation among the main groups (0.08 ≤ FST ≤ 0.12). Our results highlight an important fraction of the Spanish apple germplasm that constitutes a differentiated genepool with respect to the international and commercial apple cultivars. Moreover, the extent of the Spanish genetic diversity was spatially distributed along the northern Iberian Peninsula, suggesting an extensive migration of genotypes along the country. This study is the first valuable action for genetic conservation of apple at the national scale, and constitutes a decisive step towards the definition of a Spanish core collection that will be useful for further studies in dissecting the genetic control of important horticultural traits through genome‐wide association analysis in apple.

Genomic and transcriptomic analysis of aroma synthesis in two hybrids between Saccharomyces cerevisiae and S. kudriavzevii in winemaking conditions.

BackgroundAroma is one of the most important attributes defining wine quality in which yeasts play a crucial role, synthesizing aromatic compounds or releasing odourless conjugates. A present-day trend in winemaking consists of lowering fermentation temperature to achieve higher aroma production and retention. S.cerevisiae × S.kudriavzevii hybrids seem to have inherited beneficial traits from their parental species, like fermenting efficiently at low temperature or producing higher amounts of certain aromatic compounds. In this study, allelic composition and gene expression of the genes related to aroma synthesis in two genetically and phenotypically different S.cerevisiae × S.kudriavzevii hybrids, Lalvin W27 and VIN7, were compared and related to aroma production in microvinifications at 12 and 28 °C. In addition, the contribution of the allele coming from each parental to the overall expression was explored by RT-PCR.ResultsThe results indicated large differences in allele composition, gene expression and the contribution of each parental to the overall expression at the fermentation temperatures tested. Results obtained by RT-PCR showed that in ARO1 and ATF2 genes the S.kudriavzevii allele was more expressed than that of S.cerevisiae particularly at 12 °C.ConclusionsThis study revealed high differences regarding allele composition and gene expression in two S.cerevisiae × S.kudriavzevii hybrids, which may have led to different aroma profiles in winemaking conditions. The contribution of the alleles coming from each parental to the overall expression has proved to differently influence aroma synthesis. Besides, the quantitative contribution to the overall gene expression of the alleles coming from one parental strain or the other was clearly determined by the fermentation temperature for some genes.

Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic Killifish (Fundulus heteroclitus)

BackgroundThe most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed.ResultsSince the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs.ConclusionsThe observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.

High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.)

Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic polymorphism in plant genomes. SNP markers are valuable tools for genetic analysis of complex traits of agronomic importance, linkage and association mapping, genome-wide selection, map-based cloning, and marker-assisted selection. Current challenges for SNP genotyping in polyploid outcrossing species include multiple alleles per loci and lack of high-throughput methods suitable for variant detection. In this study, we report on a high-resolution melting (HRM) analysis system for SNP genotyping and mapping in outcrossing tetraploid genotypes. The sensitivity and utility of this technology is demonstrated by identification of the parental genotypes and segregating progeny in six alfalfa populations based on unique melting curve profiles due to differences in allelic composition at one or multiple loci. HRM using a 384-well format is a fast, consistent, and efficient approach for SNP discovery and genotyping, useful in polyploid species with uncharacterized genomes. Possible applications of this method include variation discovery, analysis of candidate genes, genotyping for comparative and association mapping, and integration of genome-wide selection in breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-011-9566-x) contains supplementary material, which is available to authorized users.

Electrophoretic studies on two sibling species Thera variata and Thera obeliscata (Lepidoptera, Geometridae) with special reference to phosphoglucomutase and phosphoglucose isomerase.

Ten enzymes from the two sibling species Thera obeliscata and T. variata were compared by means of starch gel electrophoresis. Only one enzyme indicated an absolute interspecific difference, whereas interspecific differences in allele composition of two allelomorphic enzymes were established. The allozyme variation of phosphoglucomutase and phosphoglucose isomerase in three populations of Thera obeliscata was analysed. No differences between the populations were found. In Thera variata only phosphoglucomutase shows allozyme variation. This was analysed in 12 populations. A diffuse geographic as well as a year to year pattern of variation was revealed. The year to year variation is explained as due to selection against the Pgm- 3,5 heterozygote, since this type has been found in deficit compared to Hardy-Weinberg ratios in all samples.

Rapid Evolution of the MH Class I Locus Results in Different Allelic Compositions in Recently Diverged Populations of Atlantic Salmon

We compared major histocompatibility class I allelic diversity in two currently reproductively isolated Atlantic salmon (Salmo salar) populations (Irish and Norwegian) with a common postglacial origin in order to test for among-population differences in allelic composition and patterns of recombination and point mutation. We also examined the evidence for adaptive molecular divergence at this locus by analyzing the rate of amino acid replacement in relation to a neutral expectation. Contrary to our prediction, and in contrast to the situation for other genetic markers, the two populations have almost nonoverlapping sets of major histocompatibility class I alleles. Although there is a strong signal of point mutation that predates population divergence, recent recombination, acting in similar, but not identical, ways in both populations appears to be a significant force in creating new alleles. Moreover, selection acting on peptide-binding residues seems to favor new recombinant alleles and is likely to be responsible for the rapid divergence between populations.

Characterization of simple sequence repeats in Japanese chestnut

SummaryFifteen SSR (simple sequence repeat) loci were developed in Japanese chestnut (Castanea crenata Sieb et Zucc.) using a genomic library enriched for (AG)/(TC). The SSR loci obtained produced 1–16 alleles per locus, of which 14 showed polymorphisms. The average values of heterozygosity and polymorphic information content among the 14 loci were 0.50 and 0.54, respectively. Genetic relatedness was evaluated for 30 Japanese chestnut accessions using 14 polymorphic SSR loci, with no distinct differences in allele composition observed between cultivated and wild natures as well as between Japanese and Korean origins. SSR loci developed in the Japanese chestnut could be successfully transferable to other Castanea species. Diversity and genetic relationship in Castanea pp. was examined based on the nucleotide sequences of putative SSR alleles.

Allozymic and Isozymic Evidence for Polytypy in the North American Catostomid Genus Cycleptus

Abstract To assess patterns of geographic variation in the wide-ranging North American catostomid genus Cycleptus, 23 specimens were obtained from six locations among four drainage systems that exit into the Gulf of Mexico. Starch gel electrophoresis was used to compare gene products of 47 loci. A contingency chi-square test showed that the 23 samples did not come from a single, random-breeding population. Tests using exact probabilities showed that all samples from within each of the four drainage systems were in agreement with Hardy-Weinberg equilibrium expectations. Pairwise combinations showed that only two of the drainages could be combined and still result in equilibrium. Three allopatric genetic units are recognized: (1) Rio Grande drainage, (2) Mississippi drainage, and (3) the Alabama plus Pascagoula drainages. All three units can be distinguished by differences in allelic composition at certain enzymatic loci, levels of heterozygosity, number of genes expressed (some genes have been silenced in ...

Genetic differentiation among northern and southern populations of the moor frog Rana arvalis Nilsson in central Europe.

Starch gel electrophoresis and morphometric characters were used to assess the geographical variation between 14 populations of the moor frog, Rana arvalis, from northern and southern areas in Central Europe. Six of the 13 screened allozyme loci were polymorphic (95% criterion). No fixed differences in allele composition between the two regions were found. Some of the alleles were region specific. Genetic variability as measured by expected heterozygosity (He) and number of alleles per locus was significantly lower in the southern samples than in northern ones (He=0.104 and He=0.156, alleles/locus=1.6 and 1.8 respectively). This is interpreted as a consequence of the different past history of these two groups during the Pleistocene. Population subdivision, as measured by FST, was substantial (0.124 and 0.078 for the southern and northern group, respectively); 59.9% of the between-locality variation is attributed to this division into two geographical groups. Isolation-by-distance was detected by significant negative correlation between the estimate of gene flow (log M) and log(geographical distance) only for the southern population groups. This indicates that the northern populations have recently recolonized their contemporary distribution area. The mean genetic distance between the northern and southern group of populations was DN=0.062. Despite the relatively low genetic distance between them, the two population groups form two distinct clusters in the maximum likelihood (ML) tree. Discriminant analysis on 11 size adjusted body measurements showed considerable overlap between populations from different geographical areas. An isolated Romanian Reci population which genetically belongs to the southern group of populations was morphologically situated in an intermediate position between northern and other southern populations.

Population genetics of Atlantic cod using amplified single locus minisatellite VNTR analysis

Atlantic cod, Gadus morhua, have been examined extensively over the last two decades using allozyme electrophoresis. More recently, several populations have been studied using mitochondrial DNA (RFLP and sequence) analysis, together with multilocus minisatellite DNA and also microsatellite DNA analyses. The declining status of cod populations in many areas highlights the need for powerful genetic markers capable of discriminating between cod populations, in order to facilitate the design of effective management strategies. Single locus minisatellite DNA analysis offers a potentially powerful alternative to the already mentioned techniques, by combining the power of detection of hypervariable DNA, with non‐radioactive techniques in a cost‐effective way. As a preliminary investigation into the feasibility of using this approach, four Atlantic cod samples (North Norway, Irish Sea, Scotian Shelf and Northern Cod) were screened at a single polymerase chain reaction (PCR) amplified minisatellite locus (Mmer‐AMP2), using primers designed for the flanking regions of a whiting Merlangius merlangus L., minisatellite DNA locus. PCR products separated by agarose electrophoresis and viewed by ethidium bromide fluorescence under UV illumination, consisted of one or two bands per individual (corresponding to homozygotes and hétérozygotes, respectively). Twenty‐two alleles were resolved in 119 cod, and sample heterozygosity ranged from 0.76 to 0.90. Samples from opposite sides of the Atlantic showed highly significant differences in allelic composition. The results suggest that single locus minisatellite DNA analysis may be of substantial benefit to furthering our knowledge of the population genetics of Atlantic cod.

Allelic variation at Glu-1 loci in some Yugoslav wheat cultivars

The high molecular weight (HMW) subunits of glutenin extracted from flour of 36 Yogoslav wheat cultivars were separated by SDS-PAGE to identify their alleles, and the frequency of each allele was calculated. Eleven alleles from the three Glu-loci were recognized, three at the Glu-A1 locus, six at the Glu-B1 locus and two at the Glu-D1 locus. The most frequent allele was “a” (55.5%) from Glu-D1, which controls synthesis of subunits 2+12. The Glu-1 quality score varied from 4 (KG-III/27, KG-75, Morava and KG-101/7) to 10 (Lepenica). The mean Glu-1 quality score of cultivars and lines from Kragujevac was 6.8, for cultivars from Zagreb 7.2, and for cultivars from Novi Sad was 7.9. Most of the genotypes with a quality score of 8 or above, had high sedimentation values (Zeleny test). There were no significant differences in allelic composition at the Glu-1 loci among wheat genotypes from Kragujevac, Novi Sad and Zagreb.

Polymorphism of mannose phosphate isomerase in North Sea and Baltic Sea populations of the amphipods Gammarus zaddachi and G. salinus

Genetic variation at the mannosephosphate isomerase (MPI) locus was examined in the euryhaline sibling species Gammarus zaddachi Sexton and G. salinus Spooner. Both crustacean amphipods share identical enzyme mobilities, following electrophoresis on vertical starch gels. The MPI locus turned out to be highly polymorphic; it is encoded by 6 alleles in G. zaddachi and 7 alleles in G. salinus. Geographic variation of allelic diversity was studied in samples from 9 G. zaddachi and 10 G. salinus populations, primarily obtained from Baltic Sea and North Sea sites. Patterns of inter- and intraspecific heterogeneity are described. Differences in allelic composition exist between Baltic and North Sea samples of G. salinus. In G. zaddachi, levels of polymorphism are higher in North Sea populations than in those from Baltic Sea areas. The significance of these findings is discussed in the light of previous biochemical genetic investigations on the population structure of the two amphipods considered.