Biometric-genetic analysis of genotype dissimilarity in diallel crosses of spring wheat

A new biometric-genetic model and parameters described in [1] have been used for analysis of pair dissimilarity between spring wheat cultivars and F1 hybrids obtained by diallel crossing. The dissimilarity between the reactions of different genotypes estimated by a growth trait (plant height) served as a metric. The mode of inheritance of dissimilarity has been determined, and the cultivars that are the most dissimilar in allelic composition have been detected.     

Biometric-genetic analysis of genotype dissimilarity: The model and parameters

An additive-dominant model and parameters for biometric-genetic analysis of pair dissimilarity between genotypes have been developed. The analyzed dissimilarity metrics are presumed to be determined by the quantitative traits of plant lines and F₁ hybrids obtained by diallel crossing. Relationships between dissimilarity parameters have been determined, and algorithms for estimating their use, in particular, for detecting the most heterozygous hybrids are suggested.     

Genetic Diversity of Kenaf (Hibiscus cannabinus) Evaluated by Inter-Simple Sequence Repeat (ISSR)

Understanding genetic diversity is very useful for scientific utilization for breeding. In this study, we estimated the genetic distances in a panel of 84 kenaf accessions collected from 26 countries and regions using ISSR markers. The results of UPGMA analysis showed that kenaf germplasm had abundant genetic variation, with genetic dissimilarity coefficients ranging from 0.01 to 0.62. The in-group dissimilarity coefficient (0.29) was observed in 84 kenaf accessions, and all the accessions could be divided into three groups: cultivars (L_1–1), relatively wild species (L_1–2 and L_1–3), and wild species (the others). Further in-group analysis in group L_1–1 (0.19) revealed that the kenaf cultivars could be divided into five subgroups with distinct regional characteristics. It is imperative that genes be exchanged among all kinds of tested varieties from different origins. The results provide a useful basis for kenaf germplasm research and breeding.     

The effect of species composition dissimilarity on plant–herbivore network structure is not consistent over time

The structural organization of several antagonistic networks has been demonstrated to be largely conserved through time and space even when species beta-diversity is high. This might occur either because species are replaced by others that fulfill similar network roles or because interaction probabilities are given by species relative abundances rather than by their functional traits. Alternatively, if species-specific traits are important drivers of realized interactions, any change in species composition should promote a certain degree of network structural dissimilarity. Here, we used a spatial-temporal system comprising asteraceous plants and flower head herbivores from remnants of Brazilian Cerrado to investigate whether the relationship between spatial beta-diversity of species and network structural dissimilarity changes over time. We measured species beta-diversity using Sørensen's dissimilarity index (β_sor) and its components of species replacement (β_-3) and richness differences (β_rich). Network structural dissimilarity was estimated using three different metrics: connectance, modularity, and web asymmetry. We show that, in general, the effect of species beta-diversity on network structure was time-dependent: While some periods presented a positive relationship between spatial beta-diversity and network structural dissimilarity, others presented no significant relationship. This indicates that functionally similar species may present different turnover rates at distinct periods, and different non-exclusive processes affect plant–herbivore network organization across time.     

Genetic Structure of Remnant Populations and Cultivars of Switchgrass (Panicum virgatum) in the Context of Prairie Conservation and Restoration

Switchgrass (Panicum virgatum L.) is a dominant, perennial C₄ grass of North American tallgrass prairies with cultivars that are widely used in grassland restoration, pastures, and landscaping. However, these cultivars may be genetically dissimilar to small, remnant populations, raising concerns about altered genetic composition of native populations through gene flow. To address this issue on a local scale in Ohio and Illinois, we used microsatellite markers to characterize genetic diversity and differentiation of 10 remnant prairie populations (5 in each state) and 8 common cultivars. The bulk of genetic variation was found to reside within rather than among wild populations, consistent with the outcrossing breeding system of switchgrass. Genetic diversity was similar among the remnant populations despite large differences in area (approximately 2–2,590 ha), highlighting the importance of small native populations as reservoirs of variation and potential seed sources for prairie restoration. Cultivars generally had similar levels of variation to the wild populations, but we found clear genetic dissimilarity between wild and cultivated gene pools (especially for Kanlow, but also Trailblazer, Blackwell, Dacotah, Summer, and Sunburst cultivars). This suggests that using cultivars in local prairie restoration efforts may alter the genetic composition of wild populations. Whether such changes are deemed as negative depends on the cultivar under consideration and specific conservation goals for preserving native switchgrass populations. Patterns of genetic variation in remnant prairie populations and potential cultivar sources can be used to develop guidelines for restoration as well as future planting of cultivars for biofuels.     

Identification of Cultivar Differences in Seed Polypeptide Composition of Peanuts (Arachis hypogaea L.) by Two-Dimensional Polyacrylamide Gel Electrophoresis

Seed polypeptides from several cultivars of peanut (Arachis hypogaea L.) have been compared by means of a two-dimensional polyacrylamide gel electrophoresis. Protein was extracted from the defatted peanut meal by homogenizing in 5 millimolar K₂CO₃-9.5 molar urea. After addition of Nonidet P-40 (2%, v/v) and dithiothreitol (0.5%, w/v) the solution was centrifuged at 25,000 g. This procedure led to solubilization of more than 95% of the total protein. The clear supernatant fraction was then subjected to two-dimensional polyacrylamide gel electrophoresis, employing isoelectric focusing in the first dimension and electrophoresis in presence of sodium dodecyl sulfate in the second. After examining several cultivars, it was possible to construct a composite map to include all of the polypeptide species found among all of the cultivars examined. At least 74 major and between 100 and 125 minor components were detectable by Coomassie blue staining. The majority of these had isoelectric points between pH 4.4 and 8.0, and molecular weights between 16,000 and 75,000. Several different cultivars have been compared using this method and it has been shown that considerable variation exists among the major polypeptides present. The method should prove valuable for analyzing different genotypes and selecting varieties with a particular storage protein make-up, as well as for following compositional changes that occur during seed development and germination.     

Biometric-genetic analysis of genotype dissimilarity: the model and parameters

An additive-dominant model and parameters for biometric--genetic analysis of pair dissimilarity between genotypes have been developed. The analyzed dissimilarity metrics are presumed to be determined by the quantitative traits of plant lines and F1 hybrids obtained by diallel crossing. Relationships between dissimilarity parameters have been determined, and algorithms for estimating their use, in particular, for detecting the most heterozygous hybrids are suggested.     

Mapping of QTL associated with heading time in winter wheat

The duration of periods to heading has been investigated for 107 winter wheat cultivars of different origins. To reveal the DNA markers to QTL associated with the heading rate, the cultivars and individual plants of the F₂ progeny from a cross between the Omskaya Ozimaya and Numbu Komugi cultivars, which contrasted most in respect of the analyzed trait, have been analyzed by SSR-PCR. Two revealed loci—Xgwm512 and Xgwm429—explain 19.3% (8.9% and 10.4%, respectively) of all differences in the duration of periods to heading, which were observed in individual F₂ plants under field conditions.     

Performance of pairwise shape dissimilarity morphometrics on nonmammalian taxa (Insecta: Neuroptera: Mantispidae)

Morphometric dissimilarity metrics aim to quantify the variation between compared specimens such that inferences about their relatedness and alpha taxonomy can be made. Recently, the technique has developed metrics that purport to quantify shape dissimilarity between specimens—employing the use of least squares regression analysis. These metrics have been well applied by studies in the hominin fossil record with an arguably unsubstantiated backing for the technique. Originally postulated was the log₁₀ se_m metric which subsequently led to the standard error test of the null hypothesis metric. Following this, the standard deviation of logged ratios (S_LR) metric arose as a pairwise dissimilarity metric that constrains the regression to a zero‐intercept, that is, a significant development in the robustness of the technique. This metric was tested on extant primates in order to evaluate its effectiveness alongside the two other metrics. It was shown to be the most reliable for comparisons between specimens of primates, but was unable to discriminate between heterospecific and conspecific comparisons. Arguably, an alternative model organism with which to compare the technique is lacking. This study considers shape dissimilarity metrics with respect to a group of nonmammalian organisms (mantidflies) and tests the metrics against three lines of evidence (morphology, CO1‐DNA, and geographic distribution) that can delimit the species‐level taxonomy for the group. It is shown that the metrics are unable to discriminate between pairwise comparisons of closely related species, resulting in biologically erroneous groupings, and contradicting the groupings derived from morphological, CO1‐DNA, and distributional comparisons. It is thus asserted that the technique is unsuitable for use in alpha taxonomy as an additional line of evidence in mantidflies. It is further supposed that morphometrics in general should be employed with caution in studies of evolutionary history as phylogeny is not the only information contained within morphometric data. J. Morphol. 276:1482–1494, 2015. © 2015 Wiley Periodicals, Inc.     

Genetic dissimilarity of putative gamma-ray-induced 'Preciosa-AAAB-Pome type' banana (Musa sp) mutants based on multivariate statistical analysis

Bananas are among the most important fruit crops worldwide, being cultivated in more than 120 countries, mainly by small-scale producers. However, short-stature high-yielding bananas presenting good agronomic characteristics are hard to find. Consequently, wind continues to damage a great number of plantations each year, leading to lodging of plants and bunch loss. Development of new cultivars through conventional genetic breeding methods is hindered by female sterility and the low number of seeds. Mutation induction seems to have great potential for the development of new cultivars. We evaluated genetic dissimilarity among putative 'Preciosa' banana mutants generated by gamma-ray irradiation, using morphoagronomic characteristics and ISSR markers. The genetic distances between the putative 'Preciosa' mutants varied from 0.21 to 0.66, with a cophenetic correlation coefficient of 0.8064. We found good variability after irradiation of 'Preciosa' bananas; this procedure could be useful for banana breeding programs aimed at developing short-stature varieties with good agronomic characteristics.     

Genetic Diversity in Grapevine Germplasm Resources in the Coruh Valley Revealed by RAPD Markers

Random amplified polymorphic DNA analysis was carried out in 35 autochthonous table grapevine cultivars grown in Coruh valley. Fifty-five oligonucleotide primers were screened on cultivars, and among them, 12 primers showed clear polymorphic patterns. PCR amplification with 12 primers generated a total of 157 polymorphic bands. There was genetic variation among the cultivars with values of genetic diversity ranging from 0.19 to 0.72 using the Jaccard coefficient. UPGMA analysis of the distance matrix resulted in a dendrogram with two main clusters. The first cluster included 28 cultivars and the second 7 cultivars. The greatest genetic similarity was observed between cultivars Gah and Kolik, while the greatest dissimilarity was observed between cultivars Gah and Siyah Kus Uzumu. The dendrogram revealed that the cultivars present in Coruh valley can be distinguished to a relatively high degree.     

Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches

Beta diversity and nestedness are central concepts of ecology and biogeography and evaluation of their relationships is in the focus of contemporary ecological and conservation research. Beta diversity patterns are originated from two distinct processes: the replacement (or turnover) of species and the loss (or gain) of species leading to richness differences. Nested distributional patterns are generally thought to have a component deriving from beta diversity which is independent of replacement processes. Quantification of these phenomena is often made by calculating a measure of beta diversity, and the resulting value being subsequently partitioned into a contribution by species replacement plus a fraction shared by beta diversity and nestedness. Three methods have been recently proposed for such partitioning, all of them based on pairwise comparisons of sites. In this paper, the performance of these methods was evaluated on theoretical grounds and tested by a simulation study in which different gradients of dissimilarity, with known degrees of species replacement and species loss, were created. Performance was also tested using empirical data addressing land‐use induced changes in endemic arthropod communities of the Terceira Island in the Azores. We found that the partitioning of β_cc (dissimilarity in terms of the Jaccard index) into two additive fractions, β_‐3 (dissimilarity due to species replacement) plus β_rich (dissimilarity due to richness differences) reflects the species replacement and species loss processes across the simulated gradients in an ecologically and mathematically meaningful way, whilst the other two methods lack mathematical consistency and prove conceptually self‐contradictory. Moreover, the first method identified a selective local extinction process for endemic arthropods, triggered by land‐use changes, while the latter two methods overweighted the replacement component and led to false conclusions. Their basic flaw derives from the fact that the proposed replacement and nestedness components (deemed to account for species loss) are not scaled in the same way as the measure that accounts for the total dissimilarity (Sørensen and Jaccard indices). We therefore recommend the use of β_cc=β_‐3+β_rich, since its components are scaled in the same units and their responses are proportional to the replacement and the gain/loss of species.     

Cellular double-stranded RNA in Phaseolus vulgaris

Summary High molecular weight double-stranded (ds) RNAs have been detected in apparently virus-free French (common) bean Phaseolus vulgaris cv. Black Turtle Soup (BTS). Several other bean cultivars were free of detectable high molecular weight dsRNAs. The dsRNAs have been partially characterized and have homology to the BTS genome as well as to the genomes of other bean cultivars. The T _m of hybrids formed between BTS DNA and denatured dsRNA have been estimated.     

Partial molecular characterization of some kiwi fruit cultivars by RAPD markers

Molecular variability among seven cultivars of A. deliciosa var. deliciosa was investigated through RAPD markers. Thirty four decamer primers were screened generating polymorphic patterns of amplified DNA for these cultivars. Twenty one selected primers gave clear and reporducible patterns. A total of 430 bands were produced and 29.37% of them were polymorphic. The patterns distinguished between the cultivars and their analysis established an approach to classification within A. deliciosa var. deliciosa based on RAPD markers. The dendrogram clearly differentiated male from female cultivars. While abbot and allison female cultivars were closely related, bruno and abbot female cultivars showed maximum dissimilarity.     

Evaluating the use of pairwise dissimilarity metrics in paleoanthropology

Questions of alpha taxonomy are best addressed by comparing unknown specimens to samples of the taxa to which they might belong. However, analysis of the hominin fossil record is riddled with methods that claim to evaluate whether pairs of individual fossils belong to the same species. Two such methods, log se_m and the related STET method, have been introduced and used in studies of fossil hominins. Both methods attempt to quantify morphological dissimilarity for a pair of fossils and then evaluate a null hypothesis of conspecificity using the assumption that pairs of fossils that fall beneath a predefined dissimilarity threshold are likely to belong to the same species, whereas pairs of fossils above that threshold are likely to belong to different species. In this contribution, we address (1) whether these particular methods do what they claim to do, and (2) whether such approaches can ever reliably address the question of conspecificity. We show that log se_m and STET do not reliably measure deviations from shape similarity, and that values of these measures for any pair of fossils are highly dependent upon the number of variables compared. To address these issues we develop a measure of shape dissimilarity, the Standard Deviation of Logged Ratios (s_LR). We suggest that while pairwise dissimilarity metrics that accurately measure deviations from isometry (e.g., s_LR) may be useful for addressing some questions that relate to morphological variation, no pairwise method can reliably answer the question of whether two fossils are conspecific.     

AFLP analysis of genetic variability in New Guinea impatiens

New Guinea impatiens ( Impatiens hawkeri) is an economically important floral crop, however, little work has been conducted to further our understanding of the genetics of this crop. In this study, we used amplified fragment length polymorphism (AFLP) technology to investigate the level of polymorphism present among 41 commercial cultivars of New Guinea impatiens, study their genetic relatedness, and assess the genetic diversity in this material. An efficient DNA extraction protocol was developed, and a total of 48 EcoRI and MseI primer combinations were used for PCR amplification. Amplification products were then subjected to polyacrylamide gel electrophoresis. The AFLP analysis showed that all 41 cultivars generated between 73 and 130 scoreable polymorphic bands per primer combination. Gower's Genetic Dissimilarity estimates for the entire set of cultivars ranged between 0.940 and 0.488. A dendogram was generated from these dissimilarity data that revealed four groupings among these 41 cultivars. The implications of these results on genotypic variation, genetic relationships, and genetic diversity in New Guinea impatiens will be discussed.     

Geographical patterns of turnover and nestedness-resultant components of allelic diversity among populations

The analysis of geographical patterns in population divergence has always been a powerful way to infer microevolutionary processes involved in population differentiation, and several approaches have been used to investigate such patterns. Most frequently, multivariate spatial patterns of population differentiation are analyzed by computing pairwise genetic distances or F_ST (or related statistics, such as ?_ST from AMOVA), which are then correlated with geographical distances or landscape features. However, when calculating distances, especially based on presence-absence of alleles in local populations, there would be a confounding effect of allelic richness differences in the population differentiation. Moreover, the relative magnitude of these components and their spatial patterns can help identifying microevolutionary processes driving population differentiation. Here we show how recent methodological advances in ecological community analyses that allows partitioning dissimilarity into turnover (turnover) and richness differences, or nestedness-resultant dissimilarity, can be applied to allelic variation data, using an endemic Cerrado tree (Dipteryx alata) as a case study. Individuals from 15 local populations were genotyped for eight microsatellite loci, and pairwise dissimilarities were computed based on presence-absence of alleles. The turnover of alleles among populations represented 69?% of variation in dissimilarity, but only the richness difference component shows a clear spatial structure, appearing as a westward decrease of allelic richness. We show that decoupling richness difference and turnover components of allelic variation reveals more clearly how similarity among populations reflects geographical patterns in allelic diversity that can be interpreted in respect to historical range expansion in the species.     

Changes in free and bound fractions of aroma compounds of four Vitis vinifera cultivars at the last ripening stages

The volatile composition of white Agudelo, Blanco lexitimo, Godello and red Serradelo cultivars (NW Spain) harvested at two different stages of ripening have been evaluated. C₆-compounds, alcohols, volatile fatty acids, monoterpenes, C₁₃-norisoprenoids, volatile phenols and carbonyl compounds were identified and quantified in free and glycosidically bound forms by gas chromatography–mass spectrometry (GC–MS). The total volatile concentration showed a significant increase between the two ripening stages studied for all cultivars. The free volatile composition increased during maturity for Godello and Serradelo cultivars; however the glycosidically bound concentration increases for all cultivars with exception of B. lexitimo. Free C₆-compounds ((E)-2-hexanal, 1-hexanol and (E)-2-hexen-1-ol) and bound alcohols (benzyl alcohol and 2-phenylethanol) showed the highest concentrations of volatile compounds for all grape cultivars in the two dates studied. Godello cultivar showed the highest change of volatile concentration between two ripening dates because of the high value of free C₆-compounds. B. lexitimo was the most terpene-rich cultivar at the last ripening stage due to linalool; however C₁₃-norisoprenoids in free form were detected in low concentrations for all cultivars but not in Godello and B. lexitimo cultivars at the last ripening stage. Free hexanoic acid increased during ripening in all cultivars. The evolution of volatiles during ripening of grape juice from the cultivars studied was not proportional to the changes in sugar content, which shows that the technological and aromatic maturities did not occur at the same time in these cultivars. The results also showed the cultivar * ripening date interaction for all, free and bound, groups of compounds.     

Genetic and ‘cultural’ similarity in wild chimpanzees

The question of whether animals possess ‘cultures’ or ‘traditions’ continues to generate widespread theoretical and empirical interest. Studies of wild chimpanzees have featured prominently in this discussion, as the dominant approach used to identify culture in wild animals was first applied to them. This procedure, the ‘method of exclusion,’ begins by documenting behavioural differences between groups and then infers the existence of culture by eliminating ecological explanations for their occurrence. The validity of this approach has been questioned because genetic differences between groups have not explicitly been ruled out as a factor contributing to between-group differences in behaviour. Here we investigate this issue directly by analysing genetic and behavioural data from nine groups of wild chimpanzees. We find that the overall levels of genetic and behavioural dissimilarity between groups are highly and statistically significantly correlated. Additional analyses show that only a very small number of behaviours vary between genetically similar groups, and that there is no obvious pattern as to which classes of behaviours (e.g. tool-use versus communicative) have a distribution that matches patterns of between-group genetic dissimilarity. These results indicate that genetic dissimilarity cannot be eliminated as playing a major role in generating group differences in chimpanzee behaviour.     

Compositional dissimilarity patterns of reptiles and amphibians in insular systems around the world

Several studies have shown that taxa with poor dispersal ability have a higher level of compositional dissimilarity than good dispersers. However, compositional dissimilarity patterns between islands with respect to dispersal ability of taxa have never been investigated before. In this study, we investigated compositional dissimilarity patterns of three taxonomic groups, namely amphibians, lizards, and snakes, differing in their dispersal abilities, in various insular systems around the world. We compiled presence–absence matrices, based on which we calculated several metacommunity indices to check for differences among taxonomic groups and island types (oceanic and continental shelf) using classical statistical tests and generalized linear mixed-effects models. According to our results, compositional dissimilarity was positively affected by the isolation of the insular system, in accordance to theory. In particular, oceanic systems were characterized by a high level of compositional dissimilarity between islands and subsequently by a low level of nestedness. SIEs may be generating these patterns causing distortions from expected levels of nestedness. Similar to our predictions, compositional dissimilarity patterns were also dependent on taxon-specific dispersal ability, with good dispersers showing lower levels of between-island compositional dissimilarity than poor dispersers in continental shelf systems. However, this pattern was not observed in oceanic systems. In conclusion, compositional dissimilarity in insular systems is dependent on both taxon and island type.