Individual Heterozygosity Research Articles

Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass

The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.

The longevity gene Klotho is differentially associated with cognition in subtypes of schizophrenia

Cognitive impairment is a core feature of schizophrenia and impacts negatively the functioning of affected individuals. Cognitive decline correlates with aging, and is the primary cause of loss of independence and reduced quality of life. The klotho gene is a key modulator of aging, with expression deficiency resulting in premature aging, while overexpression extends lifespan and enhances cognition. A haplotype and functional human variant of the gene, KL-VS, increases expression and promotes longevity. KL-VS heterozygosity is associated with enhanced cognition and a larger volume of the right dorsolateral prefrontal cortex, a region involved in planning and decision-making, which is especially susceptible to shrinkage with age. We examined the effect of KL-VS heterozygosity on cognition in 497 schizophrenia patients and 316 healthy controls from the Western Australian Family Study of Schizophrenia (WAFSS) who had been comprehensively characterised by neurocognitive tests and classified into cognitively deficient (CD) and cognitively “spared” (CS) clusters. An older, cognitively normal population sample from the Health in Men Study (HIMS) was included to allow assessment of heterozygosity and memory in aged individuals. We show that heterozygosity is associated with better learning and memory in the younger WAFSS healthy controls but not in the aging HIMS sample. However, in schizophrenia patients, KL-VS has a selective effect on memory, with heterozygotes in CD and CS clusters performing worse than non-carriers. This effect was significant and more severe in the CD cluster, reinforcing the utility of subtyping patients into CD and CS clusters that may differ in their genetic underpinnings.

Viability selection creates negative heterozygosity\u2013fitness correlations in female Black Grouse Lyrurus tetrix

There is widespread interest in the relationship between individual genetic diversity and fitness–related traits (heterozygosity–fitness correlations; HFCs). Most studies have found weak continuous increases of fitness with increasing heterozygosity, while negative HFCs have rarely been reported. Negative HFCs are expected in cases of outbreeding depression, but outbreeding is rare in natural populations. Negative HFCs may also arise through viability selection acting on low heterozygosity individuals at an early stage producing a skew in the heterozygosity distribution. We tested this idea using survival and clutch parameters (egg mass, egg volume, chick mass, clutch size) in female Black Grouse Lyrurus tetrix and carried out simulations to determine how survival selection may impact the HFCs measured using clutch parameters. We show that survival is positively related to both individual heterozygosity and female body mass. There was a positive effect of body mass on all clutch parameters, but the selective mortality of females with both low heterozygosity and low body mass led to overrepresentation of high heterozygosity-low body mass females and hence a negative relationship between egg volume and heterozygosity. Using simulated data, we show that survival selection acting on both low body mass and low heterozygosity leads to a skew in the quality of breeding females, resulting in negative HFCs with egg volume. Our results indicate that survival selection can strongly influence the strength and direction of any HFCs that occur later in life and that only an integration of all aspects of individual reproductive investment and reproductive success can enable us to fully understand how heterozygosity can shape individual fitness.

Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms

In the USA, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million single nucleotide polymorphism (SNP) markers detected from exome sequencing were used to test for single-locus associations, SNP-SNP interactions, and correlation of individual heterozygosity with phenotypic traits. A total of 36 SNP-trait associations were found for specific leaf area (5 SNPs), branch angle (2), crown width (3), stem diameter (4), total height (9), carbon isotope discrimination (4), nitrogen concentration (2), and pitch canker resistance traits (7). Eleven SNP-SNP interactions were found to be associated with branch angle (1 SNP-SNP interaction), crown width (2), total height (2), carbon isotope discrimination (2), nitrogen concentration (1), and pitch canker resistance (3). Non-additive effects imposed by dominance and epistasis account for a large fraction of the genetic variance for the quantitative traits. Genes that contain the identified SNPs have a wide spectrum of functions. Individual heterozygosity positively correlated with water use efficiency and nitrogen concentration. In conclusion, multiple effects identified in this study influence the performance of loblolly pines, provide resources for understanding the genetic control of complex traits, and have potential value for assisting breeding through marker-assisted selection and genomic selection.

Polimorfisme Protein Plasma Darah pada Kelinci Rex, Lokal dan New Zealand White (POLYMORPHISM OF BLOOD PLASMA PROTEIN OF REX, LOCAL AND NEW ZEALAND WHITE RABBIT)

The objective of this study was to determine genetic diversity of rabbit by blood plasma protein variance using electrophoresis at loci of pre-albumin (Pa), albumin (Alb), ceruloplasmin (Cp), transferrin (Tf), post-transferrin (P-tf) and amylase-I (Am-I). The blood analysis was performed at the Laboratory of Physiology and Biochemistry, Faculty of Veterinary Medicine, Gadjah Mada University, Yogyakarta. The materials used were 63 blood samples of rex, local and new zealand white (NZW) rabbit, in which the number of sample in each breed was 21, respectively. Materials were taken randomly. The protein bands resulted from electrophoresis were used to calculate the value of the gene frequency. Genetic diversity was determined by using individual heterozygosity (h) and the average heterozygosity ( ) formulas. The genetic distance among breeds of rabbits was analyzed by using DISPAN and MEGA 6.06 programs. Chi-square (X2) was used to test of Hardy-Weinberg Law (HWL) equilibrium. The results showed that the loci of prealbumin (Pa), albumin (Alb), ceruloplasmin (Cp), transferrin (Tf), post-transferrin (P-tf) and amylase-I (Am-I) in Rex, local and NZW rabbits were polymorphic. Rex and NZW rabbits had close genetic relationships based on phylogeny tree analysis. Chi-square test showed that rex, local and NZW rabbits were in HWL equilibrium for locus of Pa, and Cp, while at the locus of Alb, Tf, P-tf and Amy-I were in HWL unequilibrium. In conclusion, there are genetic variability of six locuses in rex, local and NZW rabbits.

No evidence for effects of infection with the amphibian chytrid fungus on populations of yellow-bellied toads.

The parasitic chytrid fungus Batrachochytrium dendrobatidis (Bd) can cause the lethal disease chytridiomycosis in amphibians and therefore may play a role in population declines. The yellow-bellied toad Bombina variegata suffered strong declines throughout western and northwestern parts of its range and is therefore listed as highly endangered for Germany and the federal state of Hesse. Whether chytridiomycosis may play a role in the observed local declines of this strictly protected anuran species has never been tested. We investigated 19 Hessian yellow-bellied toad populations for Bd infection rates, conducted capture-mark-recapture studies in 4 of them over 2 to 3 yr, examined survival histories of recaptured infected individuals, and tested whether multi-locus heterozygosity of individuals as well as expected heterozygosity and different environmental variables of populations affect probabilities of Bd infection. Our results show high prevalence of Bd infection in Hessian yellow-bellied toad populations, but although significant decreases in 2 populations could be observed, no causative link to Bd as the reason for this can be established. Mass mortalities or obvious signs of disease in individuals were not observed. Conversely, we show that growth of Bd-infected populations is possible under favorable habitat conditions and that most infected individuals could be recaptured with improved body indices. Neither genetic diversity nor environmental variables appeared to affect Bd infection probabilities. Hence, genetically diverse amphibian specimens and populations may not automatically be less susceptible for Bd infection.

Spatio-temporal variation in parasite communities maintains diversity at the major histocompatibility complex class IIβ in the endangered Rio Grande silvery minnow.

Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species' adaptive capacity. Here, we combine genetic (MHC class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States. Infections with multiple parasites on the gills were observed and there was spatio-temporal variation in parasite communities and patterns of infection among individuals. Despite its highly endangered status and chronically low genetic effective size, Rio Grande silvery minnow had high allelic diversity at MHC class IIβ with more alleles recognized at the presumptive DAB1 locus compared to the DAB3 locus. We identified significant associations between specific parasites and MHC alleles against a backdrop of generalist parasite prevalence. We also found that individuals with higher individual neutral heterozygosity and higher amino acid divergence between MHC alleles had lower parasite abundance and diversity. Taken together, these results suggest a role for fluctuating selection imposed by spatio-temporal variation in pathogen communities and divergent allele advantage in maintenance of high MHC polymorphism. Understanding the complex interaction of habitat, pathogens and immunity in protected species will require integrated experimental, genetic and field studies.

Reduced sexual dichromatism, mutual ornamentation, and individual quality in the monogamous Zenaida doveZenaida aurita

Although variation in plumage coloration is known to occur both between and within sexes, its study remains limited to a few bird families. The Zenaida dove Zenaida aurita is a socially monogamous tropical columbid bird species, characterized by an overall cinnamon-brownish plumage and structural colorations on the head and neck. The species has been described as sexually dichromatic for plumage, although color differences between males and females are not obvious in the field. We investigated variation in the presumably melanin-based color of the crown, mantle, breast, and belly, in the iridescent dark-blue streaks on the head, and in the symmetric iridescent patches on the neck, over the whole spectrum visible to birds. Further, unlike most previous studies, we assessed covariation between plumage color and phenotypic traits in both males and females in relation to the putative signaling function of ornaments. Zenaida doves appeared to be slightly sexually dichromatic for the hue of pigment-based colored areas, with males being on average more reddish than females. However, this difference was not discernible when considering the avian visual system. Conversely, although the reflectance spectra of iridescent plumage did not significantly differ between sexes in brightness, chroma or spectral position of the peaks, color discrimination analyses showed that individuals should be able to perceive between- or within-sex differences in the color of the iridescent patch. In addition, several color parameters of brown and iridescent feathers were significantly related to territorial status, body condition, wing chord, and, albeit weakly, to individual multilocus heterozygosity. Overall, our results thus suggest that plumage color might be a reliable signal of quality in individuals of both sexes in this species. Further studies are needed to test the potential implication of plumage coloration in mate choice and mating patterns in the Zenaida dove.

MHC class II β exon 2 variation in pardalotes (Pardalotidae) is shaped by selection, recombination and gene conversion.

The high levels of polymorphism and allelic diversity which characterise genes in the major histocompatibility complex (MHC) are thought to be generated and maintained through the combined effects of different evolutionary processes. Here, we characterised exon 2 of the MHC class II β genes in two congeneric passerine species, the spotted (Pardalotus punctatus) and striated pardalote (Pardalotus striatus). We estimated the levels of allelic diversity and tested for signatures of recombination, gene conversion and balancing selection to determine if these processes have influenced MHC variation in the two species. Both species showed high levels of polymorphism and allelic diversity, as well as evidence of multiple gene loci and putative pseudogenes based on the presence of stop codons. We found higher levels of MHC diversity in the striated pardalote than the spotted pardalote, based on the levels of individual heterozygosity, sequence divergence and number of polymorphic sites. The observed differences may reflect variable selection pressure on the species, resulting from differences in patterns of movement among populations. We identified strong signatures of historical balancing selection, recombination and gene conversion at the sequence level, indicating that MHC variation in the two species has been shaped by a combination of processes.

Ontogenetic Changes in Azoxyglycoside Levels in the Leaves of Dioon edule Lindl.

Plants have multiple strategies, including phytochemicals that protect their vulnerable tissues against pathogens and herbivores. Dioon edule, like all cycads, possess unique azoxy-type compounds, azoxyglycosides (AZGs) as a chemical defense; however, the ontogenetic variability of these compounds in this long-lived cycad is unknown. Here, we investigated the effects of plant age, sex, genotype and individual heterozygosity on AZG levels in mature leaves of wild D. edule populations from eastern Mexico. Individuals were divided into three ontogenetic stages: seedlings, juveniles and adults. We established overall leaf quality by quantifying pigments associated with photosynthesis; chlorophylla, chlorophyllb and lutein. Leaf chlorophylla levels were higher in seedlings compared to adult cycads. Plants were genotyped using 11 microsatellite markers and foliar AZG levels were quantified by HPLC. AZG levels do not correlate with plant genotype or the individual's heterozygosity. Genetic analysis identified a distinction between lowland and highland individuals; foliar AZG levels were higher in lowland adult cycads compared to highland individuals. In both populations, the highest AZG levels were found in seedlings compared to adult cycads. These young cycads are highly reliant on their few leaves since seedlings bear one or two leaves for the first years of their life and, thus, are unlikely to recover from defoliation. The results suggest that cycad leaves with a greater nutritive content and a higher value for long-term survival are better protected with higher AZG levels. Female adult cycads have higher AZG levels compared to males, suggesting that the benefits of defense couldalso be linked to reproductive costs.

Microsatellite analysis of clonality and individual heterozygosity in natural populations of aspen Populus tremula L.: Identification of highly heterozygous clone

Aspen Populus tremula L. (Salicaceae) is the fast-growing tree species of environmental and economic value. Aspen is capable of reproduction by both seeds and vegetative means, forming root sprouts. In an adult stand, identification of ramets of one clone among the trees of seed origin based on their morphology is difficult. A panel of 14 microsatellite loci developed for individual identification of aspen was applied for the clonal structure analysis in four natural aspen stands of the European part of Russia: Moscow and Voronezh oblasts, the Mari-El Republic, and the Republic of Tatarstan. In 52 trees from the Moscow sample, 41 multilocus genotypes were identified; in the Voronezh sample, among 30 individuals, 25 different genotypes were detected; and in the sample from Mari-El, 32 trees were represented by 13 genotypes. In the stand from Sabinsky Forestry, Tatarstan, all of the examined 29 trees were represented by a single genotype. The ancestral tree carrier of this genotype which was the most heterozygous (0.929) among all studied aspen individuals (sample mean, 0.598) obviously has spread over a large territory during several cutting and reproduction cycles, currently occupying the area of 2.2 ha. For aspen, usually suffering from Aspen trunk rot, such high viability is evidence of resistance to the main pathogens. The revealed superclone deserves further study with karyological methods and flow cytometry to determine ploidy level and analysis of the growth rate and the quality of wood for possible use in plantation forest production.

Genomic heterozygosity and hybrid breakdown in cotton (Gossypium): different traits, different effects.

BackgroundHybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlations between genomic heterozygosity and vegetative and reproductive traits in cotton interspecific populations have not been studied. In the current study, two reciprocal F2 populations were developed using Gossypium hirsutum cv. Emian 22 and G. barbadense acc. 3–79 as parents to study hybrid breakdown in cotton. A total of 125 simple sequence repeat (SSR) markers were used to genotype the two F2 interspecific populations.ResultsTo guarantee mutual independence among the genotyped markers, the 125 SSR markers were checked by the linkage disequilibrium analysis. To our knowledge, this is a novel approach to evaluate the individual genomic heterozygosity. After marker checking, 83 common loci were used to assess the extent of genomic heterozygosity. Hybrid breakdown was found extensively in the two interspecific F2 populations particularly on the reproductive traits because of the infertility and the bare seeds. And then, the relationships between the genomic heterozygosity and the vegetative reproductive traits were investigated. The only relationships between hybrid breakdown and heterozygosity were observed in the (Emian22 × 3–79) F2 population for seed index (SI) and boll number per plant (BN). The maternal cytoplasmic environment may have a significant effect on genomic heterozygosity and on correlations between heterozygosity and reproductive traits.ConclusionsA novel approach was used to evaluate genomic heterozygosity in cotton; and hybrid breakdown was observed in reproductive traits in cotton. These findings may offer new insight into hybrid breakdown in allotetraploid cotton interspecific hybrids, and may be useful for the development of interspecific hybrids for cotton genetic improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0366-5) contains supplementary material, which is available to authorized users.

The effect of individual genetic heterozygosity on general homeostasis, heterosis and resilience in Siberian larch (Larix sibirica Ledeb.) using dendrochronology and microsatellite loci genotyping

The genetic mechanisms underlying the relationship of individual heterozygosity (IndHet) with heterosis and homeostasis are not fully understood. Such an understanding, however, would have enormous value as it could be used to identify trees better adapted to environmental stress. Dendrochronology data, in particular the individual average radial increment growth of wood measured as the average tree ring width (AvTRW) and the variance of tree ring width (VarTRW) were used as proxies for heterosis (growth rate measured as AvTRW) and homeostasis (stability of the radial growth of individual trees measured as VarTRW), respectively. These traits were then used to test the hypothesis that IndHet can be used to predict heterosis and homeostasis of individual trees. Wood core and needle samples were collected from 100 trees of Siberian larch (Larix sibirica Ledeb.) across two populations located in Eastern Siberia. DNA samples were obtained from the needles of each individual tree and genotyped for eight highly polymorphic microsatellite loci. Then mean IndHet calculated based on the genotypes of eight loci for each tree was correlated with the statistical characteristics of the measured radial growth (AvTRW and VarTRW) and the individual standardized chronologies. The analysis did not reveal significant relationships between the studied parameters. In order to account for the strong dependence of the radial growth on tree age the age curves were examined. An original approach was employed to sort trees into groups based on the distance between these age curves. No relationship was found between these groups and the groups formed based on heterozygosity. However, further work with more genetic markers and increased sample sizes is needed to test this novel approach for estimating heterosis and homeostasis.

Heterozygosity, gender, and the growth-defense trade-off in quaking aspen.

Although plant growth is generally recognized to be influenced by allocation to defense, genetic background (e.g., inbreeding), and gender, rarely have those factors been addressed collectively. In quaking aspen (Populus tremuloides Michx.), phenolic glycosides (PGs) and condensed tannins (CTs) constitute up to 30% of leaf dry weight. To quantify the allocation cost of this chemical defense, we measured growth, defense chemistry, and individual heterozygosity (H obs at 16 microsatellite loci) for male and female trees in both controlled and natural environments. The controlled environment consisted of 12 juvenile genets grown for 3years in a common garden, with replication. The natural environment consisted of 51 mature genets in wild populations, from which we sampled multiple ramets (trees) per genet. Concentrations of PGs and CTs were negatively correlated. PGs were uncorrelated with growth, but CT production represented a major cost. Across the range of CT levels found in wild-grown trees, growth rates varied by 2.6-fold, such that a 10% increase in CT concentration occurred with a 38.5% decrease in growth. H obs had a marked effect on aspen growth: for wild trees, a 10% increase in H obs corresponded to a 12.5% increase in growth. In wild trees, this CT effect was significant only in females, in which reproduction seems to exacerbate the cost of defense, while the H obs effect was significant only in males. Despite the lower growth rate of low-H obs trees, their higher CT levels may improve survival, which could account for the deficit of heterozygotes repeatedly found in natural aspen populations.

Gyrodactylus spp. diversity in native and introduced minnow (Phoxinus phoxinus) populations: no support for "the enemy release" hypothesis.

BackgroundTranslocation of native species and introduction of non-native species are potentially harmful to the existing biota by introducing e.g. diseases, parasites and organisms that may negatively affect the native species. The enemy release hypothesis states that parasite species will be lost from host populations when the host is introduced into new environments.MethodsWe tested the enemy release hypothesis by comparing 14 native and 29 introduced minnow (Phoxinus phoxinus) populations in Norway with regard to the ectoparasitic Gyrodactylus species community and load (on caudal fin). Here, we used a nominal logistic regression on presence/absence of Gyrodactylus spp. and a generalized linear model on the summed number of Gyrodactylus spp. on infected populations, with individual minnow heterozygosity (based on 11 microsatellites) as a covariate. In addition, a sample-based rarefaction analysis was used to test if the Gyrodactylus-species specific load differed between native and introduced minnow populations. An analysis of molecular variance was performed to test for hierarchical population structure between the two groups and to test for signals of population bottlenecks the two-phase model in the Wilcoxon signed-rank test was used. To test for demographic population expansion events in the introduced minnow population, we used the kg-test under a stepwise mutation model.ResultsThe native and introduced minnow populations had similar species compositions of Gyrodactylus, lending no support to the enemy release hypothesis. The two minnow groups did not differ in the likelihood of being infected with Gyrodactylus spp. Considering only infected minnow populations it was evident that native populations had a significantly higher mean abundance of Gyrodactylus spp. than introduced populations. The results showed that homozygotic minnows had a higher Gyrodactylus spp. infection than more heterozygotic hosts. Using only infected individuals, the two minnow groups did not differ in their mean number of Gyrodactylus spp. However, a similar negative association between heterozygosity and abundance was observed in the native and introduced group. There was no evidence for demographic bottlenecks in the minnow populations, implying that introduced populations retained a high degree of genetic variation, indicating that the number of introduced minnows may have been large or that introductions have been happening repeatedly. This could partly explain the similar species composition of Gyrodactylus in the native and introduced minnow populations.ConclusionsIn this study it was observed that native and introduced minnow populations did not differ in their species community of Gyrodactylus spp., lending no support to the enemy release hypothesis. A negative association between individual minnow host heterozygosity and the number of Gyrodactylus spp. was detected. Our results suggest that the enemy release hypothesis does not necessarily limit fish parasite dispersal, further emphasizing the importance of invasive fish species dispersal control.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1306-y) contains supplementary material, which is available to authorized users.

High genetic variability of vagrant polar bears illustrates importance of population connectivity in fragmented sea ice habitats

Projections by the Intergovernmental Panel on Climate Change (IPCC) and sea ice forecasts suggest that Arctic sea ice will decline markedly in coming decades. Expected effects on the entire ecosystem include a contraction of suitable polar bear habitat into one or few refugia. Such large-scale habitat decline and fragmentation could lead to reduced genetic diversity. Here we compare genetic variability of four vagrant polar bears that reached Iceland with that in recognized subpopulations from across the range, examining 23 autosomal microsatellites, mitochondrial control region sequences and Y-chromosomal markers. The vagrants' genotypes grouped with different genetic clusters and showed similar genetic variability at autosomal microsatellites (expected heterozygosity, allelic richness, and individual heterozygosity) as individuals in recognized subpopulations. Each vagrant carried a different mitochondrial haplotype. A likely route for polar bears to reach Iceland is via Fram Strait, a major gateway for the physical exportation of sea ice from the Arctic basin. Vagrant polar bears on Iceland likely originated from more than one recognized subpopulation, and may have been caught in sea ice export during long-distance movements to the East Greenland area. Although their potentially diverse geographic origins might suggest that these vagrants encompass much higher genetic variability than vagrants or dispersers in other regions, the four Icelandic vagrants encompassed similar genetic variability as any four randomly picked individuals from a single subpopulation or from the entire sample. We suggest that this is a consequence of the low overall genetic variability and weak range-wide genetic structuring of polar bears – few dispersers can represent a large portion of the species' gene pool. As predicted by theory and our demographic simulations, continued gene flow will be necessary to counteract loss of genetic variability in increasingly fragmented Arctic habitats. Similar considerations will be important in the management of other taxa that utilize sea ice habitats.

Genetic parameters for carcass traits and body weight using a Bayesian approach in the Canchim cattle.

Correlation between genetic parameters and factors such as backfat thickness (BFT), rib eye area (REA), and body weight (BW) were estimated for Canchim beef cattle raised in natural pastures of Brazil. Data from 1648 animals were analyzed using multi-trait (BFT, REA, and BW) animal models by the Bayesian approach. This model included the effects of contemporary group, age, and individual heterozygosity as covariates. In addition, direct additive genetic and random residual effects were also analyzed. Heritability estimated for BFT (0.16), REA (0.50), and BW (0.44) indicated their potential for genetic improvements and response to selection processes. Furthermore, genetic correlations between BW and the remaining traits were high (P > 0.50), suggesting that selection for BW could improve REA and BFT. On the other hand, genetic correlation between BFT and REA was low (P = 0.39 ± 0.17), and included considerable variations, suggesting that these traits can be jointly included as selection criteria without influencing each other. We found that REA and BFT responded to the selection processes, as measured by ultrasound. Therefore, selection for yearling weight results in changes in REA and BFT.

Larger lizards live longer in the group-living Egernia stokesii

Animal space use has implications for gene flow, disease dynamics, mating systems and the evolution of sociality. Given recent attention to sociality in reptiles, lizards are an important group for expanding our understanding of animal space use. Lizard space use is commonly investigated within one population over a short period and limited attention has been given to potential predictors of site fidelity. This study evaluated site fidelity in three populations of group-living Egernia stokesii (gidgee skink) between two field surveys separated by almost a decade. Of 43 recaptured lizards, 28 (65%) occupied their original space, and 15 (36%) of those shared their space with the same other lizard or lizards in both surveys. This confirmed long-term site and social bond fidelity in E. stokesii. We found that larger lizards were more likely to be recaptured. Neither body size, individual genetic heterozygosity, nor the availability of refuges strongly predicted whether lizards were recaptured in the same or a different place. The reasons why some lizards stayed in the same space while others moved are yet to be resolved.

European aspen (Populus tremula L.) genetic diversity assessed by molecular methods correlation with P. tremulae infection incidence

This study was based on different susceptibility of <i>Populus tremula</i> clones to <i>Phellinus tremulae</i>, the major pathogen of this tree species. As the conventional resistance genes detection is time consuming and expensive, it is important to find other applicable methods to recognize resistance genes of the plants. The aim of this study was the assessment of correlation between various genetic population parameters and phenotipic, resistance or highly heritable traits of individual <i>P. tremula</i> trees. In this study we investigated all Lithuanian <i>P. tremula</i> plus trees from 16 populations in 3 provenance regions. Investigated trees were analyzed using RAPD, SSR and PCR-RFLP methods, and their individual and population genetic parameters as well as infection incidence with <i>P. tremulae</i> were assessed. Determined genetic parameters were examined for correlation with <i>P. tremulae</i> infection. Only two out of 292 RAPD loci were significant for damaged and undamaged by <i>P. tremulae</i> groups of trees. The resistance of investigated European aspen plus trees with <i>P. tremulae</i> showed no dependency on the population, provenance region or individual tree heterozygosity. RAPD loci linked to infection should be investigated further, to confirm or reject their value in assesing individual tree susceptibility to <i>P. tremulae</i> and the genetic mechanisms underlying such correlation.

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.