Significant Dominance Effects Research Articles

Non-additive genetic variation in growth, carcass and fertility traits of beef cattle.

BackgroundA better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of individuals. Genome-wide panels of single nucleotide polymorphisms (SNPs) have been mainly used to map additive effects for quantitative traits, but they can also be used to investigate non-additive effects. We estimated dominance and epistatic effects of SNPs on various traits in beef cattle and the variance explained by dominance, and quantified the increase in accuracy of phenotype prediction by including dominance deviations in its estimation.MethodsGenotype data (729 068 real or imputed SNPs) and phenotypes on up to 16 traits of 10 191 individuals from Bos taurus, Bos indicus and composite breeds were used. A genome-wide association study was performed by fitting the additive and dominance effects of single SNPs. The dominance variance was estimated by fitting a dominance relationship matrix constructed from the 729 068 SNPs. The accuracy of predicted phenotypic values was evaluated by best linear unbiased prediction using the additive and dominance relationship matrices. Epistatic interactions (additive × additive) were tested between each of the 28 SNPs that are known to have additive effects on multiple traits, and each of the other remaining 729 067 SNPs.ResultsThe number of significant dominance effects was greater than expected by chance and most of them were in the direction that is presumed to increase fitness and in the opposite direction to inbreeding depression. Estimates of dominance variance explained by SNPs varied widely between traits, but had large standard errors. The median dominance variance across the 16 traits was equal to 5% of the phenotypic variance. Including a dominance deviation in the prediction did not significantly increase its accuracy for any of the phenotypes. The number of additive × additive epistatic effects that were statistically significant was greater than expected by chance.ConclusionsSignificant dominance and epistatic effects occur for growth, carcass and fertility traits in beef cattle but they are difficult to estimate precisely and including them in phenotype prediction does not increase its accuracy.

Optimal Elbow Angle for Sonographic Visualization of the Ulnar Collateral Ligament

ObjectiveTo formally examine the sonographic appearance of the elbow ulnar collateral ligament (UCL) at 30° versus 70° of elbow flexion in asymptomatic baseball pitchers. DesignA prospective, cross-sectional design. SettingSports medicine clinic in a tertiary academic medical center. ParticipantsThirty asymptomatic adolescent baseball pitchers 13-18 years of age (mean 15.8 years), with at least 3 years of continuous pitching experience and no significant history of elbow pain or injury. MethodsStatic sonographic images of the bilateral UCLs were obtained at 30° and 70° of elbow flexion by a single experienced examiner. Images were anonymized and randomized into a slide set. Three clinicians with different levels of ultrasound experience reviewed the static 30° and 70° images for each elbow and chose their preferred image based on UCL conspicuity. The clinicians reviewed a re-randomized slide set 1 week later. A different study co-investigator measured UCL cross-sectional area (CSA) on all images using ultrasound machine electronic calipers. Main Outcome MeasuresPreference for the sonographic conspicuity of the UCL at 30° versus 70° of elbow flexion, and UCL CSA at 30° versus 70° of flexion. ResultsEach clinician demonstrated a significant preference for UCL images obtained at 70° of flexion when compared to those obtained at 30° (80.3% overall preference for 70°, P < .001). There was no statistically significant effect of clinician experience or arm dominance on image preference. The sonographically determined CSA of the UCLs were on average 1.4 mm2 greater at 70° than at 30° of flexion (P < .001) when combining dominant and nondominant arms. ConclusionsStatic sonographic evaluation of the UCL at 70° of elbow flexion should be integrated into UCL imaging protocols. Furthermore, when performing sonographically guided procedures targeting the UCL, clinicians should consider positioning the elbow at >30° of flexion to optimize UCL conspicuity and CSA.

Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits

For human complex traits, non-additive genetic variation has been invoked to explain "missing heritability," but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (hSNP(2) and δSNP(2)) in unrelated individuals based on an orthogonal model where the estimate of hSNP(2) is independent of that of δSNP(2). With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of δSNP(2) averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average hSNP(2) = 0.15). There were a few traits that showed substantial estimates of δSNP(2), none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem.

Genetic analysis of yield and yield-related traits in short-season cotton (Gossypium hirsutum L.)

Six short-season cotton cultivars (Gossypium hirsutum L.) were crossed in a diallel crossing system to evaluate inheritance and interrelationship of phenotype and genotype of yield and yield-related traits (cottonseed yield, lint yield, cottonseed yield before frost, lint yield before frost, lint percentage, boll weight and boll number) and their correlation with earliness traits. The study was carried out from year 2005 to year 2008. The experiment design was a randomized complete block design with three replications. Additive, dominance and epistasis effects were analyzed with ADAA model. The results showed that yield and yield-related traits were mainly controlled by dominant genetic effects and also had a definitely proportion additive by environment interaction effects. Cottonseed yield, lint yield, cottonseed yield before frost, boll weight, lint percentage, boll number and lint yield before frost had the highest broad sense by environment interaction heritability (HBE) estimates, 0.653, 0.602, 0.600, 0.528, 0.416, 0.387 and 0.324, respectively. Lint percentage, cottonseed yield, lint yield and cottonseed yield before frost had higher narrow sense by environment interaction heritability (HNE), 0.416, 0.301, 0.263 and 0.185, respectively. Only boll weight and boll number had the highest narrow sense heritability (HN), 0.345 and 0.139, respectively. Some F1 hybrids had positive significant heterozygous dominance effects. Some F1 hybrids had significant positive epistatic effects and affected by environment. Among yield and yield-related traits, they all had significant positive genetic and phenotypic correlation, excepting lint percentage and boll weight, boll weight and boll number had significant negative genetic and phenotypic correlation. Yield and yield-related traits had a negative correlation with earliness traits except lint percentage and boll number. Lint percentage with harvested rate before frost, date of first square and number of node first sympodial branch, boll number with yield and relative traits showed significant negative genetic correlation. The results showed that the higher the lint percentage, boll weight and boll number and the higher harvested yield and the later the maturing. Based on these results, it is suggested to selection of yield and yield-related traits should be undertaken at late generation (F4, F5), and early-maturing parents A1, B1, B2 and B3 could be used to improve yield and yield-related traits in short-season cotton breeding programs.

Clinical features of de novo acute myeloid leukemia with concurrent DNMT3A, FLT3 and NPM1 mutations.

BackgroundDe novo acute myeloid leukemia (AML) with concurrent DNMT3A, FLT3 and NPM1 mutations (AMLDNMT3A/FLT3/NPM1) has been suggested to represent a unique AML subset on the basis of integrative genomic analysis, but the clinical features of such patients have not been characterized systematically.MethodsWe assessed the features of patients (n = 178) harboring mutations in DNMT3A, FLT3 and/or NPM1, including an index group of AMLDNMT3A/FLT3/NPM1 patients.ResultsPatients with AMLDNMT3A/FLT3/NPM1 (n = 35) were significantly younger (median, 56.0 vs. 62.0 years; p = 0.025), mostly women (65.7% vs. 46.9%; p = 0.045), and presented with a higher percentage of bone marrow blasts (p < 0.001) and normal cytogenetics (p = 0.024) in comparison to patients within other mutation groups in this study. Among patients <60 years old, those with AMLDNMT3A/FLT3/NPM1 had a shorter event-free survival (EFS) (p = 0.047). DNMT3A mutations and not FLT3 or NPM1 mutations were independently associated with overall survival (OS) (p = 0.026). Within mutation subgroups, patients with AMLDNMT3A/NPM1 had a significantly shorter OS compared to those with AMLFLT3-ITD/NPM1 (p = 0.047) suggesting that the adverse impact of DNMT3A mutations is more pronounced than that of FLT3-ITD among patients with NPM1 mutation.ConclusionsDNMT3A has a significant dominant effect on the clinical features and outcomes of de novo AML patients with concurrent DNMT3A, FLT3 and NPM1 mutations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13045-014-0074-4) contains supplementary material, which is available to authorized users.

Genetic analysis of fiber quality traits in short season cotton (Gossypium hirsutum L.)

Six short season cotton cultivars (Gossypium hirsutum L.) were crossed in a dillalel crossing system to evaluate inheritance and interrelationship of phenotype and genotype of fiber quality traits (fiber length, uniformity index, fiber strength, micronaire and fiber elongation) and their correlation with earliness and yield traits. The study was carried out from year 2005 to 2008. The experiment design was a randomized complete block design with three replications. Additive, dominance and epistasis effects were analyzed with ADAA model. The results showed that fiber quality traits were mainly controlled by dominant genetic effects and also had a definitely proportion additive genetic effects. Micronaire, fiber length, fiber strength and fiber elongation had the highest broad sense heritability (HB) and by environment interaction (HBE) estimates, 0.618 (HB) and 0.267 (HBE) for micronaire, 0.510 (HB) and 0.287 (HBE) for fiber length, 0.452 (HB) and 0.316 (HBE) for fiber strength, 0.294 (HB) and 0.494(HBE) for fiber elongation, respectively. Narrow sense heritability (HN) was 0.258 for fiber elongation, 0.136 for fiber length, 0.127 for fiber strength and 0.110 for micronaire. Some F1 hybrids (A1×B2), (A2×A3) and (B1×A3) for fiber length, F1 (A2×B3) and (B1×B2) for fiber strength, F1 (B1×A2), (A2×B2), (A2×B3), (B1×A3), (B2×A3) and (B1×B2) for micronaire and F1 (A1×A2), (A1×A3), (A1×B1), (A1×B3) and (B2×A3) for fiber elongation had significant positive heterozygous dominance effects and affected by environment. Some F1 hybrids (A1×A2), (A1×B1), (A1×B3), (B1×A2) and (B2×A3) for fiber length, (A1×A3), (A1×B1) and (A1×B3) for fiber strength, (A1×A3), (A1×B1), (A1×B2) and (B2×B3) for micronaire and (A2×A3), (A2×B2), (A2×B3) and (B1×B2) for fiber elongation had significant positive epistatic effects. Among fiber quality traits, fiber length with fiber strength, uniformity index with fiber strength and micronaire, fiber strength with micronaire showed a positive and significant correlation. Only elongation had a significant negative correlation with fiber quality traits. Fiber quality traits had a negative correlation with earliness traits except micronaire. Fiber length and strength showed a significant negative correlation with lint yield, lint yield before frost, lint percentage and boll number. Uniformity index, micronaire and fiber elongation had a significant positive correlation with yield traits except boll weight and lint percentage. The results showed that the higher the yield and the earlier the maturing and the worse the fiber quality. Therefore, selections of fiber properties and integration of high yield, good fiber quality and early maturing traits should be performed in higher generations in short season cotton variety breeding program.

The effect of contrast on monocular versus binocular reading performance.

The binocular advantage in reading performance is typically small. On the other hand research shows binocular reading to be remarkably robust to degraded stimulus properties. We hypothesized that this robustness may stem from an increasing binocular contribution. The main objective was to compare monocular and binocular performance at different stimulus contrasts and assess the level of binocular superiority. A secondary objective was to assess any asymmetry in performance related to ocular dominance. In a balanced repeated measures experiment 18 subjects read texts at three levels of contrast monocularly and binocularly while their eye movements were recorded. The binocular advantage increased with reduced contrast producing a 7% slower monocular reading at 40% contrast, 9% slower at 20% contrast, and 21% slower at 10% contrast. A statistically significant interaction effect was found in fixation duration displaying a more adverse effect in the monocular condition at lowest contrast. No significant effects of ocular dominance were observed. The outcome suggests that binocularity contributes increasingly to reading performance as stimulus contrast decreases. The strongest difference between monocular and binocular performance was due to fixation duration. The findings may pose a clinical point that it may be necessary to consider tests at different contrast levels when estimating reading performance.

Genetic analysis of the antioxidant enzymes, methane dicarboxylic aldehyde (MDA) and chlorophyll content in leaves of the short season cotton (Gossypium hirsutum L.)

Premature senescence is an important limited factor for the short season cotton (SSC), which decreases yield and declines fiber quality. The activity of antioxidant enzyme, methane dicarboxylic aldehyde (MDA) content and chlorophyll content is related with premature senescence. The present study is aimed to investigate the heredity and relationship of the antioxidant enzymes catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD), MDA content and chlorophyll content for breeding high yield and good quality of the SSC varieties. Six parents from two types of senescence varieties (type A, which matures early and displays premature senescence; type B, which matures early but does not display premature senescence) and their F1, F2 progenies in a diallel crossing scheme were planted in the experiment field. Phenotypic data on the traits were analyzed according to the Additive–Dominance–Epistasis and Additive–Dominance–Maternal–Paternal effects genetic model. CAT activity of dominant genetic effects were significant and large from 9 to 85 days after planting, the variance components were 34.69, 8.41, 31.93, 19.57 and 27.96 % at 9, 36, 50, 66 and 85 days, respectively. Additive-by-additive epistatic effects on CAT activity were significant and important from 9 to 85 days after planting. POD activity of additive genetic effects was significant and stable. There was not interaction by environment during 24 to 50 days after planting, the variance components were 9.82, 18.86 and 7.87 % at 24, 36 and 50 days, respectively. SOD activity of additive genetic effects was significant and stable. There was not interaction by environment during 66 to 100 days after planting, the variance components were 11.56, 11.80 and 13.84 % at 66, 85 and 100 days, respectively. MDA content of additive genetic effects was significant and stable. There was not interaction by environment during 50 to 100 days after planting, the variance components were 24.81, 13.81, 14.38 and 4.77 % at 50, 66, 85 and 100 days, respectively. Chlorophyll content was mainly controlled by significant dominance effects and main genetic effect from 9 to 66 days after planting, the dominant variance components were over 30 %. Maternal and paternal genetic effects on CAT and chlorophyll content were significant among 36–85 days after planting. Based on these results, it is suggested to selection of POD, SOD and MDA should be undertaken at early generation (F2, F3) and selection of chlorophyll and CAT should be undertaken at late generation (F4, F5) in SSC breeding programs.

Genomic heritability estimation for the early life-history transition related to propensity to migrate in wild rainbow and steelhead trout populations.

A previous genomewide association study (GWAS) identified SNP markers associated with propensity to migrate of rainbow and steelhead trout (Oncorhynchus mykiss) in a connected population with free access to the ocean in Upper Yakima River (UYR) and a population in Upper Mann Creek (UMC) that has been sequestered from its access to the ocean for more than 50 years. Applying genomic heritability estimation using the same dataset, we found that smoltification in the UYR population were almost completely determined by additive effects, with 95.5% additive heritability and 4.5% dominance heritability, whereas smoltification in the UMC population had substantial dominance effects, with 0% additive heritability and 39.3% dominance heritability. Dominance test detected one SNP marker (R30393) with significant dominance effect on smoltification (P = 1.98 × 10−7). Genomic-predicted additive effects completely separated migratory and nonmigratory fish in the UYR population, whereas genomic-predicted dominance effects achieved such complete separation in the UMC population. The UMC population had higher genomic additive and dominance correlations than the UYR population, and fish between these two populations had the least genomic correlations. These results suggested that blocking the free access to the ocean may have reduced genetic diversity and increased genomic similarity associated with the early life-history transition related to propensity to migrate.

Asymmetries in phonological development: the case of word-final cluster acquisition in Welsh–English bilingual children

This study provides the first systematic account of word-final cluster acquisition in bilingual children. To this end, forty Welsh-English bilingual children differing in language dominance and age (2;6 to 5;0) participated in a picture-naming task in English and Welsh. The results revealed significant age and dominance effects on cluster acquisition, with greater overall accuracy on the English clusters. Interestingly, although the Welsh-dominant children outperformed the English-dominant ones on the Welsh clusters, they did not exhibit a concomitant lag on the English clusters. It is argued that this asymmetry is a direct reflection of the sociolinguistic situation in Wales with English as the majority language and Welsh the minority language. The study also revealed accelerated rates of acquisition for English clusters compared with age-matched monolinguals reported elsewhere (Templin, 1957), thereby supporting claims that bilingual contexts may have a facilitative effect on phonological acquisition (Goldstein & Bunta, 2012; Grech & Dodd, 2008).

Detection of QTL on panicle number in rice (Oryza sativa L.) under different densities with single segment substitution lines

The elite indica rice variety Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs), all of which have been shown to have quantitative trait loci (QTL) for panicle number (PN), were used as crossing parents to construct a half-diallel crossing population with the aim of analyzing the expression of these QTL under different cropping densities. A total of 91 half-diallel crossing combinations were grown in two planting seasons at three cropping densities. PN was measured at the mature stage. The additive, dominant and epistatic effects of the 12 QTL as well as their interaction effects with the seasons and with the densities were estimated based on genetic effect components. Our analysis revealed that PN generally decreased with increasing cropping density. In the six single environments, eight additive QTL, nine dominant QTL and 49 pairs of epistatic QTL were detected, which were mostly associated with estimated positive, positive and negative effects, respectively. Expression of these QTL differed across planting seasons and cropping densities, implying an existing of QTL-by-environment interaction. Further analysis of the QTL effect components revealed that seven, eight and 28 pairs of QTL were present with significant additive, dominance, epistasis and/or interaction effects with densities. QTL additive and dominant effects were mostly positive, while epistatic effects were all negative. No significant QTL-by-season effects were detected. QTL Pn3-1, without any significant additive-by-density interaction effect, showed stable additive expression across densities. QTL Pn3-1, Pn3-2 and Pn6-1 showed stable dominance expression, and QTL pairs Pn2-1/Pn9, Pn2-2/Pn3-1, Pn2-2/Pn6-2, Pn3-1/Pn6-1, Pn3-1/Pn7 and Pn6-1/Pn6-3 had stable epistasis expression. The remaining significant QTL had different effects across densities. We determined that a density of 10 × 16.7 cm2 had little influence on QTL expression, that a density of 16.7 × 16.7 cm2 mostly increased QTL additive and dominant effects and decreased QTL epistatic effects and that a density of 23.3 × 16.7 cm2 had the opposite impact on QTL effects compared with 16.7 × 16.7 cm2. Additionally, the influence of density on QTL epistatic effect was generally larger than that on QTL additive or dominant effect. These results provide the information on cropping density and how it influences PN QTL expression, which may be useful information to improve rice PN via heterosis and/or QTL pyramiding.

Analysis of the associations between polymorphisms in GNAS complex locus and growth, carcass and meat quality traits in pigs

Imprinted genes are interesting candidates for marker assisted selection in farm animals. One of them-GNAS complex locus is engaged in obesity pathogenesis in humans and mice. In our study, we identified new polymorphism in porcine GNAS gene (variable number of CT repeats, accession number: rs196952953) and found that this polymorphism is in linkage disequilibrum with GNAS AM490165:g.324C>T. Statistical analysis (GLM procedure), performed on 552 animals (Large White n = 258 and Landrace n = 269), revealed that deduced haplotypes and GNAS AM490165:g.324C>T are associated with growth performance and a few carcass traits, but not with feed intake. We observed significant additive effects of GNAS AM490165:g.324C>T genotype and haplotype 2 (C/278 bp) on test daily gain (TDG), average daily gain (ADG), number of days on test, age of the slaughter (P < 0.01) and FCR ratio (P < 0.05). Animals with two copies of C/278 haplotype had significantly higher: TDG, ADG, lower feed:gain ratio and faster reached the weight of 100 kg. When carcass traits were considered, significant associations between GNAS AM490165:g.324C>T polymorphism, haplotype 2 (C/278) and weight of ham with and without backfat and skin (WH) (WH2), length of the carcass, height and the width of the loin, meat percentage, weight of the main cuts were identified. The significant dominance effects of GNAS AM490165:g.324C>T polymorphism and haplotype 2 on WH and WH2 were observed (P < 0.05). When the two breeds were analyzed separately significant associations were observed for most of the traits in Landrace while in Large White the same trends were present but the differences were mostly not significant. Among meat quality traits we found significant association between haplotype and IMF content in Landrace (P < 0.03). Our results show for the first time that GNAS complex locus may modulate economically important traits in pigs.

Short Communication: Association analyses of a single nucleotide polymorphism in the promoter of OLR1 with growth, feed efficiency, fat deposition, and carcass merit traits in hybrid, Angus and Charolais beef cattle

Vinsky, M., Islam, K., Chen, L. and Li, C. 2013. Short Communication: Association analyses of a single nucleotide polymorphism in the promoter of OLR1 with growth, feed efficiency, fat deposition, and carcass merit traits in hybrid, Angus and Charolais beef cattle. Can. J. Anim. Sci. 93: 193–197. A single nucleotide polymorphism (SNP) in the promoter region of oxidized low density lipoprotein (lectin-like) receptor 1 (OLR1) (c. −495 T&gt;C) was identified and analyzed for associations with 10 traits related to growth, feed efficiency, body fat deposition and carcass merit traits in hybrid (n=456), Angus (n=567) and Charolais (n=423) beef cattle populations. Significant allele substitution effect (P=0.023) was found for residual feed intake (RFI) in the Angus population. The allele “C”, which had a frequency of 0.24 in the Angus population, was associated with decreased RFI. The Angus steers with the “CC” genotype had a lower RFI value (i.e., more efficient) than the Angus steers carrying the ‘TT’ genotype. The SNP was also found to have significant dominance effects on final ultrasound rib-eye area (FUREA) (P=0.0004) and carcass rib-eye area (CREA) (P=0.009) in the Angus steer population. The Angus steers with the “CT” genotype had smaller rib-eye areas of both ultrasound and carcass measures than the average of the steers with the homozygous genotypes. However, the SNP did not show significant associations with the traits examined in either the hybrid or the Charolais steer population at P&lt;0.05. OLR1 plays a role in lipid metabolism, and analyses of transcript binding site based on the transcription element search system revealed that the “T” allele of the c.-495T&gt;C SNP introduces a presumptive binding site for CCAAT/enhancer binding protein alpha (C/EBPα). However, further investigation is required to delineate the possible regulatory role of the SNP on growth and efficiency of energy utilization in relation to different biological types of beef cattle.

Novel Use of Derived Genotype Probabilities to Discover Significant Dominance Effects for Milk Production Traits in Dairy Cattle

The estimation of dominance effects requires the availability of direct phenotypes, i.e., genotypes and phenotypes in the same individuals. In dairy cattle, classical QTL mapping approaches are, however, relying on genotyped sires and daughter-based phenotypes like breeding values. Thus, dominance effects cannot be estimated. The number of dairy bulls genotyped for dense genome-wide marker panels is steadily increasing in the context of genomic selection schemes. The availability of genotyped cows is, however, limited. Within the current study, the genotypes of male ancestors were applied to the calculation of genotype probabilities in cows. Together with the cows' phenotypes, these probabilities were used to estimate dominance effects on a genome-wide scale. The impact of sample size, the depth of pedigree used in deriving genotype probabilities, the linkage disequilibrium between QTL and marker, the fraction of variance explained by the QTL, and the degree of dominance on the power to detect dominance were analyzed in simulation studies. The effect of relatedness among animals on the specificity of detection was addressed. Furthermore, the approach was applied to a real data set comprising 470,000 Holstein cows. To account for relatedness between animals a mixed-model two-step approach was used to adjust phenotypes based on an additive genetic relationship matrix. Thereby, considerable dominance effects were identified for important milk production traits. The approach might serve as a powerful tool to dissect the genetic architecture of performance and functional traits in dairy cattle.

Biotic homogenization at the community scale: disentangling the roles of urbanization and plant invasion

AbstractAimUrbanization as a major global trend profoundly changes biodiversity patterns, and homogenization of urban biota due to expanding exotic species and declining native species is of increasing concern. Previous studies on this topic have mostly taken place at large scales that include high habitat heterogeneity. Here, we aimed at disentangling the effects of urbanization and plant invasion on species composition through the analysis of similarity patterns of urban plant assemblages at the community scale where species interact.LocationBerlin, Germany.MethodsWe analysed how different levels of urbanization, specific components of the urban matrix and the dominance of a native (Betula pendula) versus an exotic tree species (Robinia pseudoacacia) affect alpha and beta diversity of urban woodland understorey vegetation in sixty‐eight 100‐m2 plots.ResultsExotic dominance reduced alpha diversity, but not beta diversity of the total species pool. Comparing beta diversity among different species groups revealed significant but divergent effects of exotic dominance, habitat connectivity and levels of urbanization in native and non‐native species assemblages. In particular, urbanity proved to homogenize the native species pool, whereas the beta diversity of the non‐native species pool showed a more pronounced response to exotic dominance.Main conclusionsOur data provide evidence that both the urban context and the dominance of exotic species can modify homogenization processes at the community level. These novel insights into the mechanisms of biotic homogenization of urban floras may contribute to mitigating the effects of urbanization on biodiversity.

Novel insight into the genomic architecture of feed and nitrogen efficiency measured by residual energy intake and nitrogen excretion in growing pigs

BackgroundImprovement of feed efficiency in pigs is of great economical and environmental interest and contributes to use limited resources efficiently to feed the world population. Genome scans for feed efficiency traits are of importance to reveal the underlying biological causes and increase the rate of genetic gain. The aim of this study was to determine the genomic architecture of feed efficiency measured by residual energy intake (REI), in association with production, feed conversion ratio (FCR) and nitrogen excretion traits through the identification of quantitative trait loci (QTL) at different stages of growth using a three generation full-sib design population which originated from a cross between Pietrain and a commercial dam line.ResultsSix novel QTL for REI were detected explaining 2.7-6.1% of the phenotypic variance in REI. At growth from 60–90 kg body weight (BW), a QTL with a significant dominance effect was identified for REI on SSC14, at a similar location to the QTL for feed intake and nitrogen excretion traits. At growth from 90–120 kg BW, three QTL for REI were detected on SSC2, SSC4 and SSC7 with significant additive, imprinting and additive effects, respectively. These QTL (except for the imprinted QTL) were positionally overlapping with QTL for FCR and nitrogen excretion traits. During final growth (120–140 kg BW), a further QTL for REI was identified on SSC8 with significant additive effect, which overlapped with QTL for nitrogen excretion. During entire analysed growth (60–140 kg BW), a novel additive QTL for REI on SSC4 was observed, with no overlapping with QTL for any other traits considered.ConclusionsThe occurrence of only one overlapping QTL of REI with feed intake suggests that only a small proportion of the variance in REI was explained by change in feed intake, whereas four overlapping QTL of REI with those of nitrogen excretion traits suggests that mostly underlying factors of feed utilisation such as metabolism and protein turnover were the reason for change in REI. Different QTL for REI were identified at different growth stages, indicating that different genes are responsible for efficiency in feed utilisation at different stages of growth.

Quantitative Trait Loci Analysis of Folate Content in Dry Beans,Phaseolus vulgarisL.

Dry beans (Phaseolus vulgarisL.) contain high levels of folates, yet the level of folate may vary among different genotypes. Folates are essential vitamins and folate deficiencies may lead to a number of health problems. Among the different forms of folates, 5-methyltetrahydrofolate (5MTHF) comprises more than 80% of the total folate in dry beans. The objectives of this paper were to compare selected genotypes of dry beans for the folate content of the dry seeds and to identify quantitative trait loci (QTL) associated with the folate content in a population derived from an inter-gene-pool cross of dry beans. The folate content was examined in three large-seeded (AC Elk, Redhawk, and Taylor) and one medium-seeded (Othello) dry bean genotypes, their six F1(i.e., one-way diallel crosses), and the F2of Othello/Redhawk that were evaluated in the field in 2009. Total folate and 5MTHF contents were measured twice with one-hour time interval. The significant variation (P&lt;0.05) in the folate content was observed among the parental genotypes, their F1progeny, and members of the F2population, ranging from 147 to 345 μg/100 g. There was a reduction in the 5MTHF and total folate contents in the second compared to the first measurement. Dark red kidney variety Redhawk consistently had the highest and pinto Othello had the lowest total folate and 5MTHF contents in both measurements. A single marker QTL analysis identified three QTL for total folate and 5MTHF contents in the first measurement and one marker for the total folate in the second measurement in the F2. These QTL had significant dominance effects and individually accounted for 7.7% to 10.5% of the total phenotypic variance. The total phenotypic variance explained by the four QTL was 18% for 5MTHF and 19% for total folate in the first measurement, but only 8% for total folate in the second measurement.

Effects of polymorphisms in the bovine growth differentiation factor 9 gene on sperm quality in Holstein bulls

Members of the transforming growth factor-β (TGFβ) superfamily are critical regulators of germ cell development that act as extracellular ligands of the signal transduction pathways regulating proliferation, differentiation, apoptosis, and other aspects of cell behavior. Growth differentiation factor 9 (GDF9) is a member of the TGFβ superfamily that plays a critical role in ovarian follicular development and ovulation rate in females; however, its role in the testis has not been well elucidated. Therefore, in this study we investigated the effects of GDF9 mutations on the quality of fresh and frozen semen of Holstein bulls. Two reported single nucleotide polymorphisms of GDF9, A485TA and A625C, were analyzed in 129 Holstein bulls. Analysis of variance revealed that the A485T polymorphism had significant effects on the acrosome integrity rate (P < 0.05), whereas the A625T polymorphism was significantly associated with sperm concentration (P < 0.05). In addition, a significant additive effect on sperm concentration was detected for the A485T polymorphism (P < 0.05), whereas the polymorphisms A485TA and A625C had significant dominant effects on acrosome integrity rate and sperm motility in frozen semen, respectively (P < 0.05). This study is the first to show a significant association of GDF9 with sperm quality traits, and the results implied that GDF9 is involved in the initiation or maintenance of spermatogenesis; however, further verification is needed.

Generation Means Analysis of Oil Concentration in Peanut

The current interest in biodiesel production has resulted in a concurrent interest in increasing the oil concentration in high-yielding cultivars, which could make peanuts (Arachis hypogaea.) more desirable as a biofuel source. Currently, peanut seed is approximately 450 to 500 g kg−1 oil on a dry weight basis, depending upon location grown, and there is relatively little genetic variation for oil concentration among adapted high-yielding cultivated peanut genotypes. Thus, identifying sources of variation and elucidating the genetics of oil concentration in peanut is essential to advancing the development of high oil genotypes. The objective of this study was to determine the types of gene action governing the inheritance of oil concentration in peanut by generation means analysis. The F1, F2, and backcross generations of two different runner peanut crosses segregating for oil concentration were evaluated in College Station, Texas, in 2010. Significant differences in oil concentration among the generations were detected, and generation means analysis revealed significant additive, dominance, and epistatic effects for oil concentration in both crosses. The broad-sense heritability estimates were 0.85 and 0.78, and narrow-sense heritability estimates were 0.55 and 0.53 for each of the crosses. Our data indicate that transgressive segregants for high oil were observed, and there is sufficient additive variation present to improve the oil concentration of current runner cultivars.

Autosomal recessiveGJA1(Cx43) gene mutations cause oculodentodigital dysplasia by distinct mechanisms

Oculodentodigital dysplasia (ODDD) is mainly an autosomal dominant human disease caused by mutations in the GJA1 gene, which encodes the gap junction protein connexin43 (Cx43). Surprisingly, there have been two autosomal recessive mutations reported that cause ODDD: a single amino acid substitution (R76H) and a premature truncation mutation (R33X). When expressed in either gap junctional intercellular communication (GJIC)-deficient HeLa cells or Cx43-expressing NRK cells, the R76H mutant trafficked to the plasma membrane to form gap junction-like plaques, whereas the R33X mutant remained diffusely localized throughout the cell, including the nucleus. As expected, the R33X mutant failed to form functional channels. In the case of the R76H mutant, dye transfer studies in HeLa cells and electrical conductance analysis in GJIC-deficient N2a cells revealed that this mutant could form functional gap junction channels, albeit with reduced macroscopic and single channel conductance. Alexa 350 dye transfer studies further revealed that the R76H mutant had no detectable negative effect on the function of co-expressed Cx26, Cx32, Cx37 or Cx40, whereas the R33X mutant exhibited significant dominant or trans-dominant effects on Cx43 and Cx40 as manifested by a reduction in wild-type connexin gap junction plaques. Taken together, our results suggest that the trans-dominant effect of R33X together with its complete inability to form a functional channel may explain why patients harboring this autosomal recessive R33X mutant exhibit greater disease burden than patients harboring the R76H mutant.