Do bottlenecks increase additive genetic variance?

Because of anthropogenic factors many populations have been at least temporarily reduced to a very small population size. Such reductions could potentially decrease genetic variation and increase the probability of extinction. Analysis of molecular markers has shown a decrease in genetic variation but in many cases this has not reduced the ability of the population to recover from the bottleneck. This apparent paradox is resolved by a consideration of how population bottlenecks can affect additive genetic variance, the relevant measure of ability to respond to selective factors. A bottleneck has the potential to increase additive genetic variance in a population. This may result in an increase in fitness, particularly in populations of conservation concern that are small and lack genetic variation. Here we present a meta-analysis of experimental tests of this prediction using models designed to fit data that is strictly additive and data that has non-additive components. This analysis shows that additive genetic variance in a dataset dominated by morphological traits increases, on average, after a bottleneck event when the inbreeding coefficient is less than 0.3, but neither of the theoretical models alone can adequately explain this result. Because of our inability at present to predict the results of a population bottleneck in a specific case and the probability of extinction associated with small population size we caution against using bottlenecks to increase genetic variance, and thus the fitness, of endangered populations.     

Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines (NILs) targeting three QTLs for spikelets per panicle (SPP), namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F 2 population in which the three QTLs segregated simultaneously. The genotypes of the individual F 2 plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F 2 and F 3 popula- tions at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F 2 population and its progeny. Additive × additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F 2 population and its progeny. Both additive and additive × additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were rec- ommended for rice breeding in different ecosystems.     

Moderate potassium chloride supplementation in essential hypertension: is it additive to moderate sodium restriction?

Twenty patients with mild or moderate essential hypertension and not receiving any drug treatment, who had been moderately restricting their sodium intake to around 70 mmol(mEq) a day for at least one month and whose mean blood pressure was then 163/103 mm Hg, were entered into a double blind, randomised crossover study to compare one month''s treatment with slow release potassium chloride tablets (64 mmol potassium chloride a day) with one month''s treatment with a matching placebo. Mean (SEM) urinary sodium excretion on entry to the study was 68 (6.8) mmol/24 h. Mean urinary potassium excretion increased from 67 (6.9) mmol(mEq)/24 h with placebo to 117 (4.6) mmol/24 h with potassium chloride. Supine and standing systolic and diastolic blood pressures did not change significantly with potassium chloride supplementation when compared with pressures while receiving placebo or before randomisation. In patients who are able moderately to restrict their sodium intake doubling potassium as a chloride salt has little or no effect on blood pressure.     

Resistin up-regulates fractalkine expression in human endothelial cells: Lack of additive effect with TNF-α

Resistin is a cytokine and fractalkine (Fk) a cell adhesion molecule and chemokine that contribute to human vascular inflammation by mechanisms not clearly defined. We questioned whether resistin induces Fk expression in human endothelial cells (HEC), compared the effect with that of the pro-inflammatory cytokine, TNF-α, and evaluated the consequences of co-stimulating HEC with both activators on Fk induction and on the signalling molecules involved. We found that resistin up-regulated Fk expression at comparable level to that of TNF-α by a mechanism involving P38 and JNK MAPK and NF-κB. Co-stimulation of cells with resistin and TNF-α did not increase Fk expression induced by every single inducer. Moreover resistin reduced the expression induced by TNF-α in HEC. The new data uncover Fk as a novel molecular link between resistin and inflammation and show that resistin and TNF-α have no additive effect in Fk up-regulation or on the signalling molecules implicated.     

Marker-based adjustment of the additive relationship matrix for estimation of genetic parameters��an example using Eucalyptus cladocalyx

The effects of adjusting additive (numerator) relationship matrices (A) for inbreeding estimates taken from molecular markers were investigated using a small, model population of Eucalyptus cladocalyx. A number of individual-tree, mixed-models were compared, incorporating estimates of population- and family-level selfing and ancestral inbreeding applied either as average values to the entire population or as variable estimates for subpopulation and family groups. The consequences of ignoring inbreeding were inflated additive genetic variance estimates and underestimation of residual variance, with resulting inflation of heritability. We found models that correct for differential inbreeding at the subpopulation level give similar results to more complex ones including family-level estimates. Our analysis indicates that the commonly applied coefficient of relationship for first-generation eucalypt progeny of ρ = 1/2.5 appears to be quite suitable for correcting variance component and heritability estimates. However, if inbreeding is not specifically corrected for by adjustment of A, some minor rank changes of individual breeding values can occur, especially where levels of inbreeding vary among families, and some suboptimal selections and loss of genetic gain may ensue.     

Characterization of an acid-tolerant β-1,4-glucosidase from Fusarium oxysporum and its potential as an animal feed additive

An extracellular β-glucosidase (BGL) from Fusarium oxysporum was purified to homogeneity by a single chromatography step on a gel filtration column. The optimum activity of BGL on cellobiose was observed at pH 5.0 and 60 °C. Under the same conditions, the K _m and V _max values for p-nitrophenyl β-d-glucopyranoside and cellobiose were 2.53 mM, 268 U?mg protein^?1 and 20.3 mM, 193 U?mg protein^?1, respectively. The F. oxysporum BGL enzyme was highly stable at acidic pH (t _1/2?=?470 min at pH 3). A commercial BGL Novo188 (Novozymes) and F. oxysporum BGL were compared in their ability to supplement Celluclast 1.5 L (Novozymes). In comparison with the commercial Novo188 (267 mg?g substrate^?1), F. oxysporum BGL supplementation released more reducing sugars (330 mg?g substrate^?1) from cellulose under simulated gastric conditions. These properties make F. oxysporum BGL a good candidate as a new commercial BGL to improve the nutrient bioavailability of animal feed.     

Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’

Many rice cultivars that originated from lower-latitude regions exhibit a strong photoperiod sensitivity (PS) and show extremely late heading under long-day conditions. Under natural day-length conditions during the cropping season in Japan, the indica rice cultivar ‘Nona Bokra’ from India showed extremely late heading (202 days to heading) compared to the japonica cultivar ‘Koshihikari’ (105 days), from Japan. To elucidate the genetic factors associated with such extremely late heading, we performed quantitative trait locus (QTL) analyses of heading date using an F₂ population and seven advanced backcross progeny (one BC₁F₂ and six BC₂F₂) derived from a cross between ‘Nona Bokra’ and ‘Koshihikari’. The analyses revealed 12 QTLs on seven chromosomes. The ‘Nona Bokra’ alleles of all QTLs contributed to an increase in heading date. Digenic interactions were rarely observed between QTLs. Based on the genetic parameters of the QTLs, such as additive effects and percentage of phenotypic variance explained, these 12 QTLs are likely generate a large proportion of the phenotypic variation observed in the heading dates between ‘Nona Bokra’ and ‘Koshihikari’. Comparison of chromosomal locations between heading date QTLs detected in this study and QTLs previously identified in ‘Nipponbare’ × ‘Kasalath’ populations revealed that eight of the heading date QTLs were recognized nearby the Hd1, Hd2, Hd3a, Hd4, Hd5, Hd6, Hd9, and Hd13. These results suggest that the strong PS in ‘Nona Bokra’ was generated mainly by the accumulation of additive effects of particular alleles at previously identified QTLs.     

Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive,dominant and overdominant pattern

Heterosis is important for conventional plant breeding and is intensively used to increase the productivity of crop plants. Genetic processes shortly after fertilization might be of particular importance with respect to heterosis, because coordination of the diverse genomes establishes a basis for future performance of the sporophyte. Here we demonstrate a strong crossbreeding advantage of hybrid maize embryos as early as 6 days after fertilization in a modern maize hybrid and provide the first embryo specific analysis of associated gene expression pattern at this early stage of development. We identified differentially expressed genes between hybrid embryos and the parental genotypes by a combined approach of suppression subtractive hybridization and differential screening by microarray hybridizations. Association of heterosis in embryos with genes related to signal transduction and other regulatory processes was implied by the enrichment of these functional classes among the identified gene set. Quantitative RT-PCR analysis validated the expression pattern of 7 of 12 genes analysed and revealed predominantly additive, but also dominant and overdominant expression patterns in hybrid embryos. These patterns indicate that gene regulatory interactions among parental alleles act at this early developmental stage and the genes identified provide entry points for the exploration of gene regulatory networks associated with the specification of the phenomenon heterosis in the plant life cycle.     

Indirect selection on female extra-pair reproduction? Comparing the additive genetic value of maternal half-sib extra-pair and within-pair offspring

One specific hypothesis explaining the evolution of extra-pair reproduction (EPR) by socially monogamous females is that EPR is under indirect selection because extra-pair offspring (EPO) sired by extra-pair males have higher additive genetic value for fitness than the within-pair offspring (WPO) a female would have produced had she solely mated with her socially paired male. This hypothesis has not been explicitly tested by comparing additive genetic value between EPO and the WPO they replaced. We show that the difference in additive genetic breeding value (BV) between EPO and the WPO they replaced is proportional to the genetic covariance between offspring fitness and male net paternity gain through EPR, and estimate this covariance with respect to offspring recruitment in free-living song sparrows (Melospiza melodia). Recruitment and net paternity gain showed non-zero additive genetic variance and heritability, and negative genetic covariance. Opposite to prediction, EPO therefore had lower BV for recruitment than the WPO they replaced. We thereby demonstrate an explicit quantitative genetic approach to testing the hypothesis that EPR allows polyandrous females to increase offspring additive genetic value, and suggest that there may be weak indirect selection against female EPR through reduced additive genetic value for recruitment of EPO versus WPO in song sparrows.     

How are arthopod communities structured and why are they so diverse? Answers from Mediterranean mountains using hierarchical additive partitioning

Mountains are complex ecosystems supporting a great variety of taxa. Here, we explored the diversity patterns of arthropods in two mountains, pinpointing the spatial scale that accounts most for overall diversity variation, using an additive partitioning framework. Butterflies and Orthoptera were sampled in Rodopi (2012) and Grammos (2013) mountains. Diversity was partitioned into five hierarchical levels (mountain, elevational zone, habitat, transect and plot). We compared the estimated diversity values for each level to the respective permuted values expected by chance, for all species, as well as for species identified as “rare” or “common”. At broader spatial levels, the variation in total diversity was attributed to the beta diversity component: mountains accounted for 20.94 and 26.25% of butterfly and Orthoptera diversity, and elevational zones accounted for 28.94 and 35.87% respectively. At finer spatial scales, beta diversity was higher than expected by chance in terms of the Shannon index. The type of habitat was found to play a significant role only for rare orthopterans. Finally, common species were recognized for shaping overall species diversity. We highlight the importance of the spatial levels of elevation zone and then mountain position in conservation planning, due to the greater beta diversity recorded at this scale as compared to habitat or more finite scales. Monitoring programs might need to adapt different strategies with respect to the focal organisms, and consider patterns of common rather than rare species that found to drive the patterns of the entire community.     

Assessing the additive and dominance genetic effects of vegetative propagation ability in Eucalyptus—influence of modeling on genetic gain

To study the genetic determinism of propagation by cutting, 2,115 individuals of 83 full-sib families of the Eucalyptus urophylla?×?Eucalyptus grandis hybrid were used as stock plants and propagated by cuttings. Shoot production (PROD) and cutting success (CUT) were measured in two periods corresponding to the dry and rainy seasons. The experiments showed a significant effect of propagation period, suggesting the combined influence of environmental conditions and physiological state of stock plants. Using the linear mixed model (LMM) and the generalized one (GLMM) to take into account the non-normal distribution, the additive and dominance variances were estimated. They were significantly different from zero for PROD and CUT, as was the interaction between genetic effects and periods. The dominance variance was equal or higher than additive variance for both traits (1?σ ² _D /σ ² _A ?h ² _ss?=?0.182 and H ² _sl?=?0.443) but high with GLMM (h ² _ss?=?0.431 and H ² _sl?=?0.891). For CUT, the same trend was observed for variances but the genetic control was weaker with heritabilities smaller than 0.3. The selection accuracy (r) was affected by the statistical model, r?=?0.94 and r?=?0.42 for PROD using LMM and GLMM, respectively. Genetic correlations between PROD, CUT, and the field growth of clones at 25 months were relatively low. These results are important elements to consider for breeding strategies that target genetic gain for both field growth and cutting success.     

Identification of QTLs with additive,epistatic and QTL × development interaction effects for seed dormancy in rice

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.     

Advantages of AlaGln as an additive to cell culture medium: use with anti-CD20 chimeric antibody-producing POTELLIGENT™ CHO cell lines

l-alanyl-l-glutamine (AlaGln) is dipeptide that has better solubility and stability than Glutamine (Gln). In this study, we evaluated the utility of this dipeptide during culture of POTELLIGENT™ Chinese hamster ovary (CHO) cells expressing anti-CD20 chimeric antibody. Although AlaGln in the culture medium lowered the specific growth rate, the MAb titer was maximized when Gln was completely replaced by AlaGln in both the basal and feed media. Moreover, AlaGln augmented production of antibody not only at flask scale but also at spinner scale, although the extent of this effect was dependent on the cell clone. To explore the mechanism responsible for the effect of AlaGln on cell growth, we measured apoptosis in the early phase of cell culture on days 8, 9, and 10. The apoptotic ratio was reduced in medium containing AlaGln. Ammonia was generated in medium containing Gln when it was maintained at 37 °C, which impeded the growth and productivity of the cells. In contrast, AlaGln produced less ammonia under these conditions, which may have been one of the properties associated with its beneficial effects. We conclude that certain dipeptides can serve as superior alternative sources of amino acids in cell culture and antibody production.     

The dual impact of HIV-1 infection and aging on naïve CD4 T-cells: additive and distinct patterns of impairment

HIV-1-infected adults over the age of 50 years progress to AIDS more rapidly than adults in their twenties or thirties. In addition, HIV-1-infected individuals receiving antiretroviral therapy (ART) present with clinical diseases, such as various cancers and liver disease, more commonly seen in older uninfected adults. These observations suggest that HIV-1 infection in older persons can have detrimental immunological effects that are not completely reversed by ART. As naïve T-cells are critically important in responses to neoantigens, we first analyzed two subsets (CD45RA⁺CD31⁺ and CD45RA⁺CD31^-) within the naïve CD4⁺ T-cell compartment in young (20–32 years old) and older (39–58 years old), ART-naïve, HIV-1 seropositive individuals within 1–3 years of infection and in age-matched seronegative controls. HIV-1 infection in the young cohort was associated with lower absolute numbers of, and shorter telomere lengths within, both CD45RA⁺CD31⁺CD4⁺ and CD45RA⁺CD31^-CD4⁺ T-cell subsets in comparison to age-matched seronegative controls, changes that resembled seronegative individuals who were decades older. Longitudinal analysis provided evidence of thymic emigration and reconstitution of CD45RA⁺CD31⁺CD4⁺ T-cells two years post-ART, but minimal reconstitution of the CD45RA⁺CD31^-CD4⁺ subset, which could impair de novo immune responses. For both ART-naïve and ART-treated HIV-1-infected adults, a renewable pool of thymic emigrants is necessary to maintain CD4⁺ T-cell homeostasis. Overall, these results offer a partial explanation both for the faster disease progression of older adults and the observation that viral responders to ART present with clinical diseases associated with older adults.     

Is hunting mortality additive or compensatory to natural mortality? Effects of experimental harvest on the survival and cause-specific mortality of willow ptarmigan

1. The effects of harvest on the annual and seasonal survival of willow ptarmigan Lagopus lagopus L. were tested in a large-scale harvest experiment. Management units were randomly assigned to one of three experimental treatments: 0%, 15% or 30% harvest. Seasonal quotas were based on the experimental treatment and estimates of bird density before the hunting season. Survival rates and hazard functions for radio-marked ptarmigan were then estimated under the competing risks of harvest and natural mortality. 2. The partially compensatory mortality hypothesis was supported: annual survival of ptarmigan was 0·54 ± 0·08 SE under 0% harvest, 0·47 ± 0·06 under 15% harvest, and was reduced to 0·30 ± 0·05 under 30% harvest. Harvest mortality increased linearly from 0·08 ± 0·05, 0·27 ± 0·05 and 0·42 ± 0·06 from 0% to 30% harvest, whereas natural mortality was 0·38 ± 0·08, 0·25 ± 0·05 and 0·28 ± 0·06 under the same treatments. 3. Realized risk of harvest mortality was 0·08-0·12 points higher than our set harvest treatments of 0-30% because birds were exposed to risk if they moved out of protected areas. The superadditive hypothesis was supported because birds in the 30% harvest treatment had higher natural mortality during winter after the hunting season. 4. Natural mortality was mainly because of raptor predation, with two seasonal peaks in fall and spring. Natural and harvest mortality coincided during early autumn with little potential for compensation during winter months. Peak risk of harvest mortality was 5× higher than natural mortality. Low natural mortality during winter suggests that most late season harvest would be additive mortality. 5. Environmental correlates of natural mortality of ptarmigan included seasonal changes in snow cover, onset of juvenile dispersal, and periods of territorial activity. Natural mortality of ptarmigan was highest during autumn movements and nesting by gyrfalcons Falco rusticolus L. Mortality was low when gyrfalcons had departed for coastal wintering sites, and during summer when ptarmigan were attending nests and broods. 6. Our experimental results have important implications for harvest management of upland gamebirds. Seasonal quotas based on proportional harvest were effective and should be set at ≤ 15% of August populations for regional management plans. Under threshold harvest of a reproductive surplus, 15% harvest would be sustainable at productivity rates ≥ 2·5 young per pair. Impacts of winter harvest could be minimized by closing the hunting season in early November or by reducing late season quotas.     

Gene cloning, expression and characterization of an α-galactosidase from Pedobacter nyackensis MJ11 CGMCC 2503 with potential as an aquatic feed additive

A gene, aga-MJ11, encoding an α-galactosidase (EC 3.2.1.22) was cloned from Pedobacter nyackensis MJ11 CGMCC 2503, expressed in Escherichia coli, and biochemically characterized. The gene consisted of 2,163 nucleotides encoding a 720 amino acid–protein with a theoretical molecular weight of 82.6 kDa. The deduced amino acid sequence of Aga-MJ11 shared the highest identity of 51% to an α-galactosidase from Parabacteroides distasonis (YP_001301506), which belongs to glycoside hydrolase (GH) family 36. Purified recombinant Aga-MJ11-H showed optimal activity at pH 5.5 and 40°C, was stable at pH 4.0–10.0, retained ~80% of the maximum activity at 30°C (the optimum temperature for freshwater fish), exhibited tolerance to some proteases, and had a wide substrate specificity (pNPG, melidiose, stachyose and raffinose). All these features make Aga-MJ11 potentially useful for applications in aquaculture. The enzyme studied in the present work may represent a novel GH-36 α-galactosidase from the genus Pedobacter. X. Liu and K. Meng contributed equally to this work.     

A novel inclusion complex (β-CD/ABP-dHC-cecropin A) with antibiotic propertiess for use as an anti-Agrobacterium additive in transgenic poplar rooting medium

The increasing resistance of bacteria and fungi to currently available antibiotics is a major concern worldwide, leading to enormous effort to develop novel antibiotics with new modes of action.We recently reported that ABP-dHC-cecropin A exhibited strong antibacterial and antifungal activity, making it a candidate antibiotic substitute. In this study, β-cyclodextrin (β-CD) combined with ABP-dHC-cecropin A enhanced the physical and chemical properties of ABP-dHC-cecropin A but did not significantly decrease its antibacterial activity. Thus, β-CD/ABP-dHC-cecropin A should be considered a novel antibacterial drug. We used β-CD/ABP-dHC-cecropin A as an anti-Agrobacterium compound to supplementtransgenic poplar medium. Sideeffects of the inclusion complex had little impact on plantgrowth. Thus, β-CD/ABP-dHC-cecropin A may be used as traditional antibiotics forpoplar transplantation with greater antibbacterial effects.