Identification of selection signatures in livestock species

The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.     

Maximal oxygen consumption in relation to subordinate traits in lines of house mice selectively bred for high voluntary wheel running.

We studied relations between maximal O2 consumption (VO2 max) during forced exercise and subordinate traits associated with blood O2 transport and cellular respiration in four lines of mice selectively bred for high voluntary wheel running (S lines) and their four nonselected control (C) lines. Previously, we reported VO2 max of 59 females at three Po2 (hypoxia = 14% O2, normoxia = 21%, hyperoxia = 30%). Here, we test the hypothesis that variation in VO2 max can be explained, in part, by hemoglobin concentration and Po2 necessary to obtain 50% O2 saturation of Hb (an estimate of Hb affinity for O2) of the blood as well as citrate synthase activity and myoglobin concentration of ventricles and gastrocnemius muscle. Statistical analyses controlled for body mass, compared S and C lines, and also considered effects of the mini-muscle phenotype (present only in S lines and resulting from a Mendelian recessive allele), which reduces hindlimb muscle mass while increasing muscle mass-specific aerobic capacity. Although S lines had higher VO2 max than C, subordinate traits showed no statistical differences when the presence of the mini-muscle phenotype was controlled. However, subordinate traits did account for some of the individual variation in VO2 max. Ventricle size was a positive predictor of VO2 max at all three Po2. Blood Hb concentration was a positive predictor of VO2 max in S lines but a negative predictor in C lines, indicating that the physiological underpinnings of VO2 max have been altered by selective breeding. Mice with the mini-muscle phenotype had enlarged ventricles, with higher mass-specific citrate synthase activity and myoglobin concentration, which may account for their higher VO2 max in hypoxia.     

Complete mitochondrial genome from South American catfish <Emphasis Type="Italic">Pseudoplatystoma reticulatum</Emphasis> (Eigenmann &amp; Eigenmann) and its impact in Siluriformes phylogenetic tree

The cachara (Pseudoplatystoma reticulatum) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of NAD6 and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in P. reticulatum mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete Pseudoplatystoma reticulatum mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.     

Treadmill Exercise Induces Neutrophil Recruitment into Muscle Tissue in a Reactive Oxygen Species-Dependent Manner. An Intravital Microscopy Study

Intense exercise is a physiological stress capable of inducing the interaction of neutrophils with muscle endothelial cells and their transmigration into tissue. Mechanisms driving this physiological inflammatory response are not known. Here, we investigate whether production of reactive oxygen species is relevant for neutrophil interaction with endothelial cells and recruitment into the quadriceps muscle in mice subjected to the treadmill fatiguing exercise protocol. Mice exercised until fatigue by running for 56.3±6.8 min on an electric treadmill. Skeletal muscle was evaluated by intravital microscopy at different time points after exercise, and then removed to assess local oxidative stress and histopathological analysis. We observed an increase in plasma lactate and creatine kinase (CK) concentrations after exercise. The numbers of monocytes, neutrophils, and lymphocytes in blood increased 12 and 24 hours after the exercise. Numbers of rolling and adherent leukocytes increased 3, 6, 12, and 24 hours post-exercise, as assessed by intravital microscopy. Using LysM-eGFP mice and confocal intravital microscopy technology, we show that the number of transmigrating neutrophils increased 12 hours post-exercise. Mutant gp91^phox-/- (non-functional NADPH oxidase) mice and mice treated with apocynin showed diminished neutrophil recruitment. SOD treatment promoted further adhesion and transmigration of leukocytes 12 hours after the exercise. These findings confirm our hypothesis that treadmill exercise increases the recruitment of leukocytes to the postcapillary venules, and NADPH oxidase-induced ROS plays an important role in this process.     

荷木树干CO_2释放通量与木质部液流和CO_2浓度的关系

采用红外气体分析仪,于2008年10月17-19日连续3个昼夜原位监测了荷木的树干CO_2释放通量、树干温度、木质部液流密度和CO_2浓度.结果表明:树干CO_2释放通量(EA)日变化呈S形曲线,不同径级间差异显著.EA与树干温度呈显著幂函数关系(0.24

Abstract：

By using a Li-820 infra-red CO_2 gas analyzer, an in situ measurement of Schima super-ba stem CO_2 efflux was conducted for three consecutive days from 17 to 19 October 2008. In the meantime, the stem temperature, xylem sap efflux density, and xylem CO_2 concentration were measured. The stem CO_2 efflux had a diurnal variation of "S" pattern, and differed significantly with stem diameter. There was a significant exponential relationship between stem CO_2 efflux and stem temperature (0. 24 < R~2 < 0. 78). The temperature coefficient (b) and regression coeffi-cient (R~2) were higher at nighttime than at daytime, and the Q_(10) value ranged from 2. 01 to 2. 79. The stem CO_2 efflux correlated significantly with the xylem CO_2 concentration, and the best regression curve was cubic (R~2= 0. 48). Excluding the effects of stem temperature, the stem CO_2 efflux showed a significant negative correlation with xylem sap flux density (r =-0.462). Therefore, only using simple temperature function to estimate stem CO_2 efflux would yield a significant error, and xylem sap flux should be taken into consideration in the stem CO_2 emux estimation.     

When nonshivering thermogenesis equals maximum metabolic rate: thermal acclimation and phenotypic plasticity of fossorial Spalacopus cyanus (Rodentia)

Many small mammals inhabiting fluctuating and cold environments display enhanced capacity for seasonal changes in nonshivering thermogenesis (NST) and thermoregulatory maximum metabolic rate (MMR). However, it is not known how this plasticity remains in a mammal that rarely experiences extreme thermal fluctuations. In order to answer this question, we determined body mass (m(b)), basal metabolic rate (BMR), NST, MMR, and minimum thermal conductance (C) on a Chilean fossorial caviomorph (Spalacopus cyanus) from a coastal population, acclimated to cold (15 degrees C) and warm (30 degrees C) conditions. NST was measured as the maximum response of metabolic rate (NST(max)) after injection of norepinephrine (NE) in thermoneutrality minus BMR. Maximum metabolic rate was assessed in animals exposed to enhanced heat-loss atmosphere (He-O2) connected with an open-flow respirometer. Body mass and metabolic variables increased significantly after cold acclimation with respect to warm acclimation but to a low extent (BMR, 26%; NST, 10%; and MMR, 12%). However, aerobic scope (MMR/BMR), calculated shivering thermogenesis (ST), and C did not change with acclimation regime. Our data suggest that physiological plasticity of S. cyanus is relatively low, which is in accordance with a fossorial mode of life. Although little is known about MMR and NST in fossorial mammals, S. cyanus has remarkably high NST; low MMR; and surprisingly, a nil capacity of ST when compared with other rodents.     

Genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population

The genetic parameters for growth, reproductive and maternal traits in a multibreed meat sheep population were estimated by applying the Average Information Restricted Maximum Likelihood method to an animal model. Data from a flock supported by the Programa de Melhoramento Genético de Caprinos e Ovinos de Corte (GENECOC) were used. The traits studied included birth weight (BW), weaning weight (WW), slaughter weight (SW), yearling weight (YW), weight gain from birth to weaning (GBW), weight gain from weaning to slaughter (GWS), weight gain from weaning to yearling (GWY), age at first lambing (AFL), lambing interval (LI), gestation length (GL), lambing date (LD - number of days between the start of breeding season and lambing), litter weight at birth (LWB) and litter weight at weaning (LWW). The direct heritabilities were 0.35, 0.81, 0.65, 0.49, 0.20, 0.15 and 0.39 for BW, WW, SW, YW, GBW, GWS and GWY, respectively, and 0.04, 0.06, 0.10, 0.05, 0.15 and 0.11 for AFL, LI, GL, LD, LWB and LWW, respectively. Positive genetic correlations were observed among body weights. In contrast, there was a negative genetic correlation between GBW and GWS (-0.49) and GBW and GWY (-0.56). Positive genetic correlations were observed between AFL and LI, LI and GL, and LWB and LWW. These results indicate a strong maternal influence in this herd and the presence of sufficient genetic variation to allow mass selection for growth traits. Additive effects were of little importance for reproductive traits, and other strategies are necessary to improve the performance of these animals.     

Linking major nutrients (C,H, N,and P) to trace metals (Fe,Mn, and Cu) in lake seston in southern Brazil

We investigated the relationships between major nutrients (C, H, N, and P) and trace metals (Cu, Fe, and Mn) in seston samples from ten lake/lagoon systems in southern Brazil. The systems were characterized by a diverse set of limnological features, including surface areas from 10⁻¹ to 10² km², water color, a _CDOM(440), from 1.4 to 12.9 m⁻¹, and electrical conductivity from 50 to 100 000 μS cm⁻¹. Seston concentrations also varied a great deal, 32-fold. The elemental (C: N, C: P, and N: P) and C: Chl-a ratios in the seston samples indicated, however, common features; i.e., most of the lakes were N-and/or P-limited, and the seston organic fraction was composed of nonvascular plants (e.g., phytoplankton). Our intersystem comparison revealed that the relative content of organic matter in seston and seston concentrations in lake water tended to correlate positively and negatively, respectively, with trace metal concentrations across the seston samples. Possible influences of elemental and C: Chl-a ratios on the association of metals with seston matrices, although theoretically important, were only partially evidenced here; positive correlations were found between C: N and also Org-H: N ratios with trace metal concentrations. We speculate that such results could be circumstantial, as the nature of the seston matrices appeared to be very similar among them. This hypothesis should thus be the theme of further research. In short, our findings suggest that C: N and Org-H: N ratios as well as the relative content of major nutrients in seston and seston concentrations can be importantly related to trace metal concentrations in seston samples. In discussing the results, however, we consider that metal-seston relationships depend on a variety of physical, chemical, and biological factors and/or variables other than those measured in this study, which could also contribute for defining and explaining variations in metal-seston concentrations in lake ecosystems.