Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline

sam βada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r ‐package providing a pipeline for landscape genomic analysis based on sam βada , spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).     

Manifestations of resistance to Haemonchus contortus in sheep: Worm populations and abomasal changes in sheep superinfected with 1,000,000 larvae of H. contortus

The super-infecting dose produced a marked rise in gastric pH in all sheep from the 3rd day after administration of larvae. Expulsion of the existing population of adult worms may have begun on the 4th day but was still only completed in 3/6 sheep on the 5th day. The larvae caused extensive damage in the individual glands which they parasitised. Very few of the 10⁶ larvae survived for 27 days and only in 1/8 sheep had they developed beyond early 4th stage at 27 days. Extensive histological changes were seen in the fundic mucosa beginning as early as 2 days after the superinfection. While the pH change preceded expulsion of the adults and was consistent in its timing, the timing of the expulsion was irregular. This throws doubt on the hypothesis that the change in physico-chemical conditions produced by the superinfecting larvae is the only cause of the expulsion of the adult worms.     

Introduced and native herbivores have different effects on plant composition in low productivity ecosystems

Questions

Understanding how livestock grazing alters plant composition in low productivity environments is critical to managing livestock sustainably alongside native and introduced wild herbivore populations. We asked four questions: (1) does recent livestock and rabbit grazing reduce some plant attributes more strongly than others; (2) does grazing by introduced herbivores (i.e. livestock and rabbits) affect plants more strongly than native herbivores (i.e. kangaroos); (3) do the effects of recent livestock grazing differ from the legacy effects of livestock grazing; and (4) does the probability of occurrence of exotic plants increase with increasing net primary productivity (NPP)?

Location

South‐eastern Australia.

Methods

We measured the recent grazing activity of co‐occurring livestock (cattle, sheep, goats), rabbits and kangaroos by counting faecal pellets; historic grazing activity by measuring livestock tracks; and derived NPP from satellite imagery. We used a hierarchical GLMM to simultaneously model the presence or absence (i.e. probability of occurrence) of all plant species as a function of their attributes (growth form, lifespan and origin) to assess their average response to recent grazing, historic grazing and productivity in a broad‐scale regional study.

Results

Recent and historic livestock grazing, rabbit grazing and increasing NPP reduced the average probability of occurrence of plant species, although responses varied among plant attributes. Both recent and historic livestock grazing strongly reduced the average probability of occurrence of native species, and forbs and geophytes, but differed in their relative effects on other growth forms. Recent livestock grazing, rabbit grazing and NPP had similar effects, strongly reducing native species and forbs, geophytes, shrubs and sub‐shrubs. The overall effects of recent kangaroo grazing were relatively weak, with no clear trends for any given plant attribute.

Conclusion

Our results highlight the complex nature of grazing by introduced herbivores compared with native herbivores on different plant attributes. Land managers need to be aware that domestic European livestock, rabbits and other free‐ranging introduced livestock such as goats have detrimental impacts on native plant communities. Our results also show that kangaroo grazing has a relatively benign effect on plant occurrence.     

急性低氧对高原土生动物藏系绵羊血气的影响

为了探讨急性低氧时藏系绵羊(Ovis aries)的血气特点,揭示其低氧适应机制,将7只雄性藏系绵羊和5只雄性移居绵羊分别置于高低压氧舱内,测定模拟海拔0、2 300和4 500 m时各动物清醒状态下的血气指标。用热稀释法测定心输出量。使用血气分析仪和EG7血样板,测定动脉及混合静脉血的血气指标,按Ficks方法计算氧耗量。结果显示,随着模拟海拔高度的升高,藏羊和移居羊的动静脉血氧饱和度(So2)、氧分压(Po2)、二氧化碳分压(Pco2)都呈明显下降趋势(P<0.05),血红蛋白浓度(Hb)、血液pH、心输出量及氧耗量虽无明显的差异性改变,但它们在4 500 m处的绝对值是增加的。在相同海拔,藏羊的Hb明显低于移居羊(P<0.05),4 500 m时藏羊的动脉血氧饱和度(Sao2)及组织摄氧量显著高于移居羊(P<0.05)。表明藏羊在急性低氧时表现出的高Sao2及高组织摄氧量,低Hb、低pH是它适应高原低氧的生理基础。     

Tumor Necrosis Factor-α, Interleukins-12(p40), 6, and 10 levels in cerebrospinal fluid and outcome prediction in Ossimi sheep with encephalitic listeriosis

Encephalitic listeriosis in sheep is a life-threatening disease. However, little is known about the cytokine response and their predictive value in this disease. The aim of present study was to assess the prognostic significance of Tumor Necrosis Factor-α (TNF-α), Interleukin-12(p40) (IL-12 p40), Interleukin-6 (IL-6), and Interleukin 10 (IL-10) levels in cerebrospinal fluid (CSF) in sheep with encephalitic listeriosis. Fifty-nine ewes in 14 flocks were diagnosed clinically as having listeriosis. CSF was collected and subjected to bacteriological examination and estimation of selected cytokines. Twenty-eight ewes were confirmed to be infected with Listeria monocytogenes. Based on antimicrobial sensitivity test, sheep were treated and the outcome was recorded as survivors (n = 10) and non-survivors (n = 18). Cutoff points for CSF cytokines were determined by Receiver operating characteristic analysis (ROC). Association between levels of CSF cytokines and outcome of listeriosis was assessed by logistic regression. TNF-α, IL-6 and IL-12(p40) levels as well as TNF-α/IL-10 ratio were significantly higher in non-survivors than survivors (p = 0.002, 0.0021, 0.0033, and 0.001, respectively). However, IL-10 level was significantly lower in non-survivors than survivors (p = 0.0058). ROC analysis revealed that IL-6 and TNF-α/IL-10 ratio had the highest AUC values (0.98, 0.984, respectively). Final multivariate logistic regression model showed that TNF-α/IL-10 ratio was the only variable that has predictive value for mortality in diseased sheep (p: 0.001; OR: 7.2; 95% CI: 5.7–9.8). TNF-α showed a positive correlation with IL-12β (r = 0.917) and IL-6 (r = 0.965). IL-12 (p40) showed also a positive correlation with IL-6 (r = 0.906). However, IL-10 showed a negative correlation with TNF-α (r = −0.915), IL-12(p40) (r = −0.790), and IL-6 (r = −0.902). In conclusion, TNF-α/IL-10 ratio may provide predictive information about outcome of encephalitic listeriosis in sheep.     

Preference by sheep for endophyte-infected tall fescue grown adjacent to or at a distance from alfalfa

Two experiments were conducted to assess preference by sheep for endophyte-infected tall fescue growing in monoculture at least 5 m away from alfalfa (fescue-middle (FM)) over endophyte-infected tall fescue growing adjacent (0.2 to 1 m; fescue–alfalfa (FA)) to alfalfa (FA), and the effect of legume scent on preference for endophyte-infected tall fescue. In Experiment 1, 10 six-month-old lambs were offered for 12 days a choice of freshly harvested FA and FM. On days 13 and 14, lambs were offered the same choice, except cages (to allow access only to scent) containing freshly harvested alfalfa were put in the feeders containing FA, whereas cages containing freshly harvested FM were included with the feeders containing FM. Forage intake was measured 1 h after feeding and at three consecutive 2-h intervals thereafter. FA contained greater (P<0.002) concentrations of the alkaloid ergovaline (360±27 ppm) and CP (8±0.4%) than FM (219±27 ppm and 6±0.4%, respectively). Lambs preferred (P<0.05) FA to FM during the 1^st hour of feeding, but the differences became smaller and disappeared in later feeding periods (P<0.005). Lambs offered FA with alfalfa scent or FM with FM scent preferred (P<0.05) FA but only on the 2^nd day. In Experiment 2, 10 six-month-old lambs were offered a choice of FM with cages (to allow access only to scent) containing freshly harvested alfalfa or FM for 8 days. During the following 4 days, FM in the cages was replaced with freshly harvested sainfoin. Preference was greater (P<0.05) for FM offered with alfalfa scent than for FM offered with FM scent only on days 4 and 8. When lambs were offered FM with alfalfa or sainfoin in cages, they preferred (P<0.05) tall fescue with sainfoin scent over fescue with alfalfa scent, but intake was variable across hours and days (P<0.001). It is concluded that (1) lambs adjusted their intake of and preference for FA and FM over successive feeding bouts within each day, likely owing to an attempt to balance intakes of nutrients and alkaloids and (2) olfactory cues influenced preference, but to a lesser extent than nutrients and alkaloids in endophyte-infected tall fescue.     

Net mineral requirements for the growth and maintenance of Somali lambs

Minerals are limiting factors in animal production, and the knowledge of mineral requirements for livestock is crucial to the success of a commercial enterprise. Hair sheep may have different mineral requirements than those presents by the international committees. A study was carried to evaluate the net calcium (Ca), phosphorus (P), magnesium (Mg), sodium (Na), potassium (K), zinc (Zn), iron (Fe), manganese (Mn) and copper (Cu) requirements for the growth and maintenance of Brazilian Somali lambs. A total of 48 hair lambs (13.5±1.8 kg) aged 60±15 days were allocated to individual pens. Eight animals were slaughtered at the beginning of the experiment to serve as a reference group to estimate initial empty BW (EBW) and initial body composition. The remaining lambs (n=40) were assigned to a completely randomized design with eight replications in five levels of metabolizable energy (ME; 4.93, 8.65, 9.41, 10.12 and 11.24 MJ/kg DM). When the lambs of a given treatment reached an average BW of 28 kg, they were slaughtered. Initial body composition was used to calculate the retention of minerals. Mineral body composition was fit using a logarithmic equation in the form of a nonlinear model. The maintenance requirements were estimated from regressions of mineral retention in the empty body on mineral intake. The body mineral concentration decreased in lambs with a BW ranging from 15 to 30 kg. The net mineral requirements (100 g/day of average daily gain (ADG)) decreased from 0.52 to 0.51 g for Ca, 0.28 to 0.23 g for P, 0.02 to 0.02 g for Mg, 0.09 to 0.08 g for Na, 0.11 to 0.09 g for K, 1.30 to 1.08 mg for Zn, 3.77 to 3.22 mg for Fe, 0.08 to 0.06 mg for Mn and 0.09 to 0.08 mg for Cu when BW increased from 15 to 30 kg. The daily net requirements for maintenance per kilogram of BW were 30.13 mg of Ca, 27.58 mg of P, 1.26 mg of Mg, 4.12 mg of Na, 8.11 mg of K, 0.133 mg of Zn, 0.271 mg of Fe, 0.002 mg of Mn and 0.014 mg of Cu. The results of this study indicate that the net mineral requirements for weight gain and maintenance in Brazilian Somali lambs are different than the values that are commonly recommended by the main evaluation systems for feed and nutritional requirements for sheep. These results for the nutritional requirements of minerals may help to optimize mineral supply for hair sheep.     

Effects of rotational and continuous grazing on herbage quality,feed intake and performance of sheep on a semi-arid grassland steppe

Compared to continuous grazing (CG), rotational grazing (RG) increases herbage production and thereby the resilience of grasslands to intensive grazing. Results on feed intake and animal performance, however, are contradictory. Hence, the objective of the study was to determine the effects of RG and CG on herbage mass, digestibility of ingested organic matter (dOM), organic matter intake (OMI) and live weight gain (LWG) of sheep in the Inner Mongolian steppe, China. During June–September 2005–2008, two 2-ha plots were used for each grazing system. In RG, plots were divided into four 0.5-ha paddocks that were grazed for 10 days each at a moderate stocking rate. Instead, CG sheep grazed the whole plots throughout the entire grazing season. At the beginning of every month, dOM was estimated from faecal crude protein concentration. Faeces excretion was determined using titanium dioxide in six sheep per plot. The animals were weighed every month to determine their LWG. Across the years, herbage mass did not differ between systems (p = 0.820). However, dOM, OMI and LWG were lower in RG than in CG (p ≤ 0.005). Thus, our study showed that RG does not improve herbage growth, feed intake and performance of sheep and suggests that stocking rates rather than management system determine the ecological sustainability of pastoral livestock systems in semi-arid environments.     

Synthesis and secretion of the mouse whey acidic protein in transgenic sheep

The synthesis of foreign proteins can be targeted to the mammary gland of transgenic animals, thus permitting commercial purification of otherwise unavailable proteins from milk. Genetic regulatory elements from the mouse whey acidic protein (WAP) gene have been used successfully to direct expression of transgenes to the mammary gland of mice, goats and pigs. To extend the practical usefulness of WAP promoter-driven fusion genes and further characterize WAP expression in heterologous species, we introduced a 6.8 kb DNA fragment containing the genomic form of the mouse WAP gene into sheep zygotes. Two lines of transgenic sheep were produced. The transgene was expressed in mammary tissue of both lines and intact WAP was secreted into milk at concentrations estimated to range from 100 to 500 mg/litre. Ectopic WAP gene expression was found in salivary gland, spleen, liver, lung, heart muscle, kidney and bone marrow of one founder ewe. WAP RNA was not detected in skeletal muscle and intestine. These data suggest that unlike pigs, sheep may possess nuclear factors in a variety of tissues that interact with WAP regulatory sequences. Though the data presented are based on only two lines, these findings suggest WAP regulatory sequences may not be suitable as control elements for transgenes in sheep bioreactors.     

Rumen Ciliate Fauna of Alaskan Moose (Alces americana), Musk-Ox (Ovibos moschatus) and Dall Mountain Sheep (Ovis dalli)*

Total numbers, generic distribution and percentage species distribution were determined for the ciliate protozoa in rumen contents obtained from Alaskan moose (Alces americana), musk-ox (Ovibos moschatus) and Dall mountain sheep (Ovis dalli). The musk-ox has a fauna somewhat similar to that previously observed in reindeer and caribou. In contrast, only protozoa in the genus Entodinium were observed in moose, while Dall mountain sheep have a fauna unique among Alaskan ruminants studied to date. Other than Entodinium exiguum which was common to all animals, only 2 additional species of Entodinium, observed in the moose and musk-ox, occurred in more than one animal species. Four new species of protozoa are described, Entodinium dalli sp.n., Entodinium constrictum sp.n. and Polyplastron alaskum sp.n. from the Dall mountain sheep and Entodinium alces sp.n. from moose.