The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world. The high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome. The first contig has 40 overlapping BAC clones covering an approximately 2.9 Mb region of MHC class I, class III, and class IIa, and the second contig has 7 BAC clones covering an approximately 500 Kb genomic region that harbours MHC class IIb. The relative position of each BAC corresponding to the MHC sequence was determined by comparative mapping using PCR screening of the BAC library of 192,000 clones, and the order of BACs was determined by DNA fingerprinting. The overlaps of neighboring BACs were cross-verified by both BAC-end sequencing and co-amplification of identical PCR fragments within the overlapped region, with their identities further confirmed by DNA sequencing. We report here the successful construction of a high-quality physical map for the addax MHC region using BACs and comparative mapping. The addax MHC physical map we constructed showed one gap of approximately 18 Mb formed by an ancient autosomal inversion that divided the MHC class II into IIa and IIb. The autosomal inversion provides compelling evidence that the MHC organizations in all of the ruminant species are relatively conserved.

Concerted conservation efforts have brought the giant panda (Ailuropoda melanoleuca) back from the brink of extinction, but pandas continue to face anthropogenic threats in the wild and breeding success in captivity remains low. Because stress can have detrimental impacts on reproduction, monitoring stress- and sex-steroid levels would help assess the effectiveness of conservation mitigation measures in panda populations as well as monitor the welfare and reproductive health of captive animals. In this proof-of-concept study, we used faecal sex steroid and cortisol concentrations (n = 867 samples collected from five males and five females at Beijing Zoo every 4 days over the course of 12 months) as a reference to investigate if testosterone, estradiol, progesterone and cortisol can be meaningfully measured in panda hair (n = 10) using radio-immuno-assays. Additionally, we calculated the ratio of testosterone to cortisol (T:C ratio) for each male, which can provide a biomarker of stress and physical performance. Our findings revealed distinct monthly variations in faecal sex-steroid and cortisol concentrations, reflecting reproductive seasonality and visitor-related stress among individual pandas. Notably, the oldest male had a significantly lower T:C ratio than other males. Our results confirm that the level of sex steroids and cortisol can be assayed by panda hair, and the hair cortisol concentrations correlate significantly with that in faeces with one month lag behind (r = 0.68, P = 0.03). However, the concentrations of hormones detected in saliva are lower than those in faeces by two orders of magnitude, making it difficult to ensure accuracy. By assessing the applicability of hair, faecal and salivary sampling, we can infer their utility in monitoring the reproductive status and acute and chronic stress levels of giant pandas, thereby providing a means to gauge the success of ongoing habitat restoration efforts and to discuss the feasibility of sample collection from wild populations.

The giant panda (Ailuropoda melanoleuca) has evolved a large number of mucous glands in the intestinal lining to adapt to the digestion of high-fiber foods. However, in captive pandas, excessive mucus might form a mass and then be eliminated, which is often accompanied by discomfort and decreased activity. This event is called ‘mucous excretion’. The causes of mucus excretions in captive pandas, however, remain unknown. The aims of this study were to document the occurrence of mucus excretion and to investigate its possible associations with pandas’ age, gender, and feces output. Eighteen giant pandas were studied at the Beijing Zoo from April 2003 to June 2017, and a total of 900 occurrences of mucous excretion and 32,856 daily defecation outputs in weight were recorded. The likelihood of mucous excretion occurrence decreased by 11.34% for each 1 kg of fecal output (Z = −4.12, p < 0.0001), while it increased by 5.89% per year of age (Z = 4.02, p < 0.0001). However, individual differences in gender had no significant effect on the mucous occurrence (Z = −0.75, p = 0.4508). A monthly change in mucus occurrence was also found. The mean frequency of mucus occurrence was significantly higher in October. In August, time (month) change showed the biggest negative influence on feces output but the biggest positive influence on mucus excretion (seasonal factors were −2.261 and 0.0126, respectively). Our results documented the occurrence of mucous excretions and confirmed their possible associations with the pandas’ age and fecal output based on a 15-year prospective study. This study not only adds to our knowledge of panda physiology but also suggests the need for further studies examining the causes of the excretion of mucous stools in captive pandas. Reducing the incidence of mucous excretion would promote ex situ conservation and enhance panda welfare.

Background: The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Fewer than 2500 giant pandas are known to exist, many of which are bred in captivity as a means to preserve and repopulate the species. Like other captive mammals, giant pandas acquire age-related cataracts, reducing their quality of life. Recent comparative genome-wide methylation analysis revealed 110 differentially methylated genes associated with cataract formation including six also associated with the formation of age-related cataracts in humans. Results: To investigate the pathological pathway in greater detail, here we used RNA-Seq analysis to investigate the differential expression profiles of genes in three giant pandas with cataracts and three healthy controls. We identified more than 700 differentially expressed genes, 29 of which were selected for further analysis based on their low q-value. We found that many of the genes encoded regulatory and signaling proteins associated with the control of cell growth, migration, differentiation and apoptosis, supporting previous research indicating a key role for apoptosis in cataract formation. Conclusion: The identification of genes involved in the formation of age-related cataracts could facilitate the development of predictive markers, preventative measures and even new therapies to improve the life of captive animals.

Giant pandas feed preferentially on bamboo but choose different species and organs depending on factors such as the altitude and season, suggesting preferential selection according to their nutritional requirements. However, the mechanism of selection is unclear. Pandas cannot directly sense the nutritional quality of bamboo shoots but tend to sniff their food before consumption, inferring that odors inform their choice, which is then reinforced by the selection of positive and negative taste cues. To investigate the basis of selection, we observed the effects of 10 different bamboo species on feeding behavior, including food item selection, feeding frequency, portion size, food processing time per bite, and amount consumed per meal. Three of the bamboos were preferred, another four were consumed when the preferable bamboos were unavailable, and the remaining three were always rejected. We then characterized the volatile components of the bamboo leaves as well as the primary and secondary metabolites, allowing us, for the first time, to correlate feeding behavior with metabolomics. The three groups shared some volatile compounds but 21 volatiles were unique to the preferred leaves and appeared to confer sweet and fresh aromas, whereas the inedible leaves produced 20 unique volatiles that were pungent or floral, which appeared to discourage feeding. The three groups also shared many common nonvolatile metabolites, but pairwise comparisons revealed both qualitative and quantitative differences in metabolite abundance that resulted in the preferred leaves accumulating compounds associated with a sweet taste in humans (e.g., sugars), while the inedible leaves contained metabolites often associated with sour and bitter tastes (e.g., certain flavonoids and acids). Following attraction by certain volatiles, giant pandas may therefore consolidate their selection of leaves that are potentially more nutritious by consuming those with sweeter, less bitter and less sour tastes.

Approximately 20% of aged captive giant pandas (Ailuropoda melanoleuca) have cataracts that impair their quality of life. To identify potential biomarkers of cataract formation, we carried out a quantitative proteomics analysis of 10 giant pandas to find proteins differing in abundance between healthy and cataract-bearing animals. We identified almost 150 proteins exceeding our threshold for differential abundance, most of which were associated with GO categories related to extracellular localization. The most significant differential abundance was associated with components of the proteasome and other proteins with a role in proteolysis or its regulation, most of which were depleted in pandas with cataracts. Other modulated proteins included components of the extracellular matrix or cytoskeleton, as well as associated signaling proteins and regulators, but we did not find any differentially expressed transcription factors. These results indicate that the formation of cataracts involves a complex post-transcriptional network of signaling inside and outside lens cells to drive stress responses as a means to address the accumulation of protein aggregates triggered by oxidative damage. The modulated proteins also indicate that it should be possible to predict the onset of cataracts in captive pandas by taking blood samples and testing them for the presence or absence of specific protein markers.