QTL for live weight traits in Père David's x red deer interspecies hybrids

Interspecies hybrids between Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus) have proved to be a powerful resource in the search for quantitative trait loci (QTL) in deer. Several regions of the genome with significant effects on live weight and growth rates in backcross hybrids were detected. These include putative QTL for 6-month live weight (LOD 3.90) on linkage group 12, for 14-month live weight (LOD 3.19) on linkage group 1, three putative QTL for growth rate from 3 to 6 months (LOD 4.19 on linkage group 12, LOD 3.92 on linkage group 12, and LOD 3.34 on linkage group 5). In addition, linkage groups 20 and 1 appear to be associated with live weight traits between 9 and 16 months. The variance in traits explained by these QTL ranged between 5.3% and 11.2%. Allele substitution with Père David's alleles at different loci had both positive and negative effects on live weights and growth rates.     

A QTL study of growth and body shape in the inter-species hybrid of Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus)

An interspecies deer hybrid resource population developed from a cross of Père David's and red deer was used to detect QTL that account for species differences. A genome scan, coupled with composite interval mapping, was conducted to search for QTL controlling body measurements at pre-pubescent age (6 months of age) and puberty (15 months of age) in this interspecies hybrid. Five linkage groups that harbour QTL affecting morphology were identified. A joint-traits analysis was used to search for putative pleiotropic QTL on four of these linkage groups, and three were significantly associated with pleiotropic QTL for nose width and foot length (metacarpal and phalanges), which collectively accounted for 29-58% of the phenotypic difference between the two deer species. This study suggests that a few loci with large pleiotropic effects may be responsible for species-specific differences in growth and structure-related traits.     

Seasonal changes of reproductive behavior and fecal steroid concentrations in Père David's deer.

From July 1997 to September 1997 and from March 1998 to July 1998, we studied reproductive behaviors of Père David's deer in Dafeng, China. During the field behavioral observations, we collected fresh voided fecal samples from the Père David's stags and hinds periodically and kept those samples under -20 degrees C until laboratory analysis. We analyzed the fecal testosterone, estradiol, and progesterone concentrations in those samples using radioimmunoassay. During this study, we also recorded 17 types of male reproductive behaviors and nine types of female reproductive behaviors. Reproductive behaviors and the fecal steroid concentrations showed overt seasonal fluctuations. There were statistically significant correlations between some male reproductive behaviors, such as anogenital sniffing, urine sniffing, urine spraying, wallowing, bellowing, antler adorning, Antler swags mud, chasing, herding hinds, chin resting, mounting and copulating, with the fecal testosterone concentrations. These results suggested that seasonal reproductive behaviors in stags are strongly associated with circulating testosterone. We also found that some female reproductive behaviors fluctuate corresponding with changes in fecal estrogen concentrations. Although there was no direct evidence to confirm the correlations between female reproductive behaviors and fecal estrogen in our experiment, we could not rule out that reproductive activities of hinds were largely related to ovarian estrogen secretion, and estrogen is necessary for inducing female reproductive behaviors.     

cDNA cloning, recombinant expression and bioactivity of Père David's deer BAFF

B cell activating factor (BAFF), a member of the TNF family, is a critical cytokine for the survival, proliferation, maturation, and differentiation of B cells. In the present study, Père David's deer BAFF (miBAFF) was amplified from Elaphurus davidianus using RT-PCR. This is the first BAFF cloned from a member of Cervidae family. The open reading frame (ORF) of the miBAFF cDNA consists of 843 bases that encode a 280-amino acid protein bearing typical TNF homology domain. Sequence alignment shows that miBAFF shares 39.3%-97% sequence homology with the BAFF sequences of other mammals. Comparative protein modeling predicted that the 3D structure of the soluble mature portion of miBAFF (misBAFF) is very similar to that of human BAFF (hsBAFF). Recombinant misBAFF fused to a SUMO-tag was efficiently expressed in Escherichia coli BL21 (DE3) cells. The protein molecular weight of ~36 KDa was determined using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. In vitro, purified misBAFF was shown to promote the survival and proliferation of Père David's deer peripheral blood lymphocytes and mouse B cells. These results indicate that miBAFF plays an important role in the survival/proliferation of mouse B cells and, shows highly conserved evolutionarily, leading to functional cross-reactivity that exists between mouse and Père David's deer BAFF.     

Diet composition and selection of Père David's deer in Hubei Shishou Milu National Nature Reserve,China

Hubei Shishou Milu National Nature Reserve is an ideal place to restore the wild population of Père David's deer (Elaphurus davidianus). Understanding foraging ecology and diet composition is essential for assessing population development or establishing long-term effective conservation measures for endangered species. However, little is known about the diet composition of Père David's deer and its diet selection mechanism. In this study, we used stable isotope technology to investigate the diet composition of Père David's deer according to various tissues (i.e., fur, muscle, liver, heart, and feces) and seasons, and evaluated the correlation between the nutrient composition of plants and diet composition. Bayesian isotope analysis showed that the autumn and winter diet estimated by fur and fecal samples indicated a diet dominated by C₃ grasses (42.7%–57.2%, mean), while the summer diet estimated by muscle and liver samples was dominated by C₃ forbs (30.9%–41.6%, mean). The Pearson correlation test indicated that the contribution of winter diet composition reflected by fur and fecal samples was associated with correlations with crude protein (r = .666, p < .01) and soluble sugars (r = .695, p < .01). The results indicated that crude protein and soluble sugars were important factors influencing the winter diet selection of Père David's deer. In the context of the current reintroduction facing many challenges, such as habitat fragmentation, wetland degradation, and human disturbance, comprehensively evaluating the diet selection mechanism of Père David's deer under different resource specificities and temporal changes should be considered in the future.     

Oestrous cycles and the breeding season of the Père David's deer hind (Elaphurus davidianus)

Reproductive cycles were studied in a group of tame Père David's deer hinds. The non-pregnant hind is seasonally polyoestrous and, in animals studied over 2 years, the breeding season began in early August (2 August +/- 3.3 days; s.e.m., N = 9) and ended in mid-December (18 December +/- 5.7 days; N = 8) and early January (6 January +/- 3.2 days; N = 11) in consecutive years. During the anoestrous period, plasma progesterone concentrations were low (0.2 +/- 0.01 ng/ml) or non-detectable. There was a small, transient increase in progesterone values before the onset of the first cycle of the breeding season. In daily samples taken during an oestrous cycle in which hinds were mated by a marked vasectomized stag, progesterone concentrations remained low (less than 0.5 ng/ml) for a period of about 6 days around the time of oestrus, showed a significant increase above oestrous levels by Day 4 (Day 0 = day of oestrus) and then continued to increase for 18 +/- 2.8 days to reach mean maximum luteal levels of 3.5 +/- 0.6 ng/ml. The plasma progesterone profiles from a number of animals indicated that marking of the hinds by the vasectomized stag did not occur at each ovulation during the breeding season and therefore an estimate of the cycle length could not be determined by this method. In the following year, detection of oestrus in 5 hinds was based on behavioural observations made in the absence of the stag. A total of 19 oestrous cycles with a mean length of 19.5 +/- 0.6 days was observed.(ABSTRACT TRUNCATED AT 250 WORDS)     

A novel HURRAH protocol reveals high numbers of monomorphic MHC class II loci and two asymmetric multi-locus haplotypes in the Père David's deer

The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated "HURRAH" based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1) All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2) these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ～ DRB1 ～ DRB3 ～ DQA1 ～ DQB2 (H1) and DRA1*02 ～ DRB2 ～ DRB4 ～ DQA2 ～ DQB1 (H2). The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.     

Assaying progesterone,estradiol and cortisol concentrations in hair of Père David deer hinds: an alternative way to reflect seasonality of steroid secretion

The use of a hair hormone concentration assay is increasingly recognized as a useful and noninvasive technique for monitoring the endocrinological status of animals. However, few studies have focused on reproductive and stress hormones together. We used a chemiluminescent immunoassay to determine whether the progesterone, estradiol, and cortisol concentrations could be measured from hair and whether these hormone concentrations varied in different hair segments of captive Père David deer hinds. We found that progesterone, estradiol, and cortisol could be measured in the hair samples and that the progesterone concentration varied but the estradiol and cortisol concentrations did not among different hair segments. Contrary to the segmental decline in hair cortisol found in many studies, we found that progesterone concentration was higher near the tip than at the base of hair in Père David deer. This suggests that the variation in segmental hair steroid hormone concentration in seasonal molting animals may be mainly due to internal reproductive cycles and that hair steroid hormones may reflect long-term physiological changes and can thus be used for the conservation and management of wildlife.     

The Père David's deer MHC class I genes show unexpected diversity patterns, with monomorphic classical genes but polymorphic nonclassical genes and pseudogenes

Père David's deer (Elaphurus davidianus) is a highly inbred species that arose from 11 founders but now comprises a population of about 3,000 individuals, making it interesting to investigate the adaptive variation of this species from the major histocompatibility complex (MHC) perspective. In this study, we isolated Elda-MHC class I loci using magnetic bead-based cDNA hybridization, and examined the molecular variations of these loci using single-strand conformation polymorphism (SSCP) and sequence analysis. We obtained seven MHC class I genes, which we designated F1, F12, G2, I7, AF, I8, and C1. Our analyses of stop codons, phylogenetic trees, amino acid conservation, and G+C content revealed that F1, F12, G2, and I7 were classical genes, AF was a nonclassical gene, and I8 and C1 were pseudogenes. Our subsequent molecular examinations showed that the diversity pattern in the Père David's deer was unusual. Most mammals have more polymorphic classical class I loci vs. the nonclassical and neutral genes. In contrast, the Père David's deer was found to be monomorphic at classical genes F1, F12, G2, and I7, dimorphic at the nonclassical AF gene, dimorphic at pseudogene I8, and tetramorphic at pseudogene C1. The adverse polymorphism patterns of Elda-I genes might provide evidence for selection too faster deplete MHC variation than drift in the bottlenecked populations, while the postbottleneck tetramorphism of the C1 pseudogene appears to be evidence of strong historical balancing selection.     

LH secretion and response to GnRH during seasonal anoestrus of the Pére David's deer hind (Elaphurus davidianus)

The pattern of LH secretion and response to exogenous GnRH was determined on 5 occasions during seasonal anoestrus of the Père David's deer hind. LH pulse frequency was low (3.3 +/- 0.6 pulses/18 h) in early anoestrus (February), increased significantly in mid-anoestrus (April; 8.4 +/- 1.4 pulses/18 h) and thereafter declined slightly in late anoestrus (June; 6.3 +/- 0.25 pulses/18 h). Mean LH concentrations also showed significant changes during anoestrus with higher levels in mid-anoestrus (April; 0.85 +/- 0.12 ng/ml) when compared with other times (0.53 +/- 0.05, 0.60 +/- 0.10, 0.68 +/- 0.06 and 0.71 +/- 0.05 ng/ml for February, March, May and June, respectively). LH pulse amplitude showed no significant changes during the study. The LH response to intravenous injections of 2 micrograms GnRH was lowest in early anoestrus (February), increased significantly in mid-anoestrus (April) and remained high through late anoestrus. The response during the luteal phase was similar to that seen during late anoestrus. These results indicate that seasonal anoestrus in the Père David's deer hind is not a uniform state but is characterized by an early period of 'deep' anoestrus.     

Detecting QTL for feed intake traits and other performance traits in growing pigs in a Piétrain-Large White backcross

Knowing the large difference in daily feed intake (DFI) between Large White (LW) and Piétrain (PI) growing pigs, a backcross (BC) population has been set up to map QTL that could be used in marker assisted selection strategies. LW × PI boars were mated with sows from two LW lines to produce 16 sire families. A total of 717 BC progeny were fed ad libitum from 30 to 108 kg BW using single-place electronic feeders. A genome scan was conducted using genotypes for the halothane gene and 118 microsatellite markers spread on the 18 porcine autosomes. Interval mapping analyses were carried out, assuming different QTL alleles between sire families to account for within breed variability using the QTLMap software. The effects of the halothane genotype and of the dam line on the QTL effect estimates were tested. One QTL for DFI (P < 0.05 at the chromosome-wide (CW) level) and one QTL for feed conversion ratio (P < 0.01 at the CW level) were mapped to chromosomes SSC6 - probably due to the halothane alleles - and SSC7, respectively. Three putative QTL for feed intake traits were detected (P < 0.06 at the CW level) on SSC2, SSC7 and SSC9. QTL on feeding traits had effects in the range of 0.20 phenotypic s.d. The relatively low number of QTL detected for these traits suggests a large QTL allele variability within breeds and/or low effects of individual loci. Significant QTL were detected for traits related to carcass composition on chromosomes SSC6, SSC15 and SSC17, and to meat quality on chromosome SSC6 (P < 0.01 at the genome-wide level). QTL effects for body composition on SSC13 and SSC17 differed according to the LW dam line, which confirmed that QTL alleles were segregating in the LW breed. An epistatic effect involving the halothane locus and a QTL for loin weight on SSC7 was identified, the estimated substitution effects for the QTL differing by 200 g between Nn and NN individuals. The interactions between QTL alleles and genetic background or particular genes suggest further work to validate QTL segregations in the populations where marker assisted selection for the QTL would be applied.     

Seasonal home range patterns of the reintroduced and rewild female Père David’s deer Elaphurus davidianus

To learn the seasonal home range pattern and its role in the ecological adaptation of rewild Père David’s deer, we took the investigation from spring to winter in three-collared females that released into the coastal wetlands of the Yellow Sea, China. Using GPS collars, minimum convex polygons and fixed kernel estimation, we recorded the movement and estimated the home ranges of the deer. The results showed that the collared deer inhabited only 42.85% of the coastal wetland habitat that had been designated for them. The home ranges were larger during winter and spring than in autumn and summer. In summer and autumn, the collared deer remained in the reserve, which was dominated by spartina grass. In the spring and winter, they were lured by the green leaves of wheat in the farmlands outside the reserve but were then driven back by people. Home range patterns reflected the seasonality of the availability of food resources and human activity. In addition to the frequently utilized habitats, much larger wetland areas are required for such deer. As the population density increases gradually, more available space will be needed to meet the fundamental needs of the seasonal dispersal of rewild Père David’s deer.     

Congruence in QTL for adventitious rooting in Pinus elliottii × Pinus caribaea hybrids resolves between and within-species effects

Targeting between-species effects for improvement in synthetic hybrid populations derived from outcrossing parental tree species may be one way to increase the efficacy and predictability of hybrid breeding. We present a comparative analysis of the quantitative trait loci (QTL) which resolved between from within-species effects for adventitious rooting in two populations of hybrids between Pinus elliottii and P. caribaea, an outbred F₁ (n=287) and an inbred-like F₂ family (n=357). Most small to moderate effect QTL (each explaining 2–5% of phenotypic variation, PV) were congruent (3 out of 4 QTL in each family) and therefore considered within-species effects as they segregated in both families. A single large effect QTL (40% PV) was detected uniquely in the F₂ family and assumed to be due to a between-species effect, resulting from a genetic locus with contrasting alleles in each parental species. Oligogenic as opposed to polygenic architecture was supported in both families (60% and 20% PV explained by 4 QTL in the F₂ and F₁ respectively). The importance of adventitious rooting for adaptation to survive water-logged environments was thought in part to explain oligogenic architecture of what is believed to be a complex trait controlled by many hundreds of genes.     

Mapping and characterisation of QTL × E interactions for traits determining grain and stover yield in pearl millet

A mapping population of 104 F(3) lines of pearl millet, derived from a cross between two inbred lines H 77/833-2 x PRLT 2/89-33, was evaluated, as testcrosses on a common tester, for traits determining grain and stover yield in seven different field trials, distributed over 3 years and two seasons. The total genetic variation was partitioned into effects due to season (S), genotype (G), genotype x season interaction (G x S), and genotype x environment-within-season interaction [G x E(S)]. QTLs were determined for traits for their G, G x S, and G x E(S) effects, to assess the magnitude and the nature (cross over/non-crossover) of environmental interaction effects on individual QTLs. QTLs for some traits were associated with G effects only, while others were associated with the effects of both G and G x S and/or G, G x S and G x E(S) effects. The major G x S QTLs detected were for flowering time (on LG 4 and LG 6), and mapped to the same intervals as G x S QTLs for several other traits (including stover yield, harvest index, biomass yield and panicle number m(-2)). All three QTLs detected for grain yield were unaffected by G x S interaction however. All three QTLs for stover yield (mapping on LG 2, LG 4 and LG 6) and one of the three QTLs for grain yield (mapping on LG 4) were also free of QTL x E(S) interactions. The grain yield QTLs that were affected by QTL x E(S) interactions (mapping on LG 2 and LG 6), appeared to be linked to parallel QTL x E(S) interactions of the QTLs for panicle number m(-2) on (LG 2) and of QTLs for both panicle number m(-2) and harvest index (LG 6). In general, QTL x E(S) interactions were more frequently observed for component traits of grain and stover yield, than for grain or stover yield per se.     

Use of trial clustering to study QTL × environment effects for grain yield and related traits in maize

A population of 300 F_3:4 lines derived from the cross between maize inbred lines F2 and F252 was evaluated for testcross value in a large range of environmental conditions (11 different locations in 2 years: 1995 and 1996) in order to study (1) the magnitude of genotype × environment and (2) the stability of quantitative trait loci (QTL) effects. Several agronomic traits were measured: dry grain yield (DGY), kernel weight, average number of kernels per plant, silking date (SD) and grain moisture at harvest. A large genotype × environment interaction was found, particularly for DGY. A hierarchical classification of trials and an additive main effects and multiplicative interaction (AMMI) model were carried out. Both methods led to the conclusion that trials could be partitioned into three groups consistent with (1) the year of experiment and (2) the water availability (irrigated vs non-irrigated) for the trials sown in 1995. QTL detection was carried out for all the traits in the different groups of trials. Between 9 and 15 QTL were detected for each trait. QTL × group and QTL × trial effects were tested and proved significant for a large proportion of QTL. QTL detection was also performed on coordinates on the first two principal components (PC) of the AMMI model. PC QTL were generally detected in areas where QTL × group and QTL × trial interactions were significant. A region located on chromosome 8 near an SD QTL seemed to play a key role in DGY stability. Our results confirm the key role of water availability and flowering earliness on grain yield stability in maize.     

Effects of heterodimerization and proteolytic processing on Derrière and Nodal activity: implications for mesoderm induction in Xenopus

Derrière is a recently discovered member of the TGFbeta superfamily that can induce mesoderm in explant assays and is expressed at the right time and location to mediate mesoderm induction in response to VegT during Xenopus embryogenesis. We show that the ability of Derrière to induce dorsal or ventral mesoderm depends strictly on the location of expression and that a dominant-negative Derrière cleavage mutant completely blocks all mesoderm formation when ectopically expressed. This differs from the activity of similar Xnr2 cleavage mutant constructs, which are secreted and retain signaling activity. Additional analysis of mesoderm induction by Derrière and members of the Nodal family indicates that these molecules are involved in a mutual positive-feedback loop and antagonism of either one of the signals can reduce the other. Interaction between Derrière and members of the Nodal family is also shown to occur through the formation of heterodimeric ligands. Using an oocyte expression system we show direct interaction between the mature Derrière ligand and members of both the Nodal and BMP families. Taken together, these findings indicate that Derrière and Nodal proteins probably work cooperatively to induce mesoderm throughout the marginal zone during early Xenopus development.     

Effects of spatial scale and sample size in GPS-based species distribution models: are the best models trivial for red deer management?

Species distribution models (SDMs) are popular in conservation and management of a wide array of taxa. Often parameterized with coarse GIS-based environmental maps, they perform well in macro-ecological settings but it is debated if the models can predict distribution within broadly suitable “known” habitats of interest to local managers. We parameterized SDMs with GIS-derived environmental variables and location data from 82 GPS-collared female red deer (Cervus elaphus) from two study areas in Norway. Candidate GLM models were fitted to address the effect of spatial scale (landscape vs. home range), sample size, and transferability between study areas, with respect to predictability (AUC) and explained variance (Generalized R ² and deviance). The landscape level SDM captured variation in deer distribution well and performed best on all diagnostic measures of model quality, caused mainly by a trivial effect of avoidance of non-habitat (barren mountains). The home range level SDMs were far less predictable and explained comparatively little variation in space use. Landscape scale models stabilized at the low sample size of 5–10 individuals and were highly transferrable between study areas implying a low degree of individual variation in habitat selection at this scale. It is important to have realistic expectations of SDMs derived from digital elevation models and coarse habitat maps. They do perform well in highlighting potential habitat on a landscape scale, but often miss nuances necessary to predict more fine-scaled distribution of wildlife populations. Currently, there seems to be a trade-off between model quality and usefulness in local management.     

The induction of male sexual behavior in red deer (Cervus elaphus) by the administration of testosterone to hinds and estradiol-17β to stags

One-gram implants of testosterone were placed subcutaneously in two adult intact and one castrated red deer hinds, and 100-mg implants of estradiol-17β were given to three castrated and two intact red deer stags. Their sexual behavior was then observed in the wild and in captivity for up to 3 years. Testosterone initially produced prolonged and intense estrous behavior in the hinds; this gradually gave way to behavior normally shown only by rutting stags, such as flehmen, herding threats, and roaring. Testosterone-implanted hinds rose in the dominance hierarchy as measured by competition for food. Pregnancy, or the administration of progestagens, suppressed most of this testosterone-induced behavior. Testosterone also induced development of male secondary sexual characteristics such as formation of small antler pedicles (but not antlers), hypertrophy of the clitoris and neck musculature, and development of a neck mane and male rutting odor. Estradiol-17β mimicked the behavioral effects of testosterone when given to castrated stags, stimulating all components of rutting behavior. In intact stags, the only effects were to abolish antler casting and stimulate roaring; normal rutting behavior continued unchanged. In contrast to the effects of testosterone, estradiol-17β did not influence the social status of either intact or castrated stags. The distinctions between the behavioral effects of androgens and estrogens are ill defined and are determined more by the prior sexual differentiation of the brain and the duration of steroid treatment, than by the nature of the steroid.     

Porcine OGN and ASPN: mapping, polymorphisms and use for quantitative trait loci identification for growth and carcass traits in a Meishan x Piétrain intercross

The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.