Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model

Background

Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line.

Methods

The following traits were analyzed: egg production, egg weight, egg color, shell strength, age at sexual maturity, body weight, albumen height, and yolk weight. Predictions appropriate for early or late selection were compared. A total of 2,708 birds were genotyped for 23,356 segregating SNP, including 1,563 females with records. Phenotypes on relatives without genotypes were incorporated in the analysis (in total 13,049 production records).The data were analyzed with a Reduced Animal Model using a relationship matrix based on pedigree data or on marker genotypes and with a Bayesian method using model averaging. Using a validation set that consisted of individuals from the generation following training, these methods were compared by correlating EBV with phenotypes corrected for fixed effects, selecting the top 30 individuals based on EBV and evaluating their mean phenotype, and by regressing phenotypes on EBV.

Results

Using high-density SNP genotypes increased accuracies of EBV up to two-fold for selection at an early age and by up to 88% for selection at a later age. Accuracy increases at an early age can be mostly attributed to improved estimates of parental EBV for shell quality and egg production, while for other egg quality traits it is mostly due to improved estimates of Mendelian sampling effects. A relatively small number of markers was sufficient to explain most of the genetic variation for egg weight and body weight.     

Grazing by Kangaroos Limits the Establishment of the Grass Trees Xanthorrhoea gracilis and X. preissii in Restored Bauxite Mines in Eucalypt Forest of Southwestern Australia

This study examined factors affecting germination, survival, and growth of the grass trees Xanthorrhoea gracilis and X. preissii on newly rehabilitated bauxite mine pits in the jarrah forest of southwestern Australia. Grazing by kangaroos (Macropus fuliginosus) was the major factor in reducing survival and growth of both species during the first 2 years. Provision of artificial grazing protection increased survival and growth (plant mass) of both species by 3‐fold. Grazing by native vertebrates has not previously been identified as affecting mine restoration in Western Australia. Initial germination rates from sown seeds of X. preissii at eight replicate sites ranged from 25 to 64% with a mean of 42%. Corresponding figures for X. gracilis were 5–42% with a mean of 17%. Germination of X. gracilis was greater on heavier, moister soils, but X. preissii germinated better on sandier soils. High levels of initial germination did not ensure high survival. Plants of both species grew bigger and survived better on the lighter, sandy soils. Xanthorrhoea seedlings located in the depressions created by the ripping process grew larger than seedlings on the slopes of the riplines. The presence of plants of other species did not have a significant effect on survival. However, these plants facilitated the growth of both species when artificial grazing protection was unavailable. Plants of other species reduced the growth rates of Xanthorrhoea seedlings where artificial grazing protection was provided. Artificial shade by itself had no significant effect on growth of either species. In rehabilitated bauxite mines in the jarrah forest, the provision of grazing protection is recommended to ensure successful establishment and early survival of Xanthorrhoea spp.     

Associations of BF2 alleles with antibody titres and production traits in commercial pure line broiler chickens

Three commercial broiler pure lines were evaluated for associations of sire BF2 (major histocompatibility complex class I) alleles with progeny phenotypic traits. Significant BF2 associations with a subset of traits were observed in two lines. The BF2*21 allele was positively associated with antibody titre to infectious bursal disease virus in both lines. Other associations were line-specific.     

Guiding the prioritization of the most endangered and evolutionary distinct birds for new zoo conservation programs

Zoos have played a pivotal role in the successful reinforcement and reintroduction of species threatened with extinction, but prioritization is required in the face of increasing need and limited capacity. One means of prioritizing between species of equal threat status when establishing new breeding programs is the consideration of evolutionary distinctness (ED). More distinct species have fewer close relatives such that their extinction would result in a greater overall loss to the Tree of Life. Considering global ex situ holdings of birds (a group with a complete and well‐detailed evolutionary tree), we investigate the representation of at‐risk and highly evolutionarily distinct species in global zoo holdings. We identified a total of 2,236 bird species indicated by the Zoological Information Management System as being held in zoological institutions worldwide. As previously reported, imperiled species (defined as those possessing endangered or critically endangered threat status) in this database are less likely to be held in zoos than non‐imperiled species. However, we find that species possessing ED scores within the top 10% of all bird species are more likely to be held in zoos than other species, possibly because they possess unique characteristics that have historically made them popular exhibits. To assist with the selection of high priority ED species for future zoo conservation programs, we provide a list of imperiled species currently not held in zoos, ranked by ED. This list highlights species representing particular priorities for ex situ conservation planners, and represents a practical tool for improving the conservation value of zoological collections.     

Evolutionary history of fire‐stimulated resprouting,flowering, seed release and germination

Fire has shaped the evolution of many plant traits in fire‐prone environments: fire‐resistant tissues with heat‐insulated meristems, post‐fire resprouting or fire‐killed but regenerating from stored seeds, fire‐stimulated flowering, release of on‐plant‐stored seeds, and germination of soil‐stored seeds. Flowering, seed release and germination fit into three categories of response to intensifying fire: fire not required, weakly fire‐adapted or strongly fire‐adapted. Resprouting also has three categories but survival is always reduced by increasing fire intensity. We collated 286 records for 20 angiosperm and two gymnosperm families and 50 trait assignments to dated phylogenies. We placed these into three fire‐adapted trait types: those associated with the origin of their clade and the onset of fire‐proneness [primary diversification, contributing 20% of speciation events over the last 120 million years (My)], those originating much later coincident with a change in the fire regime (secondary diversification, 30%), and those conserved in the daughter lineage as already adapted to the fire regime (stabilisation, 50%). All four fire‐response types could be traced to >100 My ago (Mya) with pyrogenic flowering slightly younger because of its dependence on resprouting. There was no evidence that resprouting was always an older trait than either seed storage or non‐sprouting throughout this period, with either/both ancestral or derived in different clades and times. Fire‐adapted traits evolved slowly in the Cretaceous, 120–65 Mya, and rapidly but fitfully in the Cenozoic, 65–0 Mya, peaking over the last 20 My. The four trait‐types climaxed at different times, with the peak in resprouter speciation over the last 5 My attributable to fluctuating growing conditions and increasing savanna grasslands unsuitable for non‐sprouters. All experienced a trough in the 40–30‐Mya period following a reduction in world temperatures and oxygen levels and expected reduced fire activity. Thick bark and serotiny arose in the Mid‐Cretaceous among extant Pinaceae. Heat‐stimulated germination of hard seeds is ancestral in the 103‐My‐old Fabales. Smoke‐(karrikin)‐stimulated germination of non‐hard seeds is even older, and includes the 101‐My‐old Restionaceae–Anarthriaceae. A smoke/karrikin response is detectable in some fire‐free lineages that prove to have a fire‐prone ancestry. Among clades that are predominantly fire‐prone, absence of fire‐related traits is the advanced condition, associated either with increased fire frequency (loss of serotiny and soil storage), or migration to fire‐free habitats (loss of thick bark, pyrogenic flowering, serotiny or soil storage). Protea (Africa) and Hakea (Australia) illustrate the importance of stabilisation processes between resprouting/non‐sprouting in accounting for speciation events over the last 20 My and highlight the frequent interchange possible between these two traits. Apart from Pinus, most ancestral trait reconstruction relative to fire has been conducted on predominantly Southern Hemisphere clades and this needs to be redressed. Despite these limitations, it is clear that fire has had a profound effect on fire‐related trait evolution worldwide, and set the platform for subsequent evolution of many non‐fire‐related traits. Genetics of the triggering mechanisms remain poorly understood, except the karrikin system for smoke‐stimulated germination. We exhort biologists to include fire‐proneness and fire‐related traits in their thinking on possible factors controlling the evolution of plants.     

The Cysteine Dioxygenase Homologue from Pseudomonas aeruginosa Is a 3-Mercaptopropionate Dioxygenase

Thiol dioxygenation is the initial oxidation step that commits a thiol to important catabolic or biosynthetic pathways. The reaction is catalyzed by a family of specific non-heme mononuclear iron proteins each of which is reported to react efficiently with only one substrate. This family of enzymes includes cysteine dioxygenase, cysteamine dioxygenase, mercaptosuccinate dioxygenase, and 3-mercaptopropionate dioxygenase. Using sequence alignment to infer cysteine dioxygenase activity, a cysteine dioxygenase homologue from Pseudomonas aeruginosa (p3MDO) has been identified. Mass spectrometry of P. aeruginosa under standard growth conditions showed that p3MDO is expressed in low levels, suggesting that this metabolic pathway is available to the organism. Purified recombinant p3MDO is able to oxidize both cysteine and 3-mercaptopropionic acid in vitro, with a marked preference for 3-mercaptopropionic acid. We therefore describe this enzyme as a 3-mercaptopropionate dioxygenase. Mössbauer spectroscopy suggests that substrate binding to the ferrous iron is through the thiol but indicates that each substrate could adopt different coordination geometries. Crystallographic comparison with mammalian cysteine dioxygenase shows that the overall active site geometry is conserved but suggests that the different substrate specificity can be related to replacement of an arginine by a glutamine in the active site.     

Porphyromonas gingivalis promotes invasion of oral squamous cell carcinoma through induction of proMMP9 and its activation

Recent epidemiological studies have revealed a significant association between periodontitis and oral squamous cell carcinoma (OSCC). Furthermore, matrix metalloproteinase 9 (MMP9) is implicated in the invasion and metastasis of tumour cells. We examined the involvement of Porphyromonas gingivalis, a periodontal pathogen, in OSCC invasion through induced expression of proMMP and its activation. proMMP9 was continuously secreted from carcinoma SAS cells, while P. gingivalis infection increased proenzyme expression and subsequently processed it to active MMP9 in culture supernatant, which enhanced cellular invasion. In contrast, Fusobacterium nucleatum, another periodontal organism, failed to demonstrate such activities. The effects of P. gingivalis were observed with highly invasive cells, but not with the low invasivetype. P. gingivalis also stimulated proteinase‐activated receptor 2 (PAR2) and enhanced proMMP9 expression, which promoted cellular invasion. P. gingivalis mutants deficient in gingipain proteases failed to activate MMP9. Infected SAS cells exhibited activation of ERK1/2, p38, and NF‐kB, and their inhibitors diminished both proMMP9‐overexpression and cellular invasion. Together, our results show that P. gingivalis activates the ERK1/2‐Ets1, p38/HSP27, and PAR2/NF‐kB pathways to induce proMMP9 expression, after which the proenzyme is activated by gingipains to promote cellular invasion of OSCC cell lines. These findings suggest a novel mechanism of progression and metastasis of OSCC associated with periodontitis.     

A Systematic Analysis of miRNA Transcriptome in Marek’s Disease Virus-Induced Lymphoma Reveals Novel and Differentially Expressed miRNAs

Marek’s disease is a lymphoproliferative neoplastic disease of the chicken, which poses a serious threat to poultry health. Marek’s disease virus (MDV)-induced T-cell lymphoma is also an excellent biomedical model for neoplasia research. Recently, miRNAs have been demonstrated to play crucial roles in mediating neoplastic transformation. To investigate host miRNA expression profiles in the tumor transformation phase of MDV infection, we performed deep sequencing in two MDV-infected samples (tumorous spleen and MD lymphoma from liver), and two non-infected controls (non-infected spleen and lymphocytes). In total, 187 and 16 known miRNAs were identified in chicken and MDV, respectively, and 17 novel chicken miRNAs were further confirmed by qPCR. We identified 28 down-regulated miRNAs and 11 up-regulated miRNAs in MDV-infected samples by bioinformatic analysis. Of nine further tested by qPCR, seven were verified. The gga-miR-181a, gga-miR-26a, gga-miR-221, gga-miR-222, gga-miR-199*, and gga-miR-140* were down-regulated, and gga-miR-146c was up-regulated in MDV-infected tumorous spleens and MD lymphomas. In addition, 189 putative target genes for seven differentially expressed miRNAs were predicted. The luciferase reporter gene assay showed interactions of gga-miR-181a with MYBL1, gga-miR-181a with IGF2BP3, and gga-miR-26a with EIF3A. Differential expression of miRNAs and the predicted targets strongly suggest that they contribute to MDV-induced lymphomagenesis.     

A comparison of the effects of 6 weeks of traditional resistance training, plyometric training, and complex training on measures of strength and anthropometrics

Complex training (CT; alternating between heavy and lighter load resistance exercises with similar movement patterns within an exercise session) is a form of training that may potentially bring about a state of postactivation potentiation, resulting in increased dynamic power (Pmax) and rate of force development during the lighter load exercise. Such a method may be more effective than either modality, independently for developing strength. The purpose of this research was to compare the effects of resistance training (RT), plyometric training (PT), and CT on lower body strength and anthropometrics. Thirty recreationally trained college-aged men were trained using 1 of 3 methods: resistance, plyometric, or complex twice weekly for 6 weeks. The participants were tested pre, mid, and post to assess back squat strength, Romanian dead lift (RDL) strength, standing calf raise (SCR) strength, quadriceps girth, triceps surae girth, body mass, and body fat percentage. Diet was not controlled during this study. Statistical measures revealed a significant increase for squat strength (p = 0.000), RDL strength (p = 0.000), and SCR strength (p = 0.000) for all groups pre to post, with no differences between groups. There was also a main effect for time for girth measures of the quadriceps muscle group (p = 0.001), the triceps surae muscle group (p = 0.001), and body mass (p = 0.001; post hoc revealed no significant difference). There were main effects for time and group × time interactions for fat-free mass % (RT: p = 0.031; PT: p = 0.000). The results suggest that CT mirrors benefits seen with traditional RT or PT. Moreover, CT revealed no decrement in strength and anthropometric values and appears to be a viable training modality.