A low-tech, cost-effective and efficient method for safeguarding genetic diversity by direct cryopreservation of poultry embryonic reproductive cells

Chickens are an important resource for smallholder farmers who raise locally adapted, genetically distinct breeds for eggs and meat. The development of efficient reproductive technologies to conserve and regenerate chicken breeds safeguards existing biodiversity and secures poultry genetic resources for climate resilience, biosecurity, and future food production. The majority of the over 1600 breeds of chicken are raised in low and lower to middle income countries under resource-limited, small-scale production systems, which necessitates a low-tech, cost-effective means of conserving diversity is needed. Here, we validate a simple biobanking technique using cryopreserved embryonic chicken gonads. The gonads are quickly isolated, visually sexed, pooled by sex, and cryopreserved. Subsequently, the stored material is thawed and dissociated before injection into sterile host chicken embryos. By using pooled GFP and RFP-labelled donor gonadal cells and Sire Dam Surrogate mating, we demonstrate that chicks deriving entirely from male and female donor germ cells are hatched. This technology will enable ongoing efforts to conserve chicken genetic diversity for both commercial and smallholder farmers, and to preserve existing genetic resources at poultry research facilities

Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds

In macrolecithal species, cryopreservation of the oocyte and zygote is not possible due to the large size and quantity of lipid deposited within the egg. For birds, this signifies that cryopreserving and regenerating a species from frozen cellular material are currently technically unfeasible. Diploid primordial germ cells (PGCs) are a potential means to freeze down the entire genome and reconstitute an avian species from frozen material. Here, we examine the use of genetically engineered (GE) sterile female layer chicken as surrogate hosts for the transplantation of cryopreserved avian PGCs from rare heritage breeds of chicken. We first amplified PGC numbers in culture before cryopreservation and subsequent transplantation into host GE embryos. We found that all hatched offspring from the chimera GE hens were derived from the donor rare heritage breed broiler PGCs, and using cryopreserved semen, we were able to produce pure offspring. Measurement of the mutation rate of PGCs in culture revealed that 2.7 × 10-10 de novo single-nucleotide variants (SNVs) were generated per cell division, which is comparable with other stem cell lineages. We also found that endogenous avian leukosis virus (ALV) retroviral insertions were not mobilized during in vitro propagation. Taken together, these results show that mutation rates are no higher than normal stem cells, essential if we are to conserve avian breeds. Thus, GE sterile avian surrogate hosts provide a viable platform to conserve and regenerate avian species using cryopreserved PGCs

Avian primordial germ cells are bipotent for male or female gametogenesis

In birds, males are the homogametic sex (ZZ) and females are the heterogametic sex (ZW). Here, we investigate the role of chromosomal sex and germ cell competition on avian germ cell differentiation. We recently developed genetically sterile layer cockerels and hens for use as surrogate hosts for primordial germ cell (PGC) transplantation. Using in vitro propagated and cryopreserved PGCs from a pedigree Silkie broiler breed, we now demonstrate that sterile surrogate layer hosts injected with same sex PGCs have normal fertility and produced pure breed Silkie broiler offspring when directly mated to each other in Sire Dam Surrogate mating. We found that female sterile hosts carrying chromosomally male (ZZ) PGCs formed functional oocytes and eggs, which gave rise to 100% male offspring after fertilization. Unexpectedly, we also observed that chromosomally female (ZW) PGCs carried by male sterile hosts formed functional spermatozoa and produced viable offspring. These findings demonstrate that avian PGCs are not sexually restricted for functional gamete formation and provide new insights for the cryopreservation of poultry and other bird species using diploid stage germ cells

Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis

Background: Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there are commercial incentives to breed chickens with greater resistance to this important production disease. To identify phenotypic biomarkers that are associated with the production impacts of coccidiosis, and to assess their covariance and heritability, 942 Cobb500 commercial broilers were subjected to a defined challenge with Eimeria tenella (Houghton). Three traits were measured: weight gain (WG) during the period of infection, caecal lesion score (CLS) post mortem, and the level of a serum biomarker of intestinal inflammation, i.e. circulating interleukin 10 (IL-10), measured at the height of the infection.Results: Phenotypic analysis of the challenged chicken cohort revealed a significant positive correlation between CLS and IL-10, with significant negative correlations of both these traits with WG. Eigenanalysis of phenotypic covariances between measured traits revealed three distinct eigenvectors. Trait weightings of the first eigenvector, (EV1, eigenvalue = 59%), were biologically interpreted as representing a response of birds that were susceptible to infection, with low WG, high CLS and high IL-10. Similarly, the second eigenvector represented infection resilience/resistance (EV2, 22%; high WG, low CLS and high IL-10), and the third eigenvector tolerance (EV3, 19%; high WG, high CLS and low IL-10), respectively. Genome-wide association studies (GWAS) identified two SNPs that were associated with WG at the suggestive level.Conclusions: Eigenanalysis separated the phenotypic impact of a defined challenge with E. tenella on WG, caecal inflammation/pathology, and production of IL-10 into three major eigenvectors, indicating that the susceptibility-resistance axis is not a single continuous quantitative trait. The SNPs identified by the GWAS for body weight were located in close proximity to two genes that are involved in innate immunity (FAM96B and RRAD)

Cosmological Synergies Enabled by Joint Analysis of Multi-probe data from WFIRST, Euclid, and LSST

WFIRST, Euclid, and LSST are all missions designed to perform dedicated cosmology surveys that offer unprecedented statistical constraining power and control of systematic uncertainties. There is a growing realization that these missions will be significantly more powerful when the data are processed and analyzed in unison

Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.Funding for this study was provided by Cobb-Vantress, Inc. Authors RH and RO are commercially affiliated with the funder. The funder provided support in the form of salaries for SDS, and RH and RO, employed by the funder had active roles in the study as stated in the authors’ contributions.Peer reviewe

Derivation of parentage and breed-of-origin of alleles in a crossbred broiler dataset

Pig and poultry breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes include DNA from two to four different breeds, depending on the crossbreeding scheme. SNP information allows: 1) derivation of parentage, provided that genotypes of parents are available, and 2) derivation of breed-of-origin of alleles in crossbreds, provided that sufficient genotypes of purebred animals are available to determine frequencies of segregating haplotypes for each of the parental breeds. We derived both parentage and breed-of-origin of alleles in a broiler dataset that comprised 5882 purebred and 10,943 three-way crossbred offspring that were generated by natural mating of 164 purebred sires to 660 purebred and 1031 F1 crossbred hens. Numbers of offspring per sire had a very skewed distribution, ranging from 1 to 275 crossbreds and 1 to 155 purebreds. Breed-of-origin could be derived for 99.74% of the alleles of the 1031 F1 crossbred hens and for 98.10% of the alleles of the 10,943 three-way crossbred offspring. Visual inspection of the assigned breed-of-origin, however, suggested that there are some errors in assignment of the maternal alleles. Further tuning of the algorithm, or adding more purebred animals of the dam lines to the analysis, may help to resolve those errors. The achieved percentage of assignment to the sire line appears sufficient to proceed with subsequent analyses requiring only the breed-of-origin of the paternal alleles to be known

Chicken muscle mitochondrial content appears co-ordinately regulated and is associated with performance phenotypes

Mitochondrial content is a fundamental cellular bioenergetic phenotype. Previous work has hypothesised possible links between variation in muscle mitochondrial content and animal performance. However, no population screens have been performed in any production species. Here, we have designed a high throughput molecular approach to estimate mitochondrial content in commercial broilers. Technical validity was established using several approaches, including its performance in monoclonal DF-1 cells, cross-tissue comparisons in tissues with differing metabolic demands (white fa