An Evaluation of the Genetic Structure of Geese Maintained in Poland on the Basis of Microsatellite Markers

Developmental changes in tibia and humerus of goose: morphometric, densitometric, and mechanical analysis

The skeletal system of young animals undergoes a series of intensive and rapid changes. In this study, we aimed to verify the hypothesis that geese exhibit a distinct pattern of bone growth compared to gallinaceous species. Specifically, we hypothesised that geese would experience an accelerated growth rate in the humerus bone, which can be attributed to the increased wing mobility facilitated by their rearing in free-range systems. This need for access to both ground and water environments contributes to the unique demands placed on their skeletal development. We focused on evaluating the mechanical properties and geometry of the humerus as the forelimb bone, and the tibia as the hindlimb bone. The 320 geese used in this study were divided into 12 groups according to sex (females and males) and age (0-,1-,3-,6-,8-,12-,14-week-old). To assess bone mechanical properties, a three-point bending test was performed, along with densitometry and morphological measurements. The tibiae of the geese showed the most intensive growth until 6 weeks of age and then stabilised. The wing bones (humerus) showed only slight changes in the first weeks after hatching, and then a rapid growth between the third and sixth week, both in terms of mechanical and morphological properties. This is most likely due to a change in the geese's living environment during this period, i.e., allowing them to leave their enclosures and enter open space, which gives them the opportunity to use their wings, resulting in the rapid growth of the wing bones to support increasing muscle mass in this area. This study increases our understanding of bone growth and development in domesticated birds, specifically waterfowl species, and highlights the importance of rearing methods on the proper bone development and functionality of the entire skeletal system, and thus, on their welfare.

Trait Analysis in Domestic Rabbits (Oryctolagus cuniculus f. domesticus) Using SNP Markers from Genotyping-by-Sequencing Data

Simple Summary

Rabbit breeding is an important branch of agricultural animal breeding; their fur color and weight are desirable traits for artificial breeding. Polymorphism can provide potential molecular markers for studying rabbit traits and improve rabbit breeds with such markers in the future. In this study, single-nucleotide polymorphism markers in genotyping-by-sequencing data were used to analyze rabbit traits. In total, three genes were identified to be associated with fur color and four with weight. The results of this study provide a data base for the research and improvement of rabbit breeding program.

Abstract

The domestic rabbit (Oryctolagus cuniculus f. domesticus) is a very important variety in biomedical research and agricultural animal breeding. Due to the different geographical areas in which rabbit breeds originated, and the long history of domestication/artificial breeding, rabbits have experienced strong selection pressure, which has shaped many traits of most rabbit varieties, such as color and weight. An efficient genome-wide single-nucleotide polymorphism (SNP) detection strategy is genotyping-by-sequencing (GBS), which has been widely used in many organisms. This study attempted to explore bi-allelic SNPs associated with fur color and weight-related traits using GBS in five rabbit breeds. The data consisted of a total 831,035 SNPs in 150 individuals from Californian rabbits (CF), German Zika rabbits (ZK), Qixing rabbits (QX), Sichuan grey rabbits (SG), and Sichuan white rabbits (SW). In addition, these five breeds of rabbits were obviously independent populations, with high genetic differentiation among breeds and low genetic diversity within breeds. A total of 32,144 SNP sites were identified by selective sweep among the different varieties. The genes that carried SNP loci in these selected regions were related to important traits (fur color and weight) and signal pathways, such as the MAPK/ERK signaling pathway and the Hippo signaling pathway. In addition, genes related to fur color and weight were identified, such as ASIPs, MITFs and KITs, ADCY3s, YAPs, FASs, and ACSL5s, and they had more SNP sites. The research offers the foundation for further exploration of molecular genetic markers of SNPs that are related to traits.

Genetic and Phenotypic Characterization of Domestic Geese (Anser anser) in Egypt

The objectives of this study were to achieve phenotypic characterization of three domestic Egyptian goose populations collected from three different geographical zones (Kafr El-Sheikh, Fayoum and Luxor) and to perform genetic characterization of these three populations based on mtDNA D-loop and 12 microsatellite markers. The body measurements of 402 domestic mature geese belonging to these three governorates showed that the lengths of the head, culmen and tarsus and the live body weight varied significantly among the three studied Egyptian goose populations. After alignment of a 710-base-pair segment of the goose mtDNA control region, there was a single haplotype in the three Egyptian goose populations, indicating the same maternal origins. The genotyping of the 12 microsatellite markers showed low diversity indices, including average observed (NA) and effective (NE) number of alleles and observed (HO) and expected heterozygosity (HE) (3.333, 1.760, 0.277 and 0.352, respectively), and a high inbreeding coefficient (FIS = 0.203) across the three Egyptian goose populations. The high inbreeding and low genetic and morphological differentiation of Egyptian geese could be corrected by establishing a large base population through capturing small populations with the highest genetic variation. The findings of the current study can therefore serve as an initial guide to design further investigations for developing conservation programs of Egyptian geese genetic resources.

Hypothalamus-pituitary axis transcriptomic modification dependent on growth rate in geese (Anser anser domesticus)

The hypothalamus-pituitary axis is involved in digest processing, stress response, energy storage and many other processes. In birds, this control differs from in mammals, such as regulation of appetite and satiety centre. The transcriptomics analyses of both brain structures can explain and identify the molecular processes related to body growth and development and nutritional status. Many reports describe chicken transcriptome in literature, but gene expression studies in the other poultry species are extremely rare. Therefore, the present research undertook the attempt to explain hypothalamus-pituitary processes in domestic geese-Polish White Kołuda®, main Polish line. After 16 weeks of fattening, significant differences in geese weight were observed. Therefore, transcriptome of pituitary and hypothalamus profiles could be compared between low and high growth rate geese groups. Due to the lack of domestic geese genome assembly in the public databases, we used three mapping approaches: de novo analysis, mapping to two other pink-footed and swan geese genomes. The functional examination showed that the most enriched biological process in the geese hypothalamus covered the immune response. Moreover, in the hypothalamus, proteins typical for the pituitary such as PRL and GH were differentially expressed (DE). Our study recommends one gene as a candidate for growth rate in geese-the FOS gene, which encodes Fos proto-oncogene-DE in both analysed tissues. The FOS gene is involved in regulating feeding behaviour, immune regulation, stimulating cellular proliferation and controlling growth hormone synthesis. Moreover, the present investigation indicates DE genes involved in gene expression regulation. The study delivers new information about the changes in the pituitary-hypothalamic axis in geese dependent on growth rate differences.

Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda^® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda^® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

A Genetic Evaluation System for New Zealand White Rabbit Germplasm Resources Based on SSR Markers

Simple Summary

The New Zealand white rabbit (Oryctolagus cuniculus) is one of the most important breeds of commercial and experimental rabbits in the world, and also one of the most raised rabbit breeds in China. Our goal was to develop a suite of microsatellite markers to aid future conservation genetics research for the Oryctolagus cuniculus breeds. Based on the genetic diversity of 130 New Zealand white rabbits, we obtained a set combination of 22 markers. Then, we performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations with this combination. It can be used to evaluate the breed conservation of rabbit germplasm resources.

Abstract

At present, there is an abundance of quality domestic rabbit breeds in China. However, due to the lack of technical standards for the genetic evaluation of rabbit germplasm resources, there have been a number of problems, such as poor breed conservation. By studying the genetic diversity of 130 New Zealand white rabbits (regardless of generation), we obtained the best simple sequence repeat (SSR) marker combination. We found that, when using microsatellite markers for the effective genetic evaluation of domestic rabbits, the number of records should be greater than 60 and the marker number more than 22. Through the comparative analysis of 30 combinations of 22 markers, the optimal combination of 22 markers was determined, and the 22 SSR polymorphic loci were distributed on different chromosomes. We performed a genetic analysis of 200 New Zealand white rabbits corresponding to two generations, using the best SSR polymorphic loci combination. There were no significant differences in the genetic diversity parameters between the two generations of rabbits (p > 0.05), indicating that the characteristics of this excellent rabbit germplasm have been effectively preserved. At the same time, we verified that the established method can be used to evaluate the breed conservation of rabbit germplasm resources.