Divergently selected chicken breeds are of great interest not only from an economic point of view, but also in terms of sustaining diversity of the global poultry gene pool. In this regard, it is ...essential to evaluate the classification (clustering) of varied chicken breeds using methods and models based on phenotypic and genotypic breed differences. It is also important to implement new mathematical indicators and approaches. Accordingly, we set the objectives to test and improve clustering algorithms and models to discriminate between various chicken breeds. A representative portion of the global chicken gene pool including 39 different breeds was examined in terms of an integral performance index, i.e., specific egg mass yield relative to body weight of females. The generated dataset was evaluated within the traditional, phenotypic and genotypic classification/clustering models using the k-means method, inflection points clustering, and admixture analysis. The latter embraced SNP genotype datasets including a specific one focused on the performance-associated NCAPG-LCORL locus. The k-means and inflection points analyses showed certain discrepancies between the tested models/submodels and flaws in the produced cluster configurations. On the other hand, 11 core breeds were identified that were shared between the examined models and demonstrated more adequate clustering and admixture patterns. These findings will lay the foundation for future research to improve methods for clustering as well as genome- and phenome-wide association/mediation analyses.
To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua ...non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs.
•Selection-driven chicken phenome embraces varied phenotypes including pectoral angle.•We studied PA variation across divergently selected chicken breeds.•Patterns of PA relationship with performance ...traits were analysed.•We propose a promising PA-based auxiliary index for using in layer selection.
An appreciation of the synergy between genome and phenome of poultry breed is essential for a complete understanding of their biology. Phenotypic traits are shaped under the influence of artificial, production-oriented, selection that often acts contrary to that which would occur during natural selection. In this comparative study, we analysed the phenotypic diversity of 39 chicken breeds and populations that make up a significant part of the world gene pool. Grouping patterns of breeds found within the traditional, phenotypic models of their classification/clustering required in-depth analysis using sophisticated mathematical approaches. As a result of studying performance and conformation phenotypes, a phenomenon of previously underestimated variability in pectoral angle (PA) was revealed. Moreover, patterns of PA relationship with productive traits were analysed. We propose using PA measurement as a promising new auxiliary index for selecting hens and roosters of breeding flocks in egg production improvement programs.
Abstract
Commercial breeds of chickens are staying under strong selection pressure on increasing of production level. Meanwhile aboriginal breeds are conserving unique adaptation traits, helping them ...to survive in severe climate. Local breeds combining high resistance, but lower productivity traits are widely kept in smallholders of developing countries. Improving of egg traits in such breeds should be done by selection, not crossing with commercial breeds. Aim of our studies was genetic change of QTL loci linked with yolk size (YS) and egg mass (EM) in resource chicken breeds. Studies were done using 293 samples from Pushkin, Rhode-Island, Amroks, Chinese Silk, Yurlow crawl and Russian White (RW) breeds kept in RRIFAGB Collective Use Centre ‘Genetic Collection of Rare and Endangered Chicken Breeds. EM was recorded in age of 30 weeks. YS was evaluated using ultra sound scanner. Genotyping was performed using illumina 60K Chicken Bead Chip. GWAS studies were performed on RW breed. Sufficient associations of EM were found on chromosome 4 (rs14201361, P < 1.6e-5 & GGaluGA152718, P < 3.3e-5). Correlation of YS and EM were calculated within breeds, difference were from 0.29 to 0.65. Haploblocks were analyzed in QTL region on chromosome 11 linked with YS. Due to selection and genetic drift different haplotype blocks were formed in breeds having different YS. Shown results could be used for improving egg traits in aboriginal domestic breeds. Studies were founded by RFFI project 18-016-00114 A.
Invention and subsequent development of human reproduction technologies allow people to manage reproductive risks, overcome infertility and widen alternative reproductive choice. Medicine has given ...men and women the access to programmes of saving biogenetic material, DNA-tests for identifying paternity and services for creating a genetic passport which identifies potential diseases and genetic peculiarities. However, assisted reproductive technologies, such as donorship of sex sells and surrogate motherhood, are violating the familiar integrity of reproductive process and changing the usual perception of kinship as sharing of biological substance. A distinguishing feature of the market for gamete donation and surrogate motherhood lies in the importance of both construction and deconstruction of kinship between donors, recipients of reproductive goods and services and a baby, who is born with the help of the ART methods (assisted reproductive technologies).Basing on the results of sociological research of donor sex sells market, the author of the article shows us how members of reproductive business coordinate different parts of their work (technical, emotional, legal, financial etc.), in order to solve the controversial problem of defining kinship between the participants of the donor programmes. On the one hand, medical specialists and representatives of reproductive agencies take part in destroying the kinship between a gamete donor and a baby, and on the other hand, they participate in creating and supporting kin ties between parents received donor sex sells and a baby, who doesn’t have common gens with them. Empirical study base consists of expert interviews with the employees of medical clinics and reproductive agencies in Moscow and Saint Petersburg.
Primordial germ cells (PGCs) are precursors of eggs and spermatozoa and serve as an effective means for the transgenic chickens production, including using CRISPR / Cas9 technology. The aim study is ...selection of PGCs culture media suitable for long‐term cultivation. All experiments on chickens were conducted with ethical approval of the Russian Research Institute of Farm Animal Genetics and Breeding ‐ Branch of the L.K. Ernst Federal Research Center for Animal Husbandry (Protocol Number: 2020‐3). For the work, eggs of the Pushkin breed chickens (n = 21) were selected from the Bioresource collection RRIFAGB (Pushkin, St. Petersburg). PGCs were selected from the embryos dorsal aorta for 3‐4 days of incubation (stage Hamburger‐Hamilton 14) using a microinjector (Narishige IM‐11‐2, Japan). Cells were cultured for 21 days at 37 ° C with 5% CO2. Three variants of the culture medium were used. The first basic medium was Opti‐MEM (Reduced Serum Medium, GlutaMAX Supplement) (Gibco, Thermo Fisher) with the addition of sodium pyruvate 1M, nucleosides 100X ‐ 2.5 ml, Chicken Serum (Gibco, Thermo Fisher) ‐ 2%, 2‐mercaptoethanol (NF, VWR) ‐ 3.9 μl. On day 21, the concentration of cells in the first culture reached 1,2х103, and some of the wells with cells were overgrown. The second base medium was similar to the first base medium, but with the addition of antimycotic antibiotic (Thermo Fisher) up to 1X. The medium with the use of the antibiotic‐antimycotic was less susceptible to overgrowth, on day 21, the concentration of cells in the culture reached 3.5x104. The third basic medium was KnockOut DMEM / F‐12, without L‐glutamine (Gibco, ThermoFisher) with the addition sodium pyruvate 1M, nucleosides 100X ‐ 2.5 ml, Human Activin A Recombinant Protein (Gibco, Thermo Fisher) ‐ 25 ng / μl, Human FGF‐basic (FGF‐2 / bFGF) Recombinant Protein (Gibco, Thermo Fisher) ‐ 10 ng / μl, Chicken Serum (Gibco, Thermo Fisher) ‐ 2%, 2‐mercaptoethanol (NF, VWR) ‐ 3.9 μl), antimycotic antibiotic (Thermo Fisher) up to 1X. The third medium with the addition of Activin A and FGF‐2 / bFGF supported the cell culture better, overgrowth was practically not observed, cells were actively proliferating, оn day 21, the concentration of cells in the culture reached 2.7x105. The PGCs presence was confirmed by expression high level (p≤0.01) specific marker genes PGCs such as CXCR4 (chemokine receptor CXC type 4) and PIWIL1 (Piwi‐like protein 1) in cultured cells. In a control tissue small intestine sample of an adult chicken (330 days old), the above genes expression was completely absent.
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