Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated ...feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use "Genetic Collection of Rare and Endangered Breeds of Chickens" (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large-Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross-validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1-2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.
The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their ...well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.
In the poultry industry, indicators reflecting the growth rate of young stock and the exterior characteristics of chickens are important benchmarks for breeding. Traditional selection based on ...phenotypic evaluation is characterized by low efficiency with a low character inheritance ratio and is difficult to apply in small groups of animals and birds bred in bioresource collections. The use of molecular genetic markers associated with economically important traits makes it possible to carry out early selection of birds. This entails an increase in the profitability of the poultry industry. Recently, single nucleotide polymorphisms (SNPs) have served as convenient markers for selection purposes. For five generations (P1–P5), an experimental selection of hens of the Pushkin breed was carried out for live weight. It was based on selection for single nucleotide polymorphism rs313744840 in the
MSTN
gene. As a result, a significant increase in the frequency of allele A in this gene, from 0.11 to 0.50, took place. The association of SNP markers with meat qualities in the experimental group led to changes in the exterior profile of an adult bird at 330 days of age. The individuals with the AA and AG genotypes had the greatest live weight and longest body. As a result of selection, the bird on average became larger due to an increase in the number of heterozygous individuals with long bodies and large chest girths. The depth of the chest and the width of the pelvis increased due to an increase in the frequency of allele A in the experimental population. A tendency towards an increase in these indicators with the substitution of G with A in the genotype was found. Saturation of the population with desirable alleles led to an increase in the average live weight of the chickens. Analysis of the exterior parameters of adult birds showed that this growth is achieved by increasing the depth and volume of the bird body, and not by increasing the length of the limbs. Thus, marker selection carried out for five generations in the experimental population of Pushkin breed chickens to increase body weight has reliably (p < 0.001) changed the exterior profile of adult birds.
Recently, the demand for organic products has been increasing in the world. Organic poultry farming requires additional costs due to the extensive method of poultry housing, low planting density, ...availability of paddocks and other requirements for production of organic products. Therefore, creation of specialized breeds is especially relevant today. The paper presents the experience of creating an autosex population of the Leningrad Golden-Gray (LZS) in the bioresource collection “Genetic collection of rare and endangered breeds of chickens” RRIFAGB - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry. The accuracy of separation by sex of day-old chickens reaches 98%. To create autosex chicken breed, we used breeds and populations of the bioresource collection that have marker genes of plumage color linked to the gender in the genotype. To obtain the breed status, a genome-wide study of the LZS population was conducted. Assessment of the genome homozygosity level showed compliance with the average level characteristic of consolidated groups. The study of genetic variability characterizes the population of LZS as numerous. The inbreeding coefficient of LZS chickens is at a safe level and is a consequence of intensive selection. As a result, an autosex population of LZS was created and tested, which meets the conditions for obtaining the status of a breed and allows to meet the increased requirements of organic poultry farming in the best way. The expediency of using autosex breeds for organic poultry farming has been 478 Proceedings of the National Academy of Sciences of Belarus, agrarian Series, 2021, vol. 59, no. 4 рр. 477–487 substantiated by saving feed and growing areas. The principles of creating an autosex breed from the genetic material of gene pool herds can be applied in other breeding programs.
Polymorphic variants in the myostatin, prolactin, and D2 dopamine receptor genes were analyzed in Pushkin breed chickens (
n
= 231). The rs313744840 single nucleotide polymorphism was studied in the ...myostatin gene by means of the PCR–RFLP method. The cocks with different genotypes did not differ from each other by the live weight. Chickens with AA genotype were found to be significantly larger than their coevals with AG and GG genotypes at the age of 49 days (
P
< 0.01). Polymorphism based on the insertion–deletion of a small gene region (indel-polymorphism) was considered in the prolactin and D2 dopamine receptor genes. Differences by the prolactin gene were observed at 7 days of age. The cocks homozygous by the DD deletion were significantly larger than heterozygous ID coevals (
P
< 0.05). The II cocks significantly differed by the D2 dopamine receptor gene from heterozygous ID coevals by the live weight at 49 and 110 days. In chickens, II homozygotes by the mutation in the D2 dopamine receptor gene were larger than coevals at 7 days, while they had a lower live weight at 110 days (
P
< 0.05).
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.
The genetic diversity of the Spangled Orloff chickens was for the first time studied by analyzing the polymorphism of the hypervariable region in the D-loop of mitochondrial DNA (mtDNA). Samples for ...the analysis were collected at the farms of the All-Russian Poultry Research and Technological Institute (VNITIP), the All-Russian Institute of Farm Animal Genetics and Breeding (VNIIGRZH), and the Moscow Zoo. The D-loop partial sequences (between nucleotide positions 57 and 523) were determined according to the reference sequence of Gallus gallus spadiceus mtDNA, NC_007235 in 39 individuals obtained from these populations (GenBank Accession nos. KM391754–KM391792). In the analyzed mtDNA fragment, a total of 20 polymorphic sites located between the positions 167 and 368, as well as at the position 446, were described in Orloff Spangled Chicken Breed. One polymorphic site at position 221 (haplogroup E, haplotype ORL-2) was unique. All of the identified nucleotide changes were transition-type substitutions. On the basis of the analysis of polymorphic sites in the hypervariable fragment of the D-loop of Spangled Orloff chicken mtDNA, we have found seven haplotypes belonging to four haplogroups (A, B, C, and E). Haplogroup E (haplotypes ORL-1, ORL-2, and ORL-3) was present in the majority of the studied individuals, with the frequencies of 0.77 in the total sample and 0.47 in the VNIIGRZH farm population. Haplogroups A (haplotypes ORL-4 and ORL-7), B (ORL-6), and C (ORL-5) were found only in samples from the VNIIGRZH farm. The studied mtDNA region revealed the lower level of polymorphism in the VNITIP and Moscow Zoo populations, which only had the ORL-1 and ORL-3 haplotypes belonging to Haplogroup E, respectively. Our data suggested that the studied Spangled Orloff chicken populations differed in the composition and frequencies of mtDNA haplogroups and haplotypes.
A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and ...selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and ...application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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