Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits.

Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds

The worldwide chicken gene pool encompasses a remarkable, but shrinking, number of divergently selected breeds of diverse origin. This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture, genetic variability, and detailed structure among 49 populations. These populations represent a significant sample of the world's chicken breeds from Europe (Russia, Czech Republic, France, Spain, UK, etc.), Asia (China), North America (USA), and Oceania (Australia). Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism (SNP) chip, a bioinformatic analysis was carried out. This included the calculation of heterozygosity/homozygosity statistics, inbreeding coefficients, and effective population size. It also included assessment of linkage disequilibrium and construction of phylogenetic trees. Using multidimensional scaling, principal component analysis, and ADMIXTURE-assisted global ancestry analysis, we explored the genetic structure of populations and subpopulations in each breed. An overall 49-population phylogeny analysis was also performed, and a refined evolutionary model of chicken breed formation was proposed, which included egg, meat, dual-purpose types, and ambiguous breeds. Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding. In general, whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

Whole transcriptome analysis reveals the key genes and noncoding RNAs related to follicular atresia in broilers

Broodiness, a maternal behavior, is accompanied by the atresia of follicles and the serious degradation of poultry reproductive performance. The comparison of follicles between brooding and laying hens is usually an ideal model for exploring the regulation mechanism of follicle atresia. In this study, we selected three brooding hens and three laying hens to collect their follicles for whole transcriptome sequencing. The results demonstrated different expression patterns between the follicles of brooding hens and laying hens. In the top 10 differentially expressed genes with the highest expression, MMP10 was relatively low expressed in the follicles of brooding hens, but other nine genes were relatively highly expressed, including LRR1, RACK1, SPECC1L, ABHD2, COL6A3, RPS17, ATRN, BIRC6, PGAM1 and SPECC1L. While miR-21-3p, miR-146a-5p, miR-142-5p and miR-1b-3p were highly expressed in the follicles of brooding hen, miR-106-5p, miR-451, miR-183, miR-7, miR-2188-5p and miR-182-5p were lowly expressed in brooding hen. In addition, we identified 124 lncRNAs specifically expressed in the follicles of brooding hens and 147 lncRNAs specifically expressed in the follicles of laying hens. Our results may provide a theoretical basis for further exploration of the molecular mechanism of broodiness in broilers.

Landmark native breed of the Orenburg goats: progress in its breeding and genetics and future prospects

This paper reviews information about a unique and iconic breed of the Orenburg Oblast, the homeland and the only place where the best herds of Orenburg down-hair goats in Russia are concentrated. Three types of these small ruminant animals are widespread on the territory of the region: Orenburg purebred gray goats, Orenburg purebred white goats, as well as crossbred white goats of F1 White Don × White Orenburg. Currently, at the farms of the Orenburg region, animals are selected according to their phenotype, with selected traits being color, weight and length of down hair. In recent years, the Orenburg goat breed has become an object of genetic research using various marker systems including immunogenetic, microsatellite, mtDNA and SNP markers. Overall, these studies evidence about the uniqueness of the allele pool in the landmark native breed of the Orenburg goats, which is a complex dynamic genetic system, prioritizing its further in-depth genome research and breeding applications.

Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds

Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies.

The Genetic Diversity of Stallions of Different Breeds in Russia

The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heterozygous and homozygous ROH regions, evaluated inbreeding using FROH analysis, and generated a population structure using Admixture 1.3 software. Our findings indicate that the Arabian breed is an ancestor of many horse breeds. The study of the full-genome architectonics of breeds is of great practical importance for preserving the genetic characteristics of breeds and managing breeding. Studies were carried out to determine homozygous regions in individual breeds and search for candidate genes in these regions. Fifty-six candidate genes for the influence of selection pressure were identified. Our research reveals genetic diversity consistent with breeding directions and the breeds' history of origin.

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

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.

Integrative comparative analysis of avian chromosome evolution by in-silico mapping of the gene ontology of homologous synteny blocks and evolutionary breakpoint regions

Avian chromosomes undergo more intra- than interchromosomal rearrangements, which either induce or are associated with genome variations among birds. Evolving from a common ancestor with a karyotype not dissimilar from modern chicken, two evolutionary elements characterize evolutionary change: homologous synteny blocks (HSBs) constitute common conserved parts at the sequence level, while evolutionary breakpoint regions (EBRs) occur between HSBs, defining the points where rearrangement occurred. Understanding the link between the structural organization and functionality of HSBs and EBRs provides insight into the mechanistic basis of chromosomal change. Previously, we identified gene ontology (GO) terms associated with both; however, here we revisit our analyses in light of newly developed bioinformatic algorithms and the chicken genome assembly galGal6. We aligned genomes available for six birds and one lizard species, identifying 630 HSBs and 19 EBRs. We demonstrate that HSBs hold vast functionality expressed by GO terms that have been largely conserved through evolution. Particularly, we found that genes within microchromosomal HSBs had specific functionalities relevant to neurons, RNA, cellular transport and embryonic development, and other associations. Our findings suggest that microchromosomes may have conserved throughout evolution due to the specificity of GO terms within their HSBs. The detected EBRs included those found in the genome of the anole lizard, meaning they were shared by all saurian descendants, with others being unique to avian lineages. Our estimate of gene richness in HSBs supported the fact that microchromosomes contain twice as many genes as macrochromosomes.

Application potential of chicken DNA chip in domestic pigeon species - Preliminary results

Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.

Disentangling clustering configuration intricacies for divergently selected chicken breeds

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.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

BACKGROUND

The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes.

RESULTS

Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F_ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF).

CONCLUSION

Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

Unraveling signatures of chicken genetic diversity and divergent selection in breed-specific patterns of early myogenesis, nitric oxide metabolism and post-hatch growth

Introduction: Due to long-term domestication, breeding and divergent selection, a vast genetic diversity in poultry currently exists, with various breeds being characterized by unique phenotypic and genetic features. Assuming that differences between chicken breeds divergently selected for economically and culturally important traits manifest as early as possible in development and growth stages, we aimed to explore breed-specific patterns and interrelations of embryo myogenesis, nitric oxide (NO) metabolism and post-hatch growth rate (GR). Methods: These characteristics were explored in eight breeds of different utility types (meat-type, dual purpose, egg-type, game, and fancy) by incubating 70 fertile eggs per breed. To screen the differential expression of seven key myogenesis associated genes (MSTN, GHR, MEF2C, MYOD1, MYOG, MYH1, and MYF5), quantitative real-time PCR was used. Results: We found that myogenesis associated genes expressed in the breast and thigh muscles in a coordinated manner showing breed specificity as a genetic diversity signature among the breeds studied. Notably, coordinated ("accord") expression patterns of MSTN, GHR, and MEFC2 were observed both in the breast and thigh muscles. Also, associated expression vectors were identified for MYOG and MYOD1 in the breast muscles and for MYOG and MYF5 genes in the thigh muscles. Indices of NO oxidation and post-hatch growth were generally concordant with utility types of breeds, with meat-types breeds demonstrating higher NO oxidation levels and greater GR values as compared to egg-type, dual purpose, game and fancy breeds. Discussion: The results of this study suggest that differences in early myogenesis, NO metabolism and post-hatch growth are breed-specific; they appropriately reflect genetic diversity and accurately capture the evolutionary history of divergently selected chicken breeds.

Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds

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.

Identification of Key Candidate Genes in Runs of Homozygosity of the Genome of Two Chicken Breeds, Associated with Cold Adaptation

Simple Summary

The search for genomic regions related to adaptive abilities preserved in the chicken gene pool of two breeds, which have not been under intensive selection pressure, is of great importance for breeding in the future. This study aimed to identify key candidate genes associated with the adaptation of chickens to cold environments (using the example of the Russian White breed) by using molecular genetic methods. A total of 12 key genes on breed-specific ROH (runs of homozygosity) islands were identified, which may be potential candidate genes associated with the high level of adaptability of chickens to cold environments in the early postnatal period. These genes were associated with lipid metabolism, maintaining body temperature in cold environments, non-shivering thermogenesis and muscle development and are perspectives for further research.

Abstract

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip^® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.