11 research outputs found
Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity
Simple Summary
To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds.
Abstract
Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity
Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens
Background: The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Moreover, its cold tolerance has been presumably associated with day-old chick down colour (DOCDC) white rather than yellow, the genetic basis of these traits being however poorly understood. Results: We undertook genome-wide association studies (GWASs) for eight performance traits using single nucleotide polymorphism (SNP) genotyping of 146 birds and an Illumina 60KBeadChip. Several suggestive associations (p <5.16*10(-5)) were found for YEF, AFE, BW and EW. Moreover, on chromosome 2, an association with the white DOCDC was found where there is an linkage disequilibrium block of SNPs including genes that are responsible not for colour, but for immune resistance. Conclusions: The obtained GWAS data can be used to explore the genetics of immunity and carry out selection for increasing YEF for SPF eggs production.Peer reviewe
Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations
Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60 K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD < 0.5 and LD < 0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the RussianWhite RG population, pruningwas substantial for Dataset I, and FST valueswere only positivewhen LD< 0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the RussianWhite RG populationwith the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates
Evolutionary subdivision of domestic chickens: implications for local breeds as assessed by phenotype and genotype in comparison to commercial and fancy breeds
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 and phenomenon of pectoral angle variation across different chicken phenotypes
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
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 phenomewide association/mediation analyses
[Genetic variation of the NCAPG-LCORL locus in chickens of local breeds based on SNP genotyping data] ΠΠ΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠ°Ρ ΠΈΠ·ΠΌΠ΅Π½ΡΠΈΠ²ΠΎΡΡΡ Π»ΠΎΠΊΡΡΠ° NCAPG-LCORL Ρ ΠΊΡΡ Π»ΠΎΠΊΠ°Π»ΡΠ½ΡΡ ΠΏΠΎΡΠΎΠ΄ Π½Π° ΠΎΡΠ½ΠΎΠ²Π΅ Π΄Π°Π½Π½ΡΡ SNP-Π³Π΅Π½ΠΎΡΠΈΠΏΠΈΡΠΎΠ²Π°Π½ΠΈΡ
Using SNP analysis, genomic variation of the NCAPG-LCORL locus in chickens of 49 gene pool breeds and crossbreds from the Genetic Collection of Rare and Endangered Chicken Breeds was analyzed. Genotyping was performed using an Illumina Chicken 60K SNP iSelect BeadChip. As a result of SNP scanning, five significant SNPs were identified in the NCAPG-LCORL region in all breeds and crossbreds of the analyzed groups of chickens for GGA4. Cluster analysis of admixture models revealed a subdivision of individuals according to their origin at K = 5. Chickens of the egg and meat types formed two separate clusters, which is consistent with the results of genotype frequencies. When analyzing genetic differentiation between groups of chickens with different utility types on the basis of pairwise FST values, significant differences (p < 0.05) were found for the group of egg-type chickens in comparison with meat-type (0.330), dual purpose (meat-egg, 0.178), game (0.225 ) and dual purpose (egg-meat, 0.237) chickens, as well as for meat-type relative to fancy chickens (0.153). The results showed that the compared groups differ genetically from each other, which is confirmed by the data on genotype frequencies. The population specificity of the linkage disequilibrium structure at the NCAPG-LCORL locus was revealed for 11 chicken breeds.
Π Ρ
ΠΎΠ΄Π΅ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ Ρ ΠΏΠΎΠΌΠΎΡΡΡ Π°Π½Π°Π»ΠΈΠ·Π° ΠΎΠ΄Π½ΠΎΠ½ΡΠΊΠ»Π΅ΠΎΡΠΈΠ΄Π½ΠΎΠ³ΠΎ ΠΏΠΎΠ»ΠΈΠΌΠΎΡΡΠΈΠ·ΠΌΠ° (SNP) Π±ΡΠ»Π° ΠΏΡΠΎΠ°Π½Π°Π»ΠΈΠ·ΠΈΡΠΎΠ²Π°Π½Π° Π³Π΅Π½ΠΎΠΌΠ½Π°Ρ ΠΈΠ·ΠΌΠ΅Π½ΡΠΈΠ²ΠΎΡΡΡ Π»ΠΎΠΊΡΡΠ° NCAPG-LCORL Ρ ΠΊΡΡ 49 Π³Π΅Π½ΠΎΡΠΎΠ½Π΄Π½ΡΡ
ΠΏΠΎΡΠΎΠ΄ ΠΈ Π³ΠΈΠ±ΡΠΈΠ΄Π½ΡΡ
ΡΠΎΡΠΌ ΠΈΠ· Β«ΠΠ΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠΉ ΠΊΠΎΠ»Π»Π΅ΠΊΡΠΈΠΈ ΡΠ΅Π΄ΠΊΠΈΡ
ΠΈ ΠΈΡΡΠ΅Π·Π°ΡΡΠΈΡ
ΠΏΠΎΡΠΎΠ΄ ΠΊΡΡΒ». ΠΠ΅Π½ΠΎΡΠΈΠΏΠΈΡΠΎΠ²Π°Π½ΠΈΠ΅ ΠΏΡΠΎΠ²ΠΎΠ΄ΠΈΠ»ΠΈ Ρ ΠΏΠΎΠΌΠΎΡΡΡ ΡΠΈΠΏΠ° Illumina Chicken 60K SNP iSelect BeadChip. Π ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠ΅ SNP-ΡΠΊΠ°Π½ΠΈΡΠΎΠ²Π°Π½ΠΈΡ Ρ Π²ΡΠ΅Ρ
ΠΏΠΎΡΠΎΠ΄ ΠΈ Π³ΠΈΠ±ΡΠΈΠ΄ΠΎΠ² Π°Π½Π°Π»ΠΈΠ·ΠΈΡΡΠ΅ΠΌΡΡ
Π³ΡΡΠΏΠΏ ΠΊΡΡ Π½Π° GGA4 Π² ΡΠ΅Π³ΠΈΠΎΠ½Π΅, Π²ΠΊΠ»ΡΡΠ°ΡΡΠ΅ΠΌ NCAPG-LCORL, ΠΈ Π² ΠΎΠ±Π»Π°ΡΡΠΈ ΡΡΠ΄ΠΎΠΌ Ρ ΡΡΠΈΠΌ ΡΠ΅Π³ΠΈΠΎΠ½ΠΎΠΌ ΠΎΠΏΡΠ΅Π΄Π΅Π»Π΅Π½ΠΎ ΠΏΡΡΡ Π·Π½Π°ΡΠΈΠΌΡΡ
SNPs, ΠΊΠΎΡΠΎΡΡΠ΅ ΠΌΠΎΠ³ΡΡ Π±ΡΡΡ ΠΊΠ°Π½Π΄ΠΈΠ΄Π°ΡΠ°ΠΌΠΈ Π΄Π»Ρ ΡΠ΅Π»Π΅ΠΊΡΠΈΠΈ Ρ ΠΏΠΎΠΌΠΎΡΡΡ ΠΌΠ°ΡΠΊΠ΅ΡΠΎΠ² (MAS). ΠΠ»Π°ΡΡΠ΅ΡΠ½ΡΠΉ Π°Π½Π°Π»ΠΈΠ· Π°Π΄ΠΌΠΈΠΊΡ-ΠΌΠΎΠ΄Π΅Π»Π΅ΠΉ ΠΎΠ±Π½Π°ΡΡΠΆΠΈΠ» ΡΠ°Π·Π΄Π΅Π»Π΅Π½ΠΈΠ΅ ΠΎΡΠΎΠ±Π΅ΠΉ ΡΠΎΠΎΡΠ²Π΅ΡΡΡΠ²Π΅Π½Π½ΠΎ ΠΈΡ
ΠΏΡΠΎΠΈΡΡ
ΠΎΠΆΠ΄Π΅Π½ΠΈΡ ΠΏΡΠΈ Π=5. ΠΡΡΡ ΡΠΈΡΠ½ΠΎΠ³ΠΎ ΠΈ ΠΌΡΡΠ½ΠΎΠ³ΠΎ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ²Π½ΠΎΡΡΠΈ ΡΡΠΎΡΠΌΠΈΡΠΎΠ²Π°Π»ΠΈ Π΄Π²Π° ΠΎΠ±ΠΎΡΠΎΠ±Π»Π΅Π½Π½ΡΡ
ΠΊΠ»Π°ΡΡΠ΅ΡΠ°, ΡΡΠΎ ΡΠΎΠ³Π»Π°ΡΡΠ΅ΡΡΡ Ρ ΡΠ΅Π·ΡΠ»ΡΡΠ°ΡΠ°ΠΌΠΈ ΡΠ°ΡΡΠΎΡ Π³Π΅Π½ΠΎΡΠΈΠΏΠΎΠ². ΠΡΠΈ Π°Π½Π°Π»ΠΈΠ·Π΅ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΎΠΉ Π΄ΠΈΡΡΠ΅ΡΠ΅Π½ΡΠΈΠ°ΡΠΈΠΈ ΠΌΠ΅ΠΆΠ΄Ρ Π³ΡΡΠΏΠΏΠ°ΠΌΠΈ ΠΊΡΡ ΡΠ°Π·Π»ΠΈΡΠ½ΠΎΠ³ΠΎ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ²Π½ΠΎΡΡΠΈ Π½Π° ΠΎΡΠ½ΠΎΠ²Π΅ ΠΏΠΎΠΏΠ°ΡΠ½ΡΡ
FST-Π·Π½Π°ΡΠ΅Π½ΠΈΠΉ ΠΎΡΠΌΠ΅ΡΠ΅Π½Ρ Π΄ΠΎΡΡΠΎΠ²Π΅ΡΠ½ΡΠ΅ ΡΠ°Π·Π»ΠΈΡΠΈΡ (p < 0,05) Π΄Π»Ρ Π³ΡΡΠΏΠΏΡ ΠΊΡΡ ΡΠΈΡΠ½ΠΎΠ³ΠΎ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ²Π½ΠΎΡΡΠΈ Π² ΡΡΠ°Π²Π½Π΅Π½ΠΈΠΈ Ρ ΠΌΡΡΠ½ΡΠΌΠΈ (0,330), ΠΌΡΡΠΎ-ΡΠΈΡΠ½ΡΠΌΠΈ (0,178), Π±ΠΎΠΉΡΠΎΠ²ΡΠΌΠΈ (0,225) ΠΈ ΡΠΈΡΠ½ΠΎ-ΠΌΡΡΠ½ΡΠΌΠΈ (0,237), Π° ΡΠ°ΠΊΠΆΠ΅ Π΄Π»Ρ ΠΊΡΡ ΠΌΡΡΠ½ΠΎΠ³ΠΎ Π½Π°ΠΏΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΏΡΠΎΠ΄ΡΠΊΡΠΈΠ²Π½ΠΎΡΡΠΈ ΠΎΡΠ½ΠΎΡΠΈΡΠ΅Π»ΡΠ½ΠΎ Π΄Π΅ΠΊΠΎΡΠ°ΡΠΈΠ²Π½ΡΡ
(0,153). Π Π΅Π·ΡΠ»ΡΡΠ°ΡΡ ΠΏΠΎΠΊΠ°Π·Π°Π»ΠΈ, ΡΡΠΎ ΡΡΠ°Π²Π½ΠΈΠ²Π°Π΅ΠΌΡΠ΅ Π³ΡΡΠΏΠΏΡ ΠΎΡΠ»ΠΈΡΠ°ΡΡΡΡ Π³Π΅Π½Π΅ΡΠΈΡΠ΅ΡΠΊΠΈ Π΄ΡΡΠ³ ΠΎΡ Π΄ΡΡΠ³Π°, ΡΡΠΎ ΠΏΠΎΠ΄ΡΠ²Π΅ΡΠΆΠ΄Π°Π΅ΡΡΡ Π΄Π°Π½Π½ΡΠΌΠΈ ΠΎ ΡΠ°ΡΡΠΎΡΠ°Ρ
Π³Π΅Π½ΠΎΡΠΈΠΏΠΎΠ². ΠΡΡΠ²Π»Π΅Π½Π° ΠΏΠΎΠΏΡΠ»ΡΡΠΈΠΎΠ½Π½Π°Ρ ΡΠΏΠ΅ΡΠΈΡΠΈΡΠ½ΠΎΡΡΡ ΡΡΡΡΠΊΡΡΡΡ Π½Π΅ΡΠ°Π²Π½ΠΎΠ²Π΅ΡΠΈΡ ΠΏΠΎ ΡΡΠ΅ΠΏΠ»Π΅Π½ΠΈΡ (LD) ΠΏΠΎ Π»ΠΎΠΊΡΡΡ NCAPG-LCORL Π΄Π»Ρ 11 ΠΏΠΎΡΠΎΠ΄ ΠΊΡΡ
Applying SNP array technology to assess genetic diversity in Russian gene pool of chickens
Development of high throughput next generation technologies for genome-wide genotyping opens new prospects for characterizing various gene pool populations of chickens. Use of SNP array technology allows determining the extent of their genetic diversity, differentiation, and potential for further genomic selection. Solutions derived from the identification of SNP markers and genes relevant to economically important traits, their combinations and variations can be applied to selection and improvement of lines and crosses of commercial poultry. In addition, analysis of intra- and inter-population genetic diversity of gene pool breeds of chickens using modern genomic technologies seems important because these breeds may be carriers of unique phenotypic characteristics, such as adaptability to local conditions, resistance to certain diseases, and unique productive, decorative and other features. A specific aim in the context of the problems to be solved within the current project is genotyping of 40 chicken gene pool breeds and interbreed hybrids kept at the Russian Research Institute of Farm Animal Genetics and Breeding using Illumina Chicken 60K SNP iSelect BeadChip, followed by computation of a number of population genetic parameters (Wrightβs FST-statistics, heterozygosity, inbreeding, between-breed differences, etc.). Subsequently, correlations will be identified between the calculated molecular genetic parameters, genotypes, and phenotypic characteristics of the breeds. Acknowledgements: the project is sponsored by the Russian Science Foundation grant, No. 16-16-04060
Pectoral angle: a glance at a traditional phenotypic trait in chickens from a new perspective
In meat-type poultry breeding, pectoral angle (PA) is a conventional anatomical indicator for changes in body conformation and meat traits; its correlation to egg performance is however deemed controversial. In this context, we revisited, assessed and put forward evidence for the usefulness of this classic phenotypic variable and its specific integrative index of pectoral angle-to-body weight ratio (PA/BW). Specifically, we identified respective correlations and used them for distinguishing the major categories (production types) of diverse chicken breeds under the traditional classification model (TCM) and genotypic clustering models of the global chicken gene pool subdivision. Also, the usefulness of the supplementary integrative egg mass yield index (EMY) for this objective was demonstrated. Because of estimating the total mass of eggs laid (i.e. egg number times egg weight), EMY can serve as an indicator of egg production. Direct approximation of EMY values by PA and BW values did not lead to significant correlation dependences between these indicators in each of the four breed utility types according to TCM. However, using the ratio of PA to BW, instead of PA and BW alone, resulted in significant correlation of EMY with PA/BW, allowing for distinction between egg-type and non-productive breeds. The validity of the proposed correlation-based models was supported by PCA and Neighbor Joining clustering analyses. Collectively, we suggested that PA can be a potentially correlated trait for selecting hens and roosters in breeding flocks to boost egg yield. These results can also be applied to chicken breeding as well as conservation- and phenome-related research
Evolutionary subdivision of domestic chickens: implications for local breeds as assessed by phenotype and genotype in comparison to commercial and fancy breeds
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