Disentangling clustering configuration intricacies for divergently selected chicken breeds

Vakhrameev, Anatoly B.; Narushin, Valeriy G.; Larkina, T.A.; Barkova, Olga; Peglivanyan, Grigoriy K.; Dysin, Artem P.; Дементьева, Н. В.; Макарова, А В; Shcherbakov, Yuri S.; Pozovnikova, Marina V.; Bondarenko, Yuri V.; Griffin, Darren K.; Romanov, Michael N

doi:10.1038/s41598-023-28651-8

Cited by 4 publications

(2 citation statements)

References 34 publications

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“…In general, using the results of a multilateral survey of this sample of breeds, it can be argued that phylogenetic relationships based on their genetic structure and variability reflect the known, previously postulated and discovered patterns of evolution and selection in chickens [33,42,89,[105][106][107]. These findings add to our understanding of genomic diversity, phylogeny and admixture in the genomes of unique Russian gene pool breeds with divergent selection histories and phenotypic features.…”

Section: Discussionmentioning

confidence: 78%

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

Romanov

Abdelmanova

Фисинин

et al. 2023

Biology

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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.

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Section: Discussionmentioning

confidence: 78%

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

Romanov

Abdelmanova

Фисинин

et al. 2023

Biology

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“…For this purpose, an appropriate mathematical analysis was undertaken using a new index, Narushin's IPI (Integral Performance Index). The latter was recently established by Vakhrameev et al [31] to evaluate the main economically important traits (i.e., EN, EW and female BW) in various chicken breeds and was originally designated as EY/W (where EY was the product of mean EN and EW, and W was mean female BW). Here, we renamed this index after the author of that study, Valeriy G. Narushin, who proposed this indicator, and calculated it using the corresponding formula: IPI = EN•EW BW where EN is egg number, EW is egg weight (in g), and BW is female body weight at 6 months of age (in g), all values being calculated as breed means.…”

Section: Experimental Birds and Performance Datamentioning

confidence: 99%

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

Volkova,

Romanov,

Abdelmanova

et al. 2023

Animals

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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.

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Pectoral angle: a glance at a traditional phenotypic trait in chickens from a new perspective

Vakhrameev,

Narushin,

Larkina

et al. 2023

J. Agric. Sci.

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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.

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Disentangling clustering configuration intricacies for divergently selected chicken breeds

Cited by 4 publications

References 34 publications

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

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

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

Pectoral angle: a glance at a traditional phenotypic trait in chickens from a new perspective

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