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Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

1
Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB)—Branch of the L.K. Ernst Federal Science Centre for Animal Husbandry, Pushkin, St. Petersburg 196601, Russia
2
School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
*
Author to whom correspondence should be addressed.
Animals 2020, 10(10), 1887; https://doi.org/10.3390/ani10101887
Received: 26 September 2020 / Revised: 10 October 2020 / Accepted: 12 October 2020 / Published: 15 October 2020
(This article belongs to the Special Issue Morpho-Functional and Genetic Characterization of Local Breeds)
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.
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. View Full-Text
Keywords: chicken breeds; germplasm conservation; SNPs; runs of homozygosity; linkage disequilibrium chicken breeds; germplasm conservation; SNPs; runs of homozygosity; linkage disequilibrium
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Dementieva, N.V.; Kudinov, A.A.; Larkina, T.A.; Mitrofanova, O.V.; Dysin, A.P.; Terletsky, V.P.; Tyshchenko, V.I.; Griffin, D.K.; Romanov, M.N. Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity. Animals 2020, 10, 1887.

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