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. 2025 May 24;16(6):631.
doi: 10.3390/genes16060631.

Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing

Tatiana E Deniskova  1 , Arsen V Dotsev  1 , Olga A Koshkina  1 , Anastasia D Solovieva  1 , Nadezhda A Churbakova  1 , Sergey N Petrov  1 , Alexey N Frolov  2 , Stanislav A Platonov  2 , Alexandra S Abdelmanova  1 , Maxim A Vladimirov  1 , Elena A Gladyr  1 , Igor V Gusev  1 , Svyatoslav V Lebedev  2 , Darren K Griffin  3   4   5 , Michael N Romanov  1   3   4 , Natalia A Zinovieva  1
Affiliations

Examination of Runs of Homozygosity Distribution Patterns and Relevant Candidate Genes of Potential Economic Interest in Russian Goat Breeds Using Whole-Genome Sequencing

Tatiana E Deniskova et al. Genes (Basel). .

Abstract

Background/objectives: Whole-genome sequencing (WGS) data provide valuable information about the genetic architecture of local livestock but have not yet been applied to Russian native goats, in particular, the Orenburg and Karachay breeds. A preliminary search for selection signatures based on single nucleotide polymorphism (SNP) genotype data in these breeds was not informative. Therefore, in this study, we aimed to address runs of homozygosity (ROHs) patterns and find the respective signatures of selection overlapping candidate genes in Orenburg and Karachay goats using the WGS approach.

Methods: Paired-end libraries (150 bp reads) were constructed for each animal. Next-generation sequencing was performed using a NovaSeq 6000 sequencer (Illumina, Inc., San Diego, CA, USA), with ~20X genome coverage. ROHs were identified in sliding windows, and ROH segments shared by at least 50% of the samples were considered as ROH islands.

Results: ROH islands were identified on chromosomes CHI3, CHI5, CHI7, CHI12, CHI13, and CHI15 in Karachay goats; and CHI3, CHI11, CHI12, CHI15, and CHI16 in Orenburg goats. Shared ROH islands were found on CHI12 (containing the PARP4 and MPHOSPH8 candidate genes) and on CHI15 (harboring STIM1 and RRM1). The Karachay breed had greater ROH length and higher ROH number compared to the Orenburg breed (134.13 Mb and 695 vs. 78.43 Mb and 438, respectively). The genomic inbreeding coefficient (FROH) varied from 0.032 in the Orenburg breed to 0.054 in the Karachay breed. Candidate genes associated with reproduction, milk production, immunity-related traits, embryogenesis, growth, and development were identified in ROH islands in the studied breeds.

Conclusions: Here, we present the first attempt of elucidating the ROH landscape and signatures of selection in Russian local goat breeds using WGS analysis. Our findings will pave the way for further insights into the genetic mechanisms underlying adaption and economically important traits in native goats.

Keywords: Russian local breeds; candidate genes; goat (Capra hircus); runs of homozygosity (ROHs); signatures of selection; whole-genome sequencing (WGS).

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Conflict of interest statement

The authors declare no conflicts of interest. The RSF had no role in the design of this study; in the collection, analyses, or interpretation of the data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
The representative studied goat breeds of Russian origin: (a) a family of Orenburg goats (a black male and two white females); and (b) a herd of Karachay goats.
Figure 2
Figure 2
The map with the corresponding sampling sites of goats for the Orenburg (▼) and Karachay (▼) breeds.
Figure 3
Figure 3
Individual Neighbor-Net graph using IBS distances plotted for the Orenburg and Karachay breeds based on the WGS data analysis.
Figure 4
Figure 4
Principal component analysis performed for Orenburg and Karachay goats based on the WGS data analysis: (a) for the first two principal components (PC1 and PC2); and (b) for the first and third principal components (PC1 and PC3).
Figure 5
Figure 5
Distribution of runs of homozygosity (ROH) according to length classes in Orenburg and Karachay goats based on the WGS data analysis: (a) mean number of ROHs per breed; and (b) mean length of ROHs per breed.
Figure 6
Figure 6
ROH islands identified in the Orenburg and Karachay breeds on the following chromosomes: (a) CHI3, (b) CHI5, (c) CHI7, (d) CHI11, (e) CHI12, (f) CHI13, (g) CHI15, and (h) CHI16.
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