Exploring Runs of Homozygosity and Heterozygosity in Sheep Breeds Maintained in Poland

Abstract

Objectives: The study investigates runs of homozygosity (ROH) and heterozygosity (ROHet), and their patterns in nine sheep breeds (772 animals in total) maintained in Poland (native and conserved), corresponding to their genetic diversity, inbreeding levels, and selection signatures. Methods: Genotypes were obtained using the Illumina OvineSNP50 BeadChip and quality-filtered SNPs were used to detect ROH and ROHet segments with the detectRUNS R package, following stringent parameters for segment length, SNP density, and genotype quality. Results: Significant variation in ROH characteristics was observed across breeds. Short ROH segments were predominant in all breeds, indicating historical inbreeding events. In contrast, longer ROH segments signified recent inbreeding, particularly in Swiniarka (SW) and Polish Merino of Colored Variety (MPC). The ROH-based genomic inbreeding coefficient (F_ROH) varied across breeds, with SW exhibiting the highest levels, suggesting reduced genetic diversity. ROHet analysis revealed that Uhruska (UHR) had the highest heterozygous segments span, while Black-headed (BH) sheep exhibited the lowest ROHet extent. ROH islands identified across breeds revealed regions under selection, associated with traits such as reproductive performance, wool quality, and body condition. Genes located within these islands (e.g., U6, SPP1, ABCG2) were linked to economically significant traits including milk production, growth, and carcass quality. Conclusions: The presented results highlight the genetic adaptations shaped by selection pressures, while also providing insights into the genetic architecture of sheep breeds maintained in Poland.

Keywords: ROH; autozygosity; breed diversity; inbreeding coefficient.

Figure 1

The number and length of runs of homozygosity per animal for each sheep breed. (A) represents the sum of all ROH lengths per animal; (B) represents the amount of all ROH per animal; (C) is the distribution of ROH lengths in respect to ROH length categories; (D) is the distribution of ROH numbers in respect to ROH length category. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka.

Figure 2

The proportion of the genome covered by runs of homozygosity (F_ROH) across different ROH length categories and sheep breeds. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka.

Figure 3

The number and length of runs of heterozygosity (ROHet) per animal for each sheep breed in respect to ROHet length category. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka.

Figure 4

ROH patterns in all studied sheep breeds. The dashed line represents 1% of the highest ROH occurrences in a specific breed. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka. ROH islands show gene and QTL contents.

Figure 5

Co-localization of ROH islands with known QTL regions for studied sheep breeds. Y axis represents the percent of a chromosome length. Only chromosomes on which overlaps between ROH islands and QTL were identified are presented on the graph. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka.

Figure 6

Gene intersection and breed-specific distribution of candidate genes identified in ROH islands. PMS—Polish Mountain Sheep; PZ—Podhale Zackel; CMS—Colored Mountain Sheep; SW—Swiniarka; UHR—Uhruska; MPOT—Old-type Merino; MPC—Polish Merino of Colored Variety; BH—Black-headed; WRZ—Wrzosówka.