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. 2024 Jun 29;14(13):1928.
doi: 10.3390/ani14131928.

Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection

Jelena Ramljak  1 , Marija Špehar  2 , Dora Ceranac  2 , Valentino Držaić  1 , Ivan Pocrnić  3 , Dolores Barać  2 , Boro Mioč  1 , Ivan Širić  1 , Zdravko Barać  4 , Ante Ivanković  1 , Ante Kasap  1
Affiliations

Genomic Characterization of Local Croatian Sheep Breeds-Effective Population Size, Inbreeding & Signatures of Selection

Jelena Ramljak et al. Animals (Basel). .

Abstract

The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2-4, FROH4-8, FROH8-16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440-38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection.

Keywords: OCS; ROH island; effective population size; genomic inbreeding.

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Conflict of interest statement

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

Figures

Figure 1
Figure 1
(a) Map of the Istrian Peninsula and Istrian sheep; (b) the Island of Pag and Pag sheep. Size and color of the circles are proportional to the number of sampled animals per flock.
Figure 2
Figure 2
Genetic relationship defined with multidimensional scaling (MDS) analysis between the Istrian sheep (IST) and Pag sheep (PAS).
Figure 3
Figure 3
The effective population size (Ne) estimates obtained by GONE software over the generations for Istrian and Pag sheep.
Figure 4
Figure 4
The distribution of detected ROH segments per chromosome (bars) and the average percentage of each chromosome covered by ROH (red line) for (a) Istrian sheep and (b) Pag sheep.
Figure 5
Figure 5
Runs of homozygosity islands in: (a) Istrian sheep (N = 1047) and (b) Pag sheep (N = 2323). The horizontal line corresponds to the threshold calculated as SNPs with a p-value for ROH incidence higher than 0.999.
Figure 6
Figure 6
Bubble plots displaying top three traits identified in QTL enrichment analysis. The size of bubbles represents the number QTL observed for that trait. Shade of the blue represents the p-value scale (a darker color indicates smaller p-value). Richness factor is indicated on x-axis (it represents the ratio between the number of associated QTLs for a trait and the total number of QTLs in the data base for that trait).
See this image and copyright information in PMC

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