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Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep

Heredity volume 130, pages 358–367 (2023)Cite this article

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Abstract

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1–6 Mb and another 300 in the 6–12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12–24 Mb (95) and 24–48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

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Fig. 1: Pedigree based inbreeding estimates (FPED) per generation.
Fig. 2: Population stratification.
Fig. 3: ADMIXTURE model-based clustering.
Fig. 4: Heatmap.
Fig. 5: Estimated inbreeding levels.
Fig. 6: Plot of chromosome inbreeding.
Fig. 7: Manhattan plot of % SNP in Runs.
Fig. 8: Plot of stacked runs.
Fig. 9: Plot of detected runs.

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Acknowledgements

The authors are grateful to Guilan and Bu-Ali Sina Universities for providing financial support for this study.

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Authors and Affiliations

  1. Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Gilan, Iran

    Ramin Abdoli

  2. Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, 41635-1314, Iran

    Seyed Ziaeddin Mirhoseini & Navid Ghavi Hossein-Zadeh

  3. Department of Animal Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, 65178-33131, Iran

    Pouya Zamani

  4. Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arāk, 38156-8-8349, Iran

    Mohammad Hossein Moradi

  5. AGBU, a joint venture of NSW Department of Primary Industries and University of New England, University of New England, Armidale, NSW, 2351, Australia

    Mohammad Hossein Ferdosi

  6. Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada

    Mehdi Sargolzaei

  7. Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48824, USA

    Cedric Gondro

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Contributions

Conceptualization: RA; analyses: RA, SZM, CG, MS & MHF; draft preparation: RA, SZM, NGHZ, PZ & MHM; review and editing: CG, MS, SZM & NGHZ. All authors have read and agreed to the final version of the manuscript.

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Correspondence to Ramin Abdoli or Seyed Ziaeddin Mirhoseini.

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Abdoli, R., Mirhoseini, S.Z., Ghavi Hossein-Zadeh, N. et al. Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep. Heredity 130, 358–367 (2023). https://doi.org/10.1038/s41437-023-00611-y

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