Genomic characteristics of the crossbreed sheep family as the basis for creating a resource population for identification of QTL and candidate genes associated with growth rate

Identification of quantitative trait loci (QTL) and candidate genes associated with growth rate in sheep is an important element for accelerating the breeding progress and, consequently, for increasing the production of mutton. The development and implementation of high-throughput SNP genotyping arrays revolutionized field of molecular genetic analysis and brought QTL mapping to a new level. The creation of specific resource populations to conduct genome wide associative studies (GWAS) increases level of accuracy and reduces the false positive degree. The aim of our work is a search for QTL and candidate genes associated with energy of growth of sheep, using genome wide associative studies (GWAS). We crossed fast-growing Katahdin ram with slow-growing (Romanov's ewes) to obtain F1. We established a data base of phenotypic traits including live weight at the age of 6, 42, 90, 180 and 270 days for F1 sheep. Parents and F1 individuals were genotyped with high-density DNA chip Ovine Infinium® HD SNP BeadChip (Illumina, San Diego, CA). Genotypes were obtained using GenomeStudio 2 software. Quality filtering of SNPs was performed in PLINK v1.09. Multidimensional scaling (MDS analysis) was based on identity -by-state matrix (IBS). Neighbour Net graph was created using SplitsTree 4.14.5 software. To analyze genetic structure within the sheep family, the Admixture program was used. The Admixture and MDS results were consistent: studied animals were clearly distributed according to their origin, namely: F1 individuals were located between the ram and ewes. The Neighbor Net graph showed that most individuals were clustered rather as the mother and daughter than breed groups. The next stage of our work is the crossing of F1 animals to obtain a resource population with splitting traits.

domestic sheep, SNP markers, whole genome genotyping, F1, growth rate

1. Lescheva M. Current state and perspectives of sheep breeding development in Russian modern economic conditions / M. Lescheva, A. Ivolga // Economics of Agriculture. - 2015. - №62. - P. 467-480.

2. Soller M. Strategies to assess structural variation in the chicken genome and its associations with biodiversity and biological performance / M. Soller, S. Weigend, M. N. Romanov, J. C. Dekkers, S. J. Lamont // Poult Sci. - 2006. - № 85. - P. 2061-2078.

3. Hu Z. L. Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era / Z. L. Hu, C. A. Park, X. L. Wu, J. M. Reecy // Nucleic Acids Res. - 2013. - № 41(Database issue). - P. - D871-879.

4. URL: https://www.animalgenome.org/cgi-bin/QTLdb/OA/index

5. Jonas E. Genome-wide association study and fine mapping of QTL on OAR 21 for body weight in sheep / E. Jonas, P. C. Thomson, H. W. Raadsma //In Proceeding of the 9th World Congress on Genetics Applied to Livestock Production: 1-6 August 2010; Leipzig. 2010

6. Riggio V. Genome-wide association and regional heritability mapping to identify loci underlying variation in nematode resistance and body weight in Scottish Blackface lambs / V. Riggio, O. Matika, R. Pong-Wong, M. J. Stear, S. C. Bishop // Heredity (Edinb). - 2013. - №110. - P. 420-429.

7. Gonzalez M. V. A divergent Artiodactyl MYADM-like repeat is associated with erythrocyte traits and weight of lamb weaned in domestic sheep / M. V. Gonzalez, M. R. Mousel, D. R. Herndon, Y. Jiang, B. P. Dalrymple, J. O. Reynolds, W. C. Johnson, L. M. Herrmann-Hoesing, S. N. White // PLoS One. - 2013. - №8 (8). - P. e74700.

8. Zhang L. Genome-wide association studies for growth and meat production traits in sheep / L. Zhang, J. Liu, F. Zhao, H. Ren, L. Xu, J. Lu, S. Zhang, X. Zhang, C. Wei, G. Lu, Y. Zheng, L. Du // PLoS One. - 2013. - №8 (6). - P. e66569.

9. Wang H. Genome-Wide Specific Selection in Three Domestic Sheep Breeds / H. Wang, L. Zhang, J. Cao, M. Wu, X. Ma, Z. Liu, R. Liu, F. Zhao, C. Wei, L. Du // PLoS One. - 2015. - №10 (6). - P. e0128688.

10. Al-Mamun H. A. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight / H. A. Al-Mamun, P. Kwan, S. A. Clark, M. H. Ferdosi, R. Tellam, C. Gondro // Genetics, Selection, Evolution. - 2015. - №47 (1). - P. 66.

11. Fossat N. Conditional restoration and inactivation of Rbm47 reveal its tissue-context requirement for viability and growth / N. Fossat, T. Radziewic, V. Jones, K. Tourle, P. P. L. Tam // Genesis. - 2016. - № 54(3). - P. 115-122.

12. Ledur M.C. Large-scale SNP genotyping in crosses between outbred lines: how useful is it? / M. C. Ledur, N. Navarro, M. Perez-Enciso // Heredity. - 2010. - №105. - P. 173-182.

13. Gu X. Genome-Wide Association Study of Body Weight in Chicken F2 Resource Population / X. Gu, C. Feng, L. Ma, C. Song, Y. Wang, Y. Da // PLoS ONE. - 2011. - №6 (7). - P. e21872.

14. Alexander L. J. Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population / L. J. Alexander, M. D. MacNeil, T. W. Geary, W. M. Snelling, D. C. Rule, J. A. Scanga // Animal Genetics. - 2007. - №38. - P. 506-513.

15. Houston R. D. A QTL affecting daily feed intake maps to chromosome 2 in pigs / R. D. Houston, C. S. Haley, A. L. Archibald, K. A. Rance // Mamm Genome. - 2005. - №16. - P. 464-470.

16. Qiao R. Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations /R. Qiao, J. Gao, Z. Zhang, L. Li, X. Xie, Y. Fan, L. Cui, J. Ma, H. Ai, J. Ren, L. Huang // Genet Sel Evol. - 2015. - № 47(1). - P 17.

17. Ji J. Genome-wide association study identifies 22 new loci for body dimension and body weight traits in a White Duroc×Erhualian F2 intercross population / J. Ji, L. Zhou, Y. Guo, L. Huang, J. Ma// Asian-Australas J Anim Sci. - 2017. - №30 (8). - P. 1066-1073.

18. Fan J. B. Highly parallel SNP genotyping / J. B. Fan, A. Oliphant, R. Shen et al. // Cold Spring Harb Symp Quant Biol. - 2003. - №68. - P. 69-78.

19. Purcell S. PLINK: a tool set for whole-genome association and population-based linkage analyses / S. Purcell, B. Neale, K. Todd-Brown et al. //Am J Hum Genet. - 2007. - №81 (3). - P. 559-575.

20. Huson D. H. Application of Phylogenetic Networks in Evolutionary Studies / D. H. Huson, D. Bryant // Molecular Biology and Evolution. - 2006. - № 23(2). - P. 254-267.

21. Alexander D. H. Fast model-based estimation of ancestry in unrelated individuals / D. N. Alexander, J. Novembre, K. Lange // Genome Res. - 2009. - № 19. - P. 1655-1664.

22. Francis R. M. POPHELPER: An R package and web app to analyse and visualise population structure / R. M. Francis //Mol Ecol Resour. - 2017. - №17. - P. 27-32.

23. R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria. 2012.

24. Deniskova T. E. Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping / T. E. Deniskova, A. V. Dotsev, M. I. Selionova, E. Kunz, I. Medugorac, H. Reyer, K. Wimmers, M. Barbato, A. A. Traspov, G. Brem, N. A. Zinovieva // Genet Sel Evol. - 2018. - №50 (1). - P.:29.