Genomic scanning of selection signature in Iranian skin and wool sheep using FST unbiased estimator and hapFLK methods

Document Type : Research Paper

Authors

1 Ph.D. Student, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran

2 Associate Professor, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran

3 Professor, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

4 Associate Professor, Department of Animal Science, Faculty of Agriculture, University of Arak, Arak, Iran

5 Professor, Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran

Abstract

Introduction:  The principal aim of the sheep industry worldwide is to produce high-quality meat. In addition to the meat, milk, and wool production are the economic traits in sheep breeding programs. Wool production is one of the most important economic characteristics of sheep with a complex physiological and biochemical process that is influenced by genetics, environment, and nutrition. Almost all Iranian sheep breeds are double-coated and produce carpet wool. Therefore, considering the role of wool on the country's economy, it is necessary to conduct a study to identify the genetic factors affecting this trait. Identifying the genomic regions under selection is effective in understanding the processes involved in the evolution of the genome and also in identifying the genomic regions involved in the emergence of economic traits. Selective signatures in the whole genome can help us to understand the mechanisms of selection and to identify the genomic regions that have been under natural or artificial selection for many years. Since Selective signatures are usually associated with major effect genes and important economic traits, they can provide suitable information sources to improve the performance of selection programs in the future. The objective of this study was to identify the genomic regions that have been under selection in skin and wool sheep breeds.
Materials and methods: In the present study, Illumina ovine SNP600K BeadChip genomic arrays of 80 sheep from six breeds were used, three breeds were bred for their skin (Karakul, SiahKabud, and Gray Shiraz) and three breeds were bred for their wool (Sanjabi, Kermani and Baluchi). Unbiased methods of Weir and Cockerham’s FST (Theta) and hapFLK were used to detect the selection signatures. Also, to check the genes and QTLs in the selected regions, the Biomart database, OAR 3.1 version of the sheep genome, was used, and the function of the identified genes was analyzed through a wide search in different databases such as Genecards and OMIM. Finally, the list of genes related to the selected regions was reported. For this purpose, the chromosomal position of SNPs with high numerical values of theta and hapFLK, as well as the 250 kbp region around these markers, were further investigated. Then, the DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology. Finally, Cytoscape software was used to determine gene networks.
Then, DAVID database online search was used to investigate the biological and functional processes of genes and to study the ontology.
سپس از جستجوی آنلاین پایگاه داده DAVID برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی استفاده شد.
Then, to investigate the biological and functional processes of genes and to study the ontology, DAVID database was used to search online.
سپس برای بررسی فرآیندهای بیولوژیکی و عملکردی ژن ها و مطالعه هستی شناسی از پایگاه داده DAVID برای جستجوی آنلاین استفاده شد.
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Results and discussion: The results of the Theta analysis revealed 26 genomic regions on 1, 2, 6, 19, and 24 chromosomes, and the results of hapFLK revealed seven genomic regions on 6 and 19 chromosomes. Bioinformatics analysis demonstrated that some of these genomic regions overlapped with known genes related to pigment traits and characteristics of wool (KIT on chr 6, MITF on chr 19, IGSF10 on chr 1, PDGFRA on chr 6), muscles (MICALL2 on chr 24), vasodilation and immune response (P2RY on chr 1) and cancer (MIR339 on chr 24, ELFN1 on chr 24, MAD1L1 on chr 24, GPR87 on chr 1). The investigation of reported QTLs showed that these regions are related to QTLs of important economic traits, including traits related to meat, carcass, milk, body weight, bone density, and the total number of lambs born. Also, the analysis of Gene Ontology and Enriched pathway terms in regions under positive selection were related to the pathways involved in the differentiation of melanocytes and pigments, differentiation of stem cells, cellular processes, development of the immune system, blood system, reproductive and cellular processes. The results of the gene networks with the information obtained from Theta and hapFLK statistics showed that the genes identified were significantly active in the development and morphogenesis networks of the embryonic digestive tract, the networks related to pigment and melanocyte differentiation, and the networks related to Purine and G protein. However, to identify the exact function of the identified genes and QTLs, it is recommended to carry out more investigations.
نتایج شبکه‌های ژنی با اطلاعات به‌دست‌آمده از آمار تتا و hapFLK نشان داد که ژن‌های شناسایی‌شده به‌طور معنی‌داری در شبکه‌های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه‌های مربوط به تمایز رنگدانه و ملانوسیت و شبکه‌های مربوط به
The results of the gene networks with the information obtained from theta and hapFLK statistics showed that the genes identified were significantly in the development and morphogenesis networks of the embryonic digestive system, the networks related to the differentiation of pigment and melanocytes and the networks related to
نتایج شبکه‌های ژنی با اطلاعات به‌دست‌آمده از آمار تتا و hapFLK نشان داد که ژن‌های شناسایی‌شده به‌طور معنی‌داری در شبکه‌های رشد و مورفوژنز دستگاه گوارش جنینی، شبکه‌های مربوط به تمایز رنگدانه‌ها و ملانوسیت‌ها و شبکه‌های مربوط به
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Conclusions: The results of the present study and the identified genomic regions can play an important role in the study of the effect of the selection on population differentiation in two sheep breeds that bred for skin and sheep production. Subsequently, this would direct us to identify the genomic regions associated with traits that differentiate these groups. However, these areas need to be confirmed in other independent studies with more samples. In general, the data of this research can be used in research related to genomic selection, design of mating systems, and additional reviews and evaluations to improve skin and wool production in sheep.

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Animal Production Research
Volume 12, Issue 2
September 2023
Pages 85-103

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