Identification of genomic regions related to wool quality traits in coarse and fine wool sheep breeds based on selection signature

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Mohammadi Hossein; Khaltabadi Farahani Amir Hossein

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Journal Paper

Paper Information

Journal: AGRICULTURAL BIOTECHNOLOGY JOURNAL Year:2024 | Volume:16 | Issue:3 Page(s): 133-154

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Information Journal Paper

Title

Identification of genomic regions related to wool quality traits in coarse and fine wool sheep breeds based on selection signature

Author(s)

Mohammadi Hossein | Khaltabadi Farahani Amir Hossein | Issue Writer Certificate

Keywords

hapFLK statistics

FST statistics

crimp

Candidate Gene

fiber diameter

Abstract

Objective Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. The aim of this study was to identify genomic region with a positive signature of selection related to wool quality in sheep breeds using selection signature FST and hapFLK methods. Materials and methods In this study, data from 146 Zandi and Merino animals genotyped using 50 K BeadChip were used to identify genomic regions under selection associated with wool quality traits. After quality control of the initial data using plink software, 46,793 SNP markers in 144 animals of sheep were finally entered for further analysis. To identify the signatures of selection, two statistical methods of FST and hapFLK were used under FST and hapFLK software packages, respectively. Candidate genes were identified by SNPs located at 0.1% upper range of FST and hapFLK values. GeneCards and UniProtKB databases were also used to interpret the function of the obtained genes. Results Using FST approach, we identified eight genomic regions on chromosomes 1 (two region), 1, 3 (two region), 10, 13, and 19 chromosomes, which were in the 99.9 percentile of all FST values. The identified candidate genes associated with wool trait in these genomic regions included POU1F1, FGF12, GNAS, LHX2, TMTC3, NBEA, MITF. Genes located in identified regions under selection were associated with the crimp of wool, growth and development of skin, fiber diameter, hair follicle development, growth and development of fiber, stimulation of collagen, regulation of epithelial cell and skin pigments, which can be directly and indirectly related to the trait of the wool quality. Also, the results of hapFLK statistics in this research led to the identification of four genomic regions on chromosomes 7, 10, 14, and 19. The identified candidate genes associated with the wool trait in these genomic regions included DUOX1, RHPN2 and LOC106991379. It was determined that they had different functions in collagen differentiation and gene expression of keratinocytes. Conclusions Various genes that were founded within these regions can be considered as candidates for selection based on function. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of genes obtained from association analyses. The results of our research can be used to understand the genetic mechanism controlling wool traits and using these findings could potentially be useful for genetic selection in sheep for better clean fleece yield and mean fiber diameters.

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