PSXII-7 Characterization of Runs of Homozygosity Islands in American Mink Using Whole-Genome Sequencing Data

生物 水貂 遗传学 小桶 基因组 基因 全基因组测序 纯合性运行 人口 基因本体论 单核苷酸多态性 基因表达 生态学 人口学 社会学 基因型
作者
Pourya Davoudi,Duy Ngoc,Stefanie M. Colombo,Bruce Rathgeber,Mehdi Sargolzaei,Graham Plastow,Zhiquan Wang,Younes Miar
出处
期刊:Journal of Animal Science [Oxford University Press]
卷期号:101 (Supplement_3): 351-352
标识
DOI:10.1093/jas/skad281.417
摘要

Abstract The genome-wide analysis of runs of homozygosity (ROH) islands can be an effective strategy to detect the variants shared among the individuals of a population, and thereby to reveal important genomic regions for complex traits. The current study performed ROH analysis to characterize the genome-wide patterns of homozygosity, ROH islands, and the gene content of those candidate regions using whole-genome sequencing data of 100 American mink (Neogale vison). After sequence processing, variants were called using GATK and Samtools pipelines. After quality control, 8,373,854 bi-allelic variants identified by both pipelines remained for subsequent analysis. A total of 34,652 ROH segments were identified in all individuals, among which shorter segments (0.3–1 Mb) were abundant throughout the genome, approximately accounting for 84.39% of all ROH. We identified 63 ROH islands that harbored 156 annotated genes. The genes located in ROH islands were associated with fur quality (EDNRA, FGF2, FOXA2, SLC24A4, SLC24A3, PDE5A), body size/body weight (MYLK4, PRIM2, FABP2, BBS7, EYS, PHF3), immune capacity (IL2, PTP4A1, SEMA4C, CD274, JAK2, MAD2L1, CCNA2, TNIP3), and reproduction (ADAD1, KHDRBS2, INSL6, PGRMC2, LARP1B, HSPA4L, CAMK2D). Furthermore, Gene Ontology and KEGG pathway enrichment analyses revealed multiple significant terms (P ≤ 0.05), among which cGMP-PKG signaling pathway, regulation of actin cytoskeleton, and calcium signaling pathway were highlighted due to their functional roles in growth and fur characteristics. This is the first study to present ROH islands in American mink. The candidate genes from ROH islands and functional enrichment analysis suggest possible signatures of selection in response to the mink breeding targets, such as increased body length, reproductive performance and fur quality. These findings contribute to an understanding of genetic characteristics, and provide complementary information to assist with implementation of breeding strategies for genetic improvement in American mink.
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