Assessing genome architecture and signatures of selection in the Sudan thin-tailed Desert sheep

Abstract

Thin-tail sheep are the most ancient in Africa. They are found in hot arid environments in Egypt, Morocco and Sudan and are the only type found in sub-humid and humid environments in West and Central Africa. Compared to the fat-tail sheep, their genome profile remains poorly investigated. Using 600K SNP genotypes, the genome diversity, structure and dynamics of five ecotypes of Sudan thin-tail Desert sheep were investigated. Genotypes from four breeds of Chinese fat-tail sheep were included in the study for comparative purposes. The analysis revealed moderate genetic diversity in the five Sudan thin-tail Desert sheep ecotypes. PCA, phylogenetic analysis and STRUCTURE (K = 5) revealed AL-Ahamda to be slightly genetically differentiated. Unexpectedly, a few individuals of Kabashi ecotype had a unique genetic background at K = 2. Selection signature analysis, contrasting Sudan thin-tail Desert and Chinese fat-tail Tan sheep, identified 41 candidate regions, spanning 72 potentially novel and known genes which were associated with response to heat stress (HSPA5, DNAJB14, YTHDF1), influencing lifespan (GAK, CPLX1), growth regulation (CSMD1, FGFR3, BRCA1), body weight and height variation (DIS3L2, TP53), fat deposition and tail growth (NPR2, ADD1, SNORA73), metabolic pathways (ATP1B2, G6BC, U2, STRT3, MYT3, GLI1), production (FGF9, LATS2), and reproduction (TET2, H2AFZ, OVOL1, SPAG4, EEF1A2, NPTX1, MELK, FGF2, PPP2R5D, MAPKAP1, LGR5), prolificacy (PDE6B, XRN2, EFNB3), immunity (COMMD4, ADPP1, FGB, SIGLEC1, ELF4A1) and disease resistance and inflammatory responses (POLR2A, TNFSF13, CD68, SAT2, GAA, PPT2, RABEPK, SCAI, LHX2). Our findings offer insights on the genome architecture of Sudan thin-tail Desert sheep. They call for further investigations to determine whether the observed genome structure characterize other African thin-tail sheep.