Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing

The aim of this study was to investigate the selection signatures at a genome-wide level in ‘Pishan’ sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); ‘Pishan’ sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (<i>GDF9</i>), Period Circadian Regulator 2 (<i>PER2</i>), Thyroid Stimulating Hormone Receptor (<i>TSHR</i>), and Nuclear Receptor Coactivator 1 (<i>NCOA1</i>) reside within these regions and pathways. The expression levels of <i>GDF9</i> and <i>PER2</i> genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for ‘Pishan’ sheep.