Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

Abstract

Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with the fineness of sheep wool. Whole-genome resequencing of eight sheep breeds was performed to reveal selection signals associated with wool fineness, including four coarse wool and four fine/semi-fine wool sheep breeds. Multiple methods to reveal selection signals (Fst and θπ Ratio and XP-EHH) were applied for sheep wool fineness traits. In total, 269 and 319 genes were annotated in the fine wool (F vs. C) group and the coarse wool (C vs. F) group, such as LGR4, PIK3CA, and SEMA3C and NFIB, OPHN1, and THADA. In F vs. C, 269 genes were enriched in 15 significant GO Terms (p < 0.05) and 38 significant KEGG Pathways (p < 0.05), such as protein localization to plasma membrane (GO: 0072659) and Inositol phosphate metabolism (oas 00562). In C vs. F, 319 genes were enriched in 21 GO Terms (p < 0.05) and 16 KEGG Pathways (p < 0.05), such as negative regulation of focal adhesion assembly (GO: 0051895) and Axon guidance (oas 04360). Our study has uncovered genomic information pertaining to significant traits in sheep and has identified valuable candidate genes. This will pave the way for subsequent investigations into related traits.

Genomic Characterization of Quality Wool Traits in Spanish Merino Sheep

“…The results of the present work show that the wool of the pure Spanish Merino continues to be among the finest, despite the fact that for decades, wool quality has not been used as a criterion for selection, with the fiber diameter equaling or surpassing that of other breeds previously studied, such as Akkraman [ 20 ], Chinese Merino [ 21 , 22 , 23 , 24 ], Crossed Merino [ 25 ], or Rambouillet [ 26 ]. However, the diameter of the fibers currently observed in Spanish Merino appears to be significantly coarser compared to those typically found in breeds highly selected for producing fine wool, such as Uruguayan sheep, which boast a remarkable fineness, with fibers measuring around 16.6 microns [ 27 ], or the Australian Merino, with an average fiber diameter below 16.5 microns [ 28 ].…”

Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery

“…The steps of filtering [ 25 ] are as follows: (1) remove the reads containing adapter and retain the remaining reads; (2) remove the reads containing N ratio more than 10%; (3) remove the low-quality reads (the number of bases with quality value Q ≤ 20 accounted for more than 50% of the whole read). The reference genomes chosen for the comparison were Self-assembled genome_HB, which was used as the reference for all naming and annotation results.…”

“…Then, Tajima's D was used to perform a neutral test analysis to find out whether genetic differentiation had occurred. Based on the filtered SNPs, intra-population F ST , Pi ratio and Tajima's D analyses were performed using PopGenome software [ 40 , 41 ] with sliding windows by physical length in 100 kb windows and 10 kb steps [ 25 ].…”

“…In addition, the lowest 5% of SNP loci analyzed by Tajima's D were used as candidate selection signals for both wool colors. A region of 50 kb upstream and downstream of these candidate sites was considered as the selection signal region [ 25 ]. ANNOVAR software ( https://annovar.openbioinformatics.org/en/latest/ , accessed on 10 December 2023) [ 28 ] was used to annotate the genes and the reference genome was sheep.…”

DataSheet1.ZIP

“…Hence, enhancing the fineness of livestock hair poses a challenge for wool-type livestock species breeding such as sheep (Zenda et al, 2024). Numerous domestic and international studies have been conducted on hair fineness in livestock at present, primarily focusing on the influence of genetic factors (MENGÜÇ, 2016;Ma et al, 2017;Fu et al, 2020;Li et al, 2020;Meilin et al, 2020;Hui et al, 2021;Qin et al, 2022;Shi et al, 2022;Zhang and Wong, 2022;Costa-Silva et al, 2023;Huang et al, 2023;Ma et al, 2023;Zhang et al, 2023;Zenda et al, 2024). The identification of candidate genes influencing hair fineness provides a valuable reference for the exploration of molecular markers that directly regulate fineness phenotype variation.…”