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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #410739
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep

Author
item SUN, XUELIANG - Sichuan Agricultural University
item GUO, JIAZHONG - Sichuan Agricultural University
item LI, RAN - Northwest A&f University
item ZHANG, HUANHUAN - Northwest A&f University
item ZHANG, YIFEI - Sichuan Agricultural University
item Liu, Ge - George
item EMU, QUZHE - Sichuan Agricultural University
item ZHANG, HONGPING - Sichuan Agricultural University

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2024
Publication Date: 1/29/2024
Citation: Sun, X., Guo, J., Li, R., Zhang, H., Zhang, Y., Liu, G., Emu, Q., Zhang, H. 2024. Whole-genome resequencing reveals genetic diversity and wool trait-related genes in Liangshan Semi-fine Wool Sheep. Animals. 14(3):444. https://doi.org/10.3390/ani14030444.
DOI: https://doi.org/10.3390/ani14030444

Interpretive Summary: Genetic makeup of local sheep breeds is important for the animal industry. We studied the genetic composition of the Liangshan Semi-fine wool Sheep systematically through comparative genomic analyses. These results fill our knowledge gaps and provide the foundation for incorporating new insights into the future animal breeding program. Farmers, scientists, and policy planners who need to improve animal production, health, and conservation based on genome-enabled animal selection will benefit from this study.

Technical Abstract: Understanding the genetic makeup of local sheep breeds is crucial for their scientific conservation and sustainable utilization. The Liangshan Semi-fine wool Sheep (LSS) is a Chinese semi-fine wool breed and is well-known for its soft wool. Utilizing whole-genome sequencing data from 35 LSS individuals, 84 sheep from five other domestic breeds, and 20 Asiatic mouflons, we explored the genetic composition of LSS, by investigating its population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signatures. The findings revealed that LSS displayed greater genetic similarity to Border Leicester and Romney sheep compared to Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis showcased low to moderate inbreeding coefficients ranging from 0.014 to 0.154 for this breed. For genome-wide identification of selection signals in LSS, we detected 195 candidate regions harboring 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). These genes were notably enriched in wool-related pathways, such as the WNT signaling pathway involved in dorsal/ventral axis specification and the fibroblast proliferation signaling pathway. Of particular note was a selective sweep region, exhibiting the highest XP-EHH value, which encompassed IRF2BP2, a significant candidate gene influencing fleece fiber traits. Moreover, the genotype frequency at a mutant site (c. *3317A>G, Chr25: 6,784,190 bp) within IRF2BP2 exhibited considerable differences between LSS and TIB, YNS sheep (Fisher's exact test, p < 2.2×10-16). In summary, these results lay the groundwork for further resource protection and breeding improvement of the Liangshan Semi-fine Wool Sheep (LSS).