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Polymorphism Analysis of NOTCH2 and CD1A Genes and Their Association with Wool Traits in Subo Merino Sheep
by
, , ,
Shengchao Ma
1,2,†,
Wenna Liu
1,2,†,
Asma Anwa
2,
Sen Tang
2,
Yaqian Wang
2,
Gulinigaer Aimaier
1,2,
Cuiling Wu
1,* and
Xuefeng Fu
2,* 1
Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, International Center for the Collaborative Management of Cross-Border Pest in Central Asia, College of Life Science, Xinjiang Normal University, Urumqi 830017, China
2
Xinjiang Key Laboratory of Animal Biotechnology, Key Laboratory of Genetic Breeding and Reproduction of Herbivorous Livestock of Ministry of Agriculture and Rural Affairs, Xinjiang Uygur Autonomous Region Academy of Animal Science, Urumqi 830011, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Biology 2025, 14(10), 1336; https://doi.org/10.3390/biology14101336 (registering DOI)
Submission received: 23 August 2025
/
Revised: 15 September 2025
/
Accepted: 27 September 2025
/
Published: 28 September 2025
(This article belongs to the Section Zoology)
Simple Summary
To identify the genetic factors influencing wool quality in Subo Merino sheep, this study focused on the NOTCH2 and CD1A genes. Through genetic analysis, we detected six single nucleotide polymorphisms (SNPs) within these genes and examined their associations with key wool traits. Our results indicated that specific SNPs in NOTCH2 are closely linked to the coefficient of variation of fibre diameter and greasy fleece weight, while SNPs in CD1A are significantly associated with the standard deviation of fibre diameter and crimp number. We also found that these genetic variations may alter the secondary and tertiary structures of the proteins encoded by NOTCH2 and CD1A, potentially affecting their biological functions. Furthermore, qPCR results demonstrated that CD1A is higher expressed in fine wool, reinforcing its potential role in regulating wool quality. Overall, this research identifies promising candidate SNPs that could serve as molecular markers, providing practical guidance for breeding Subo Merino sheep with improved wool traits and enhancing our understanding of the genetic mechanisms underlying wool quality.
Abstract
To identify molecular markers associated with wool traits in fine-wool sheep, we examined genetic polymorphisms in the NOTCH2 and CD1A genes in 944 Subo Merino sheep in this study. Subsequently, we performed association analyses between mutation sites in the NOTCH2 and CD1A genes and wool traits using SAS 9.4 software, followed by linkage disequilibrium (LD) analysis of different mutation sites using Haploview 4.2 software. Additionally, bioinformatics tools were employed to predict the potential impacts of missense mutations on protein secondary and tertiary structures. Finally, quantitative PCR (qPCR) was used to assess the expression levels of the NOTCH2 and CD1A genes. Genetic analysis revealed six polymorphic sites in NOTCH2 and CD1A, all of which were missense mutations. Two SNPs in NOTCH2 (SNP1 and SNP2) showed significant associations with the coefficient of variation of fibre diameter, and SNP1 was also associated with greasy fleece weight. Four SNPs in CD1A (SNP3–SNP6) were significantly associated with fibre diameter standard deviation, and SNP3, SNP4, and SNP5 were additionally associated with crimp number. LD analysis revealed that SNP3, SNP4, and SNP5 were closely linked. Bioinformatics analysis indicated that the mutations caused alterations in the secondary and tertiary structures of the NOTCH2 and CD1A proteins. qPCR results showed that the CD1A gene was highly expressed in the fine wool fibre group compared with the ultra-fine wool fibre group. In conclusion, this study revealed a genetic association between NOTCH2 and CD1A and wool traits. The results are expected to provide a theoretical foundation for breeding wool traits in Subo Merino sheep, thereby enhancing the economic value of fine wool.
Keywords:
Subo Merino sheep; NOTCH2 gene; CD1A gene; wool traits; polymorphism
