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Genome-wide association study reveals that the IBSP locus affects ear size in cattle

Heredity volume 130, pages 394–401 (2023)Cite this article

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Abstract

Ear size is a classical model for hot climate adaptation following the evolution, but the genetic basis of the traits associated with ear size remains to be elucidated. Here, we performed a genome-wide association study on 158 cattle to explain the genetic mechanism of ear size. One region on BTA6 between 36.79 and 38.80 Mb included 50 suggestive SNPs and 4 significant SNPs that were significantly associated with ear size. The most significant locus (P = 1.30 × 10−8) was a missense mutation (T250I) on the seventh exon of integrin-binding sialoprotein (IBSP), which had an allele substitution effect of 23.46 cm2 for ear size. Furthermore, this mutation will cause changes in the three-dimensional structure of the protein. To further identify genes underlying this typical feature, we performed a genome scan among nine cattle breeds with different ear sizes by using SweeD. Results suggested that IBSP was under positive selection among four breeds with relatively large ear sizes. The expression levels of IBSP in ear tissues of large- and small-ear cattle were significantly different. A haplotype diversity survey of this missense mutation in worldwide cattle breeds strongly implied that the origin of this missense mutation event was Bos taurus. These findings have important theoretical importance for the exploration of major genes associated with ear size and provide important molecular markers for the identification of cattle germplasm resources.

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Fig. 1: Statistical analysis of ear size.
Fig. 2: Genome-wide association study of ear size.
Fig. 3: Selection and conservative analysis for IBSP.
Fig. 4: Haplotype network analysis and geographical distribution of the mutation among different cattle breeds.

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Data availability

The raw whole-genome sequencing data were reported in our previous study (Chen et al. 2020) and are available at the NCBI Short Read Archive under the BioProject accession number PRJNA555741.

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Acknowledgements

We would like to thank High-Performance Computing (HPC) of Northwest A&F University (NWAFU) for providing computing resources. The study was supported by the National Natural Science Foundation of China (31872317) and China Agriculture Research System of MOF and MARA (Grant No. CARS-37).

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  1. These authors contributed equally: Jiafei Shen, Xiaoting Xia.

Authors and Affiliations

  1. Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China

    Jiafei Shen, Xiaoting Xia, Luyang Sun, Xiaohui Ma, Ningbo Chen, Hong Chen, Yu Jiang & Chuzhao Lei

  2. International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, N1 Shangcheng Road, Yiwu, Zhejiang, 322000, China

    Jiafei Shen

  3. Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, 650212, China

    Bizhi Huang & Jicai Zhang

  4. Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, 577, Pakistan

    Quratulain Hanif

  5. Academy of Science and Technology, Chuxiong Normal University, Chuxiong, Yunnan, 675000, China

    Kaixing Qu

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Contributions

YJ and CZL designed the study and supported the funding. JFS and XTX curated and analyzed the data. JFS wrote the original manuscript. QH reviewed and edited the manuscript. LYS, XHM, NBC, and HC reviewed the manuscript. BZH, KXQ, and JCZ organized sampling and conducted fieldwork. All authors commented on the manuscript and gave final approval for publication.

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Correspondence to Yu Jiang or Chuzhao Lei.

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Shen, J., Xia, X., Sun, L. et al. Genome-wide association study reveals that the IBSP locus affects ear size in cattle. Heredity 130, 394–401 (2023). https://doi.org/10.1038/s41437-023-00614-9

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