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Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle

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Abstract

The present study was carried out to identify genome-wide genetic markers and variants in candidate genes for production and reproduction traits in Sahiwal cattle using a cost-effective reduced representation sequencing method. A total of 258,231 genome-wide SNPs were identified in Sahiwal cattle with reference to Bos indicus genome, of which 150,231 were novel SNPs. Among the high-confidence SNPs identified, 91.86% and 27.30% were genotyped in 50% and 100% of the samples. Mapping of the identified SNPs revealed 525 SNPs in candidate genes related to production traits while 333 SNPs were mapped to candidate genes related to reproduction traits. The SNPs identified in this study will facilitate further insights on tropical adaptation, domestication history and population structure of indigenous cattle. The variants in candidate genes identified in this study will serve as useful genetic tools, in the quest for phenotype modifying nucleotide change and help in designing appropriate genetic improvement programs.

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Authors and Affiliations

  1. Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India

    M. R. Vineeth, T. Surya, Anshuman Kumar & I. D. Gupta

  2. ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India

    Jayakumar Sivalingam, S. K. Niranjan, S. P. Dixit, Karanveer Singh & M. S. Tantia

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  2. T. Surya
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  3. Jayakumar Sivalingam
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  4. Anshuman Kumar
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  5. S. K. Niranjan
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  6. S. P. Dixit
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  7. Karanveer Singh
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  8. M. S. Tantia
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  9. I. D. Gupta
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Corresponding author

Correspondence to Jayakumar Sivalingam.

Ethics declarations

The experimental plan was approved by NDRI and NBAGR Institutional Animal Ethics Committee (IAEC) constituted as per the article number 13 of the CPCSEA rules laid down by the Government of India. Norms concerning the ethical treatment of animals during the study were strictly followed.

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The authors declare that they have no conflict of interest.

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Vineeth, M.R., Surya, T., Sivalingam, J. et al. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod 52, 1707–1715 (2020). https://doi.org/10.1007/s11250-019-02180-x

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  • DOI: https://doi.org/10.1007/s11250-019-02180-x

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