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A genome-wide approach to screen for genetic variants in broilers (Gallus gallus) with divergent feed conversion ratio

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Abstract

Feed conversion ratio (FCR) is an economically important trait in broilers and feed accounts for a significant proportion of the costs involved in broiler production. To explore the contribution of functional variants to FCR trait, we analyzed coding and non-coding single-nucleotide variants (SNVs) across the genome by exome sequencing in seven pairs of full-sibs broilers with divergent FCR and with a sequence coverage at an average depth of fourfold. We identified 192,119 high-quality SNVs, including 30,380 coding SNVs (cSNVs) in the experimental population. We discovered missense SNVs in PGM2, NOX4, TGFBR3, and TMX4, and synonymous SNVs in TSNAX, ITA, HSP90B1, and COL18A1 associated with FCR. Haplotype analyses of genome-wide significant SNVs in PGM2, PHKG1, DGKZ, and SOD2 were also observed with suggestive evidence of haplotype association with FCR. Single-variant and FCR QTL-related genes-based association analyses of SNVs identified newly associated genes for FCR in the regions subjected to targeted exome sequencing. The top seven SNVs were next evaluated in independent replication data sets where SNV chr. 3: 13,990,160 (c. 961G>C) at TMX4 was replicated (p < 0.05). Collectively, we have detected SNVs associated with FCR in broiler as well as identification of SNVs in known FCR QTL region. These findings should facilitate the discovery of causative variants for FCR and contribute to marker-assisted selection.

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Abbreviations

BWG:

Body weight gain

CAPS:

Cleaved amplified polymorphic sequences

DHS:

DNase I–hypersensitive sites

ENCODE:

Encyclopedia of DNA Elements

EWAS:

Exome wide association study

FCR:

Feed conversion ratio

FI:

Feed intake

GWAS:

Genome-wide association study

SNV:

Single-nucleotide variation

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Acknowledgments

This study was funded by Department of Biotechnology (BT/PR15360/AAQ/01/466/2011), Ministry of Science and Technology, Government of India, India. We thank Indian Agricultural Statistics Research Institute (IASRI) for providing license of SAS and JMP Genomics software used in the current study. We thank Dr. Amrutlal K. Patel and Dr. Ramesh Menon for critical reading of manuscript and helpful suggestions.

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Authors and Affiliations

  1. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, 388 001, Gujarat, India

    Tejas M. Shah, Namrata V. Patel, Anand B. Patel, Maulik R. Upadhyay, Amitbikram Mohapatra & Chaitanya G. Joshi

  2. Marshall Breeder Pvt. Ltd., Nasik, 422 001, Maharashtra, India

    Krishna M. Singh & Sunil D. Deshpande

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  1. Tejas M. Shah
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  2. Namrata V. Patel
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  4. Maulik R. Upadhyay
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  5. Amitbikram Mohapatra
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  8. Chaitanya G. Joshi
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Correspondence to Chaitanya G. Joshi.

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The authors declare that they have no competing interests.

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All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

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Communicated by S. Hohmann.

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Shah, T.M., Patel, N.V., Patel, A.B. et al. A genome-wide approach to screen for genetic variants in broilers (Gallus gallus) with divergent feed conversion ratio. Mol Genet Genomics 291, 1715–1725 (2016). https://doi.org/10.1007/s00438-016-1213-0

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