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GWAS and gene networks for milk-related traits from test-day multiple lactations in Portuguese Holstein cattle

  • Animal Genetics • Original Paper
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Abstract

This study focused on the identification of QTL regions, candidate genes, and network related genes based on the first 3 lactations (LAC3) of milk, fat, and protein yields, and somatic cell score (SCS) in Portuguese Holstein cattle. Additionally, the results were compared with those from only first lactation (LAC1) data. The analyses were performed using the weighted single-step GWAS under an autoregressive test-day (TD) multiple lactations model. A total of 11,434,294 and 4,725,673 TD records from LAC3 and LAC1, respectively, including 38,323 autosomal SNPs and 1338 genotyped animals were used in GWAS analyses. A total of 51 (milk), 5 (fat), 24 (protein), and 4 (SCS) genes were associated to previously annotated relevant QTL regions for LAC3. The CACNA2D1 at BTA4 explained the highest proportion of genetic variance respectively for milk, fat, and protein yields. For SCS, the TRNAG-CCC at BTA14, MAPK10, and PTPN3 genes, both at BTA6 were considered important candidate genes. The accessed network refined the importance of the reported genes. CACNA2D1 regulates calcium density and activation/inactivation kinetics of calcium transport in the mammary gland; whereas TRNAG-CCC, MAPK10, and PTPN3 are directly involved with inflammatory processes widely derived from mastitis. In conclusion, potential candidate genes (TRNAG-CCC, MAPK10, and PTPN3) associated with somatic cell were highlighted, which further validation studies are needed to clarify its mechanism action in response to mastitis. Moreover, most of the candidate genes identified were present in both (LAC3 and LAC1) for milk, fat and protein yields, except for SCS, in which no candidate genes were shared between LAC3 and LAC1. The larger phenotypic information provided by LAC3 dataset was more effective to identify relevant genes, providing a better understanding of the genetic architecture of these traits over all lactations simultaneously.

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Acknowledgments

The authors acknowledge Portuguese Dairy Cattle Breeders Association (ANABLE) and Embrapa Dairy Cattle for providing the used data. We also thank Dr. Hinayah R. Oliveira (Department of Animal Sciences, Purdue University) for her valuable and constructive suggestions.

Funding

This study was partially financed by CAPES/FCT (99999.008462/2014-03) and CNPq/INCT-CA.

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Authors and Affiliations

  1. Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil

    Alessandra Alves Silva, Delvan Alves Silva, Fabyano Fonseca Silva, Hugo Teixeira Silva, Paulo Sávio Lopes & Renata Veroneze

  2. Embrapa Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil

    Cláudio Napolis Costa

  3. Research Center in Biodiversity and Genetic Resources (CIBIO-InBio), University of Porto, Vairão, Porto, Portugal

    Gertrude Thompson & Julio Carvalheira

  4. Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal

    Gertrude Thompson & Julio Carvalheira

Authors
  1. Alessandra Alves Silva
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  2. Delvan Alves Silva
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  3. Fabyano Fonseca Silva
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  4. Cláudio Napolis Costa
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  5. Hugo Teixeira Silva
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  6. Paulo Sávio Lopes
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  7. Renata Veroneze
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  8. Gertrude Thompson
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  9. Julio Carvalheira
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Contributions

AA Silva designed the study, performed the statistical analysis, interpreted the results, and wrote the manuscript. DA Silva, HT Silva, CN Costa, PS Lopes, R Veroneze, and G Thompson interpreted the results and revised the manuscript. J Carvalheira and FF Silva supervised all stages of this work. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Julio Carvalheira.

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Conflict of interest

The authors declare that they have no conflict of interests.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. The approval’s register of the Ethics Committee on the Use of Animal at the Universidade Federal de Viçosa is 001/2017.

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Communicated by: Maciej Szydlowski

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Fig. S1

GWAS results of milk production traits for the first lactation (LAC1). a milk yield, and b fat yield. Each dot represents one SNP window of 100 kb. On the y-axis is the chromosomes (Chr) (PDF 192 kb)

Fig. S2

GWAS results of milk production traits for the first lactation (LAC1). a protein yield, and b somatic cell score (SCS). Each dot represents one SNP window of 100 kb. On the y-axis is the chromosomes (Chr) (PDF 250 kb)

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Silva, A.A., Silva, D.A., Silva, F.F. et al. GWAS and gene networks for milk-related traits from test-day multiple lactations in Portuguese Holstein cattle. J Appl Genetics 61, 465–476 (2020). https://doi.org/10.1007/s13353-020-00567-3

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