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Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows

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Genotype and Environment contributing to the sustainability of dairy cow production systems through the optimal integration of genomic selection and novel management protocols based on the development
Abstract
The aim of this study was to identify genomic regions associated with 305-day milk yield and lactation curve parameters on primiparous (n = 9,910) and multiparous (n = 11,158) Holstein cows. The SNP solutions were estimated using a weighted single-step genomic BLUP approach and imputed high-density panel (777k) genotypes. The proportion of genetic variance explained by windows of 50 consecutive SNP (with an average of 165 Kb) was calculated, and regions that accounted for more than 0.50% of the variance were used to search for candidate genes. Estimated heritabilities were 0.37, 0.34, 0.17, 0.12, 0.30 and 0.19, respectively, for 305-day milk yield, peak yield, peak time, ramp, scale and decay for primiparous cows. Genetic correlations of 305-day milk yield with peak yield, peak time, ramp, scale and decay in primiparous cows were 0.99, 0.63, 0.20, 0.97 and -0.52, respectively. The results identified three windows on BTA14 associated with 305-day milk yield and the parameters of lactation curve in primi- and multiparous cows. Previously proposed candidate genes for milk yield supported by this work include GRINA, CYHR1, FOXH1, TONSL, PPP1R16A, ARHGAP39, MAF1, OPLAH and MROH1, whereas newly identified candidate genes are MIR2308, ZNF7, ZNF34, SLURP1, MAFA and KIFC2 (BTA14). The protein lipidation biological process term, which plays a key role in controlling protein localization and function, was identified as the most important term enriched by the identified genes.
Keywords
genome-wide association study, Holstein, lactation curve, milk yield, QUANTITATIVE TRAIT LOCI, SOMATIC-CELL SCORE, GENETIC-PARAMETERS, CATTLE, YIELD, SHAPE, QTL, PERSISTENCY, PREDICTIONS, ENRICHMENT

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Citation

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MLA
Atashi, Hadi, et al. “Genome-Wide Association for Milk Production and Lactation Curve Parameters in Holstein Dairy Cows.” JOURNAL OF ANIMAL BREEDING AND GENETICS, 2020.
APA
Atashi, H., Salavati, M., De Koster, J., Ehrlich, J., Crowe, M., Opsomer, G., … Hostens, M. (2020). Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows. JOURNAL OF ANIMAL BREEDING AND GENETICS.
Chicago author-date
Atashi, Hadi, Mazdak Salavati, Jenne De Koster, Jim Ehrlich, Mark Crowe, Geert Opsomer, Niamh McLoughlin, et al. 2020. “Genome-Wide Association for Milk Production and Lactation Curve Parameters in Holstein Dairy Cows.” JOURNAL OF ANIMAL BREEDING AND GENETICS.
Chicago author-date (all authors)
Atashi, Hadi, Mazdak Salavati, Jenne De Koster, Jim Ehrlich, Mark Crowe, Geert Opsomer, Niamh McLoughlin, Alan Fahey, Elizabeth Matthews, Andreia Santoro, Colin Byrne, Pauline Rudd, Roisin O’Flaherty, Sinead Hallinan, Claire Wathes, Zhangrui Cheng, Ali Fouladi, Geoff Pollott, Dirk Werling, Beatriz Sanz Bernardo, Alistair Wylie, Matt Bell, Mieke Van Eetvelde, Kristof Hermans, Geert Opsomer, Sander Moerman, Jenne De Koster, Hannes Bogaert, Jan Vandepitte, Leila Vande Velde, Bonifacius Van Ranst, Johanna Hoglund, Susanne Dahl, Soren Ostergaard, Janne Rothmann, Mogens Krogh, Else Meyer, Charlotte Gaillard, Jehan Ettema, Tine Rousing, Federica Signorelli, Francesco Napolitano, Bianca Moioli, Alessandra Crisa, Luca Buttazzoni, Jennifer McClure, Daragh Matthews, Francis Kearney, Andrew Cromie, Matt McClure, Shujun Zhang, Xing Chen, Huanchun Chen, Junlong Zhao, Liguo Yang, Guohua Hua, Chen Tan, Guiqiang Wang, Michel Bonneau, Andrea Pompozzi, Armin Pearn, Arnold Evertson, Linda Kosten, Anders Fogh, Thomas Andersen, Matthew Lucey, Chris Elsik, Gavin Conant, Jerry Taylor, Nicolas Gengler, Michel Georges, Frederic Colinet, Marilou Ramos Pamplona, Hedi Hammami, Catherine Bastin, Haruko Takeda, Aurelie Laine, Anne-Sophie Van Laere, Martin Schulze, Sergio Palma Vera, Conrad Ferris, Cinzia Marchitelli, and Miel Hostens. 2020. “Genome-Wide Association for Milk Production and Lactation Curve Parameters in Holstein Dairy Cows.” JOURNAL OF ANIMAL BREEDING AND GENETICS.
Vancouver
1.
Atashi H, Salavati M, De Koster J, Ehrlich J, Crowe M, Opsomer G, et al. Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows. JOURNAL OF ANIMAL BREEDING AND GENETICS. 2020;
IEEE
[1]
H. Atashi et al., “Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows,” JOURNAL OF ANIMAL BREEDING AND GENETICS, 2020.
@article{8633086,
  abstract     = {The aim of this study was to identify genomic regions associated with 305-day milk yield and lactation curve parameters on primiparous (n = 9,910) and multiparous (n = 11,158) Holstein cows. The SNP solutions were estimated using a weighted single-step genomic BLUP approach and imputed high-density panel (777k) genotypes. The proportion of genetic variance explained by windows of 50 consecutive SNP (with an average of 165 Kb) was calculated, and regions that accounted for more than 0.50% of the variance were used to search for candidate genes. Estimated heritabilities were 0.37, 0.34, 0.17, 0.12, 0.30 and 0.19, respectively, for 305-day milk yield, peak yield, peak time, ramp, scale and decay for primiparous cows. Genetic correlations of 305-day milk yield with peak yield, peak time, ramp, scale and decay in primiparous cows were 0.99, 0.63, 0.20, 0.97 and -0.52, respectively. The results identified three windows on BTA14 associated with 305-day milk yield and the parameters of lactation curve in primi- and multiparous cows. Previously proposed candidate genes for milk yield supported by this work include GRINA, CYHR1, FOXH1, TONSL, PPP1R16A, ARHGAP39, MAF1, OPLAH and MROH1, whereas newly identified candidate genes are MIR2308, ZNF7, ZNF34, SLURP1, MAFA and KIFC2 (BTA14). The protein lipidation biological process term, which plays a key role in controlling protein localization and function, was identified as the most important term enriched by the identified genes.},
  author       = {Atashi, Hadi and Salavati, Mazdak and De Koster, Jenne and Ehrlich, Jim and Crowe, Mark and Opsomer, Geert and McLoughlin, Niamh and Fahey, Alan and Matthews, Elizabeth and Santoro, Andreia and Byrne, Colin and Rudd, Pauline and O'Flaherty, Roisin and Hallinan, Sinead and Wathes, Claire and Cheng, Zhangrui and Fouladi, Ali and Pollott, Geoff and Werling, Dirk and Bernardo, Beatriz Sanz and Wylie, Alistair and Bell, Matt and Van Eetvelde, Mieke and Hermans, Kristof and Opsomer, Geert and Moerman, Sander and De Koster, Jenne and Bogaert, Hannes and Vandepitte, Jan and Vande Velde, Leila and Van Ranst, Bonifacius and Hoglund, Johanna and Dahl, Susanne and Ostergaard, Soren and Rothmann, Janne and Krogh, Mogens and Meyer, Else and Gaillard, Charlotte and Ettema, Jehan and Rousing, Tine and Signorelli, Federica and Napolitano, Francesco and Moioli, Bianca and Crisa, Alessandra and Buttazzoni, Luca and McClure, Jennifer and Matthews, Daragh and Kearney, Francis and Cromie, Andrew and McClure, Matt and Zhang, Shujun and Chen, Xing and Chen, Huanchun and Zhao, Junlong and Yang, Liguo and Hua, Guohua and Tan, Chen and Wang, Guiqiang and Bonneau, Michel and Pompozzi, Andrea and Pearn, Armin and Evertson, Arnold and Kosten, Linda and Fogh, Anders and Andersen, Thomas and Lucey, Matthew and Elsik, Chris and Conant, Gavin and Taylor, Jerry and Gengler, Nicolas and Georges, Michel and Colinet, Frederic and Pamplona, Marilou Ramos and Hammami, Hedi and Bastin, Catherine and Takeda, Haruko and Laine, Aurelie and Van Laere, Anne-Sophie and Schulze, Martin and Vera, Sergio Palma and Ferris, Conrad and Marchitelli, Cinzia and Hostens, Miel},
  issn         = {0931-2668},
  journal      = {JOURNAL OF ANIMAL BREEDING AND GENETICS},
  keywords     = {genome-wide association study,Holstein,lactation curve,milk yield,QUANTITATIVE TRAIT LOCI,SOMATIC-CELL SCORE,GENETIC-PARAMETERS,CATTLE,YIELD,SHAPE,QTL,PERSISTENCY,PREDICTIONS,ENRICHMENT},
  language     = {eng},
  title        = {Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows},
  url          = {http://dx.doi.org/10.1111/jbg.12442},
  year         = {2020},
}

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