A large-scale genome-wide association study of epistasis effects of production traits and daughter pregnancy rate in u.S. holstein cattle

Dzianis Prakapenka; Zuoxiang Liang; Jicai Jiang; Li Ma; Yang Da

doi:10.3390/genes12071089

A large-scale genome-wide association study of epistasis effects of production traits and daughter pregnancy rate in u.S. holstein cattle

Dzianis Prakapenka, Zuoxiang Liang, Jicai Jiang, Li Ma, Yang Da

Animal Science

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.

Original language	English (US)
Article number	1089
Journal	Genes
Volume	12
Issue number	7
DOIs	https://doi.org/10.3390/genes12071089
State	Published - Jul 2021

Bibliographical note

Funding Information:
Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals”, and USDA-ARS project 8042-31000-001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection”. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities.

Funding Information:
Funding: This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota.

Funding Information:
This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, ?Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals?, and USDA-ARS project 8042-31000-001-00-D, ?Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection?. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

Epistasis
Fertility
GWAS
Milk production

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title = "A large-scale genome-wide association study of epistasis effects of production traits and daughter pregnancy rate in u.S. holstein cattle",

abstract = "Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.",

keywords = "Epistasis, Fertility, GWAS, Milk production",

author = "Dzianis Prakapenka and Zuoxiang Liang and Jicai Jiang and Li Ma and Yang Da",

note = "Funding Information: Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals”, and USDA-ARS project 8042-31000-001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection”. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities. Funding Information: Funding: This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. Funding Information: This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, ?Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals?, and USDA-ARS project 8042-31000-001-00-D, ?Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection?. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

year = "2021",

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doi = "10.3390/genes12071089",

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AU - Jiang, Jicai

AU - Ma, Li

AU - Da, Yang

N1 - Funding Information: Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals”, and USDA-ARS project 8042-31000-001-00-D, “Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection”. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities. Funding Information: Funding: This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. Funding Information: This research was supported by grants 2018-67015-28128, 2020-67015-31133 and 2020-67015-31398 from the USDA National Institute of Food and Agriculture, and by project MIN-16-124 of the Agricultural Experiment Station at the University of Minnesota. Acknowledgments: Members of the Council on Dairy Cattle Breeding (CDCB) and the Cooperative Dairy DNA Repository (CDDR) are acknowledged for providing the data for the GWAS analysis. The Ceres high performance computing system of USDA-ARS provided computing time and storage for the data analysis. Data access and the use of USDA-ARS computing facilities by this research were supported by USDA-ARS project 8042-31000-002-00-D, ?Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals?, and USDA-ARS project 8042-31000-001-00-D, ?Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection?. The USDA is an equal opportunity provider and employer. Mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by USDA. The authors thank Paul VanRaden for help with data preparation, and John Cole, Steven Schroeder and Ransom Baldwin for help with using the USDA-ARS computing facilities. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

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N2 - Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.

AB - Epistasis is widely considered important, but epistasis studies lag those of SNP effects. Genome-wide association study (GWAS) using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits: milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FPC), protein percentage (PPC), and daughter pregnancy rate (DPR). Among the top 50,000 pairwise epistasis effects of each trait, the five production traits had large chromosome regions with intra-chromosome epistasis. The percentage of inter-chromosome epistasis effects was 1.9% for FPC, 1.6% for PPC, 10.6% for MY, 29.9% for FY, 39.3% for PY, and 84.2% for DPR. Of the 50,000 epistasis effects, the number of significant effects with log10(1/p) ≥ 12 was 50,000 for FPC and PPC, and 10,508, 4763, 4637 and 1 for MY, FY, PY and DPR, respectively, and A × A effects were the most frequent epistasis effects for all traits. Majority of the inter-chromosome epistasis effects of FPC across all chromosomes involved a Chr14 region containing DGAT1, indicating a potential regulatory role of this Chr14 region affecting all chromosomes for FPC. The epistasis results provided new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.

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DO - 10.3390/genes12071089

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ER -

A large-scale genome-wide association study of epistasis effects of production traits and daughter pregnancy rate in u.S. holstein cattle

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