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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #411184
Research Project: Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

Title: A million-cow validation of a chromosome 14 region interacting with all chromosomes for fat percentage in U.S. Holstein cows

Author
item PRAKAPENKA, DZIANIS - University Of Minnesota
item LIANG, ZUOXIANG - University Of Minnesota
item ZAABZA, HAFEDH - University Of Vermont
item JIANG, JICAI - North Carolina State University
item MA, LI - University Of Maryland
item Vanraden, Paul
item Van Tassell, Curtis - Curt
item DA, YANG - University Of Minnesota

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/2/2024
Publication Date: 1/4/2024
Citation: Prakapenka, D., Liang, Z., Zaabza, H.B., Jiang, J., Ma, L., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. A million-cow validation of a chromosome 14 region interacting with all chromosomes for fat percentage in U.S. Holstein cows. International Journal of Molecular Sciences. 25:674. https://doi.org/10.3390/ijms25010674.
DOI: https://doi.org/10.3390/ijms25010674

Interpretive Summary: Statistical tests of 75,198 genetic markers using milk production data for over 1.2 million Holstein cows confirmed that a region on chromosome 14 known to have highly significant allelic effects for fat percentage (FPC) interacted with all chromosomes for FPC. Many new results were revealed including interactions between the region on 14 and a region on chromosome 6 that was known to have highly significant effects for some production, reproduction, and health traits. This study used an unprecedentedly large sample and provided high confidence evidence that the region of chromosome 14 known to have highly significant allelic effects for FPC also had the largest allele by allele interactions across the genome.

Technical Abstract: A genome-wide association study (GWAS) of fat percentage (FPC) using 1,231,898 first lactation cows and 75,198 SNPs confirmed a previous result that a Chr14 region about 9.38 Mb region in size (0.14-9.52 Mb) had significant inter-chromosome additive × additive (A×A) effects with all chromosomes and revealed many new such effects. This study divides this 9.38 Mb into two sub-regions, Chr14a at 0.14-0.88 Mb (0.74 Mb in size) with 78% and Chr14b at 2.21-9.52 Mb (7.31 Mb in size) with 22% of the 2761 significant A×A effects. These two sub-regions were separated by a 1.3 Mb gap at 0.9-2.2 Mb without significant inter-chromosome A×A effects. The SLC4A4-GC-NPFFR2 (SGN) region of Chr06 only interacted with the 465-831 Kb region containing PPP1R16A, FOXH1, CYHR1, TONSL (PFCT), CPSF1, ADCK5, SLC52A2, DGAT1, SMPD5 and PARP10 (CASDSP) known to have highly significant additive effects for milk production traits, and the SGN region of Chr06 was known to have highly significant additive effects for some production, fertility and health traits. The most significant effects were between a SNP in GC-NPFFR2 and four SNPs in PFCT, which had the largest cluster of A×A effects with all chromosomes. The CASDSP region mostly interacted with the SGN region. The 2.28-2.42 Mb region (138.46 Kb in size) in Chr14b lacking coding genes had the largest cluster of A×A effects interacting with seventeen chromosomes. Results from this study provided high-confidence evidence towards the understanding of the genetic mechanism of FPC in Holstein cows.