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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 #415292
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: Large-sample genome-wide association study of resistance to retained placenta in U.S. Holstein cows

Author
item PRAKAPENKA, DZIANIS - University Of Minnesota
item LIANG, ZUOXIANG - University Of Minnesota
item ZAABZA, HAFEDH - Collaborator
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: 5/18/2024
Publication Date: 5/20/2024
Citation: Prakapenka, D., Liang, Z., Zaabza, H.B., Van Raden, P.M., Van Tassell, C.P., Da, Y. 2024. Large-sample genome-wide association study of resistance to retained placenta in U.S. Holstein cows. International Journal of Molecular Sciences. 25(10):5551. https://doi.org/10.3390/ijms25105551.
DOI: https://doi.org/10.3390/ijms25105551

Interpretive Summary: Retained placenta in dairy cattle refers to the failure of timely separation of the placenta from the dam after calving, and this disease causes a direct economic loss and related problems in health and fertility in U.S. Holstein cattle. The large samples of Holstein genomic evaluation data provided unprecedented opportunity to identify genetic factors affecting retained placenta in Holstein. Utilizing over six hundred thousand cows, this study identified genetic factors affecting retained placenta. The results of this study provided high-confidence evidence for the understanding of genetic factors affecting retained placenta.

Technical Abstract: A genome-wide association study of resistance to retained placenta (RETP) using 632,212 Holstein cows and 74,747 SNPs identified 200 additive effects with p-values < 10-8 on thirteen chromosomes but no dominance effect was statistically significant. The regions of 87.61-88.74 Mb of Chr09 about 1.13 Mb in size had the most significant effect in LOC112448080 and other highly significant effects in CCDC170 and ESR1, and in or near RMND1 and AKAP12. Four non-ESR1 genes in this region were reported to be involved in ESR1 fusions in humans. Chr23 had the largest number of sig-nificant effects that peaked in SLC17A1, which was involved in urate metabolism and transport that could contribute to kidney disease. The PKHD1 gene contained seven significant effects and was downstream of another six significant effects. The ACOT13 gene also had a highly significant effect. Both PKHD1 and ACOT13 were associated with kidney disease. Another highly significant effect was upstream of BOLA-DQA2. The KITLG gene of Chr05 that acts in utero in germ cell and neural cell development, and hematopoiesis was upstream of a highly significant effect, contained a sig-nificant effect, and was between another two significant effects. The results of this study pro-vided new understanding of genetic factors underlying RETP in U.S. Holstein cows.