Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins.

Autor: Seabury CM; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA., Smith JL; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA., Wilson ML; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA., Bhattarai E; Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA., Santos JEP; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA., Chebel RC; Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA., Galvão KN; Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA., Schuenemann GM; Department of Veterinary Preventative Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA., Bicalho RC; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA., Gilbert RO; Department of Clinical Sciences, School of Veterinary Medicine, Ross University, St. Kitts, West Indies, KN., Rodriguez-Zas SL; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL 61801, USA., Rosa G; Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA., Thatcher WW; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA., Pinedo PJ; Department of Animal Sciences, Colorado State University, Fort Collins, CO 80521, USA.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2023 Aug 30; Vol. 13 (9).
DOI: 10.1093/g3journal/jkad043
Abstrakt: Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination (AI) with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein cows and produce genomic heritability estimates. Moreover, we use genomic best linear unbiased prediction (GBLUP) to investigate the potential utility of the RI by performing genomic predictions with cross validation. Notably, genomic heritability estimates for the U.S. Holstein RI were moderate (h2 = 0.1654 ± 0.0317-0.2550 ± 0.0348), while single and multi-locus GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29, including the known QTL for the daughter pregnancy rate (DPR) and cow conception rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR) QTL (59 Mb). Positional candidate genes for the detected QTL included male and female fertility loci (i.e. spermatogenesis and oogenesis), meiotic and mitotic regulators, and genes associated with immune response, milk yield, enhanced pregnancy rates, and the reproductive longevity pathway. Based on the proportion of the phenotypic variance explained (PVE), all detected QTL (n = 13; P ≤ 5e - 05) were estimated to have moderate (1.0% < PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted probability of pregnancy. Genomic prediction using GBLUP with cross validation (k = 3) produced mean predictive abilities (0.1692-0.2301) and mean genomic prediction accuracies (0.4119-0.4557) that were similar to bovine health and production traits previously investigated.
Competing Interests: Conflicts of interest The authors declare no competing interests.
(© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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