Effects of ROH-based versus GRM-based future inbreeding penalties on genetic gain, variance components, and inbreeding depression in dairy cattle.

基本信息

• 作者：C Maltecca; J Jiang; J B Cole; C F Baes; L Ma; F Tiezzi
• DOI：10.3168/jds.2026-28483
• 原文链接：https://doi.org/10.3168/jds.2026-28483
• 数据来源：pubmed:pubmed-jds
• 抓取时间：2026-05-30T18:53:27+00:00
• Markdown 文件：/root/worksplace/paper-tracker/exports/obsidian/2026-05-09-effects-of-roh-based-versus-grm-based-future-inbreeding-penalties-on-genetic-gain,-variance-components,-and-i.md

摘要

Managing inbreeding while maintaining genetic gain is a critical challenge in dairy cattle breeding programs. Current North American genetic evaluations adjust breeding values for expected future inbreeding using genomic relationship matrix (GRM) approaches, but runs of homozygosity (ROH)-based methods may offer advantages for detecting recent autozygosity. This study compared ROH-based versus GRM-based inbreeding penalties across 20 generations of simulated genomic selection. Using AlphaSimR, we simulated dairy cattle populations under 3 genetic scenarios: additive only, low non-additive effects (σ 2 D/σ 2 A = 0.10, inbreeding depression = 0.30σG per 10% ΔF), and high non-additive effects (σ 2 D/σ 2 A = 0.50, inbreeding depression = 1.20σG per 10% ΔF). Each penalty method was tested at 3 intensities (0.5 ×, 1 ×, 2 × the inbreeding depression parameter) with 10 replicates per scenario-treatment combination. GRM-based penalties achieved lower inbreeding accumulation than ROH-based penalties, with differences of 0.13 to 0.22 in genomic F at matched penalty intensities. However, this enhanced inbreeding control was associated with reduced genetic gain, with GRM-based selection achieving 0.6 to 1.7 genetic standard deviations less gain than ROH-based selection. GRM-based selection retained more additive variance (66-107%) compared with ROH-based selection (63-74%), with values exceeding 100% indicating partial recovery of variance depleted during burn-in. Dominance variance retention was also greater for GRM-based selection (105-114% vs. 93-98%), reflecting maintained heterozygosity. Interestingly, GRM-based selection accumulated more inbreeding depression than ROH-based approaches despite lower inbreeding levels, potentially reflecting more effective purging under the stronger directional selection maintained by ROH-based methods. Results illustrate trade-offs between inbreeding control and genetic gain, with optimal strategy depending on breeding program objectives and trait genetic architecture.

中文整理

基础摘要（未启用或未成功调用大模型）：Managing inbreeding while maintaining genetic gain is a critical challenge in dairy cattle breeding programs. Current North American genetic evaluations adjust breeding values for expected future inbreeding using genomic relationship matrix (GRM) approaches, but runs of homozygosity (ROH)-based methods may offer advantages for detecting recent autozygosity. This study compared ROH-based versus GRM-based inbreeding penalties across 20 generations of simulated genomic selection. Using AlphaSimR, we simulated dairy cattle populations under 3 genetic scenarios: additive only, low non-additive effects (σ 2 D/σ 2 A = 0.10, inbreeding depression = 0.30σG per 10% ΔF), and high non-additive effects (

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命中 奶牛/牛只 关键词：cattle；命中 深度学习 关键词：detect