Department of Animal Sciences, Shahrekord University, Shahrekord, Iran.
Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do, Korea.
PLoS One. 2019 Oct 14;14(10):e0223352. doi: 10.1371/journal.pone.0223352. eCollection 2019.
Hanwoo, an important indigenous and popular breed of beef cattle in Korea, shows rapid growth and has high meat quality. Its yearling weight (YW) and carcass traits (backfat thickness, carcass weight- CW, eye muscle area, and marbling score) are economically important for selection of young and proven bulls. However, measuring carcass traits is difficult and expensive, and can only be performed postmortem. Genomic selection has become an appealing procedure for genetic evaluation of these traits (by inclusion of the genomic data) along with the possibility of multi-trait analysis. The aim of this study was to compare conventional best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP) methods, using both single-trait (ST-BLUP, ST-ssGBLUP) and multi-trait (MT-BLUP, MT-ssGBLUP) models to investigate the improvement of breeding-value accuracy for carcass traits and YW. The data comprised of 15,279 phenotypic records for YW and 5,824 records for carcass traits, and 1,541 genotyped animals for 34,479 single-nucleotide polymorphisms. Accuracy for each trait and model was estimated only for genotyped animals by five-fold cross-validation. ssGBLUP models (ST-ssGBLUP and MT-ssGBLUP) showed ~19% and ~36% greater accuracy than conventional BLUP models (ST-BLUP and MT-BLUP) for YW and carcass traits, respectively. Within ssGBLUP models, the accuracy of the genomically estimated breeding value for CW increased (19%) when ST-ssGBLUP was replaced with the MT-ssGBLUP model, as the inclusion of YW in the analysis led to a strong genetic correlation with CW (0.76). For backfat thickness, eye muscle area, and marbling score, ST- and MT-ssGBLUP models yielded similar accuracy. Thus, combining pedigree and genomic data via the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions, especially among young animals, for ongoing Hanwoo cattle breeding programs. MT-ssGBLUP is highly recommended when phenotypic records are limited for one of the two highly correlated genetic traits.
韩牛是韩国重要的本土牛种,具有生长速度快、肉质好的特点。其周岁体重(yearling weight,YW)和胴体性状(背膘厚、胴体重 carcass weight,CW、眼肌面积和大理石花纹评分)对青年牛和经产牛公牛的选择具有重要的经济意义。然而,测量胴体性状既困难又昂贵,而且只能在死后进行。基因组选择已成为这些性状遗传评估的一种有吸引力的方法(通过包含基因组数据),同时也有可能进行多性状分析。本研究旨在比较传统最佳线性无偏预测(BLUP)和一步法基因组 BLUP(ssGBLUP)方法,使用单性状(ST-BLUP、ST-ssGBLUP)和多性状(MT-BLUP、MT-ssGBLUP)模型,研究对胴体性状和 YW 进行育种值准确性的提高。数据包括 15279 个 YW 表型记录和 5824 个胴体性状记录,以及 1541 个基因型动物的 34479 个单核苷酸多态性。通过五重交叉验证仅对基因型动物估计每个性状和模型的准确性。ssGBLUP 模型(ST-ssGBLUP 和 MT-ssGBLUP)分别比传统 BLUP 模型(ST-BLUP 和 MT-BLUP)对 YW 和胴体性状的准确性高约 19%和 36%。在 ssGBLUP 模型中,当用 MT-ssGBLUP 模型代替 ST-ssGBLUP 模型时,CW 的基因组估计育种值的准确性提高了(19%),因为 YW 分析的纳入与 CW 之间存在很强的遗传相关性(0.76)。对于背膘厚、眼肌面积和大理石花纹评分,ST-和 MT-ssGBLUP 模型的准确性相似。因此,通过 ssGBLUP 模型结合系谱和基因组数据可能是一种有前途的方法,可以确保韩牛育种计划中持续进行的预测具有可接受的准确性,特别是在年轻动物中。当两个高度相关的遗传性状之一的表型记录有限时,强烈推荐使用 MT-ssGBLUP。