西门塔尔牛饱和脂肪酸含量的低密度芯片基因组预测

Genomic Prediction for Saturated Fatty Acid Content in Simmental using Low Density Chip

旨在探索低密度芯片标记的筛选方法并评估不同低密度芯片的准确性。本研究采用BovineHD高密度芯片,检测西门塔尔牛基因组的SNP位点及其与饱和脂肪酸含量的关联性,根据P值或效应值筛选标记构成低密度芯片,使用IBS聚类分组和随机分组进行交叉验证,估计基因组育种值并评估其准确性。结果表明,在14号染色体的MYC基因附近有5个位点与饱和脂肪酸性状显著相关,可考虑作为西门塔尔牛脂肪酸含量的候选基因进行后续研究。根据P值筛选标记并使用IBS聚类分组进行交叉验证时,估计基因组育种值准确性最高,芯片密度达到7K时准确性趋于稳定。因此,本研究发现的标记位点可能对西门塔尔牛的脂肪酸含量存在一定影响,并且为低密度芯片标记位点的筛选提供参考资料。

The objective of this study was to explore methods of selection markers and evaluate accuracies of low density（LD）chips.SNPs associated with saturated fatty acid（SFA）content were identified using BovineHD panel and genomic breeding value was evaluated using LD panels which were markers selected on the basis of P-value or effect value on Simmental bulls.Then we evaluated accuracy of genomic prediction via cross-validation（CV）methodologies based on identical by state（IBS）and random sample.A total of 5SNPs were associated with SFA and adjacent to MYC gene on BTA14,which could be considered as candidate genes.Prediction was the most accurate when markers were selected on the basis of P-value and CV was IBS-based.The accuracy of genomic value in 7 000 SNPs panel was steady.In conclusion,this study identified several SNPs associated with SFA and provided reference for marker selection in LD panels for further study.