利用高密度SNP标记分析中国荷斯坦牛基因组近交

Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle

畜禽育种中传统上利用系谱信息评估群体近交程度?近年来随着高通量单核苷酸多态(single nucleotide polymorphism,SNP)检测成本降低,使利用基因组信息分析真实的基因组近交程度成为可能?本研究利用牛54 K SNP芯片数据统计了北京地区2107头荷斯坦牛基因组上的长纯合片段(runs of homozygosity,ROH)的频率和分布,计算了2种基因组近交系数,即染色体上ROH的长度占基因组总长度的比例(Froh)及个体所有标记基因型中纯合子所占比例,即基因组纯合度(Fhom),进而分析了两种基因组近交系数之间的相关性以及基因组近交与系谱近交系数之间的相关性?结果表明,共检测到44 676个ROH片段,其长度主要分布在1~10 Mb之间?不同长度的ROH散布于个体基因组内,短ROH较长ROH更为常见?ROH在染色体上并非均匀分布,ROH频率最高的区域为10号染色体中部?两种基因组近交系数之间相关性很高(91%以上),但基因组近交与系谱近交之间的相关性较低(低于50%)?系谱完整性是影响基因组近交与系谱近交结果一致的重要因素,基因组近交系数能够反映个体真实的近交,本研究为评估群体近交水平提供了有力工具?

In livestock, inbreeding coefficient based on pedigree information is usually used to evaluate the level of inbreeding. Recently, with cost reduction of high-density SNP genotyping, it＇s possible to analyze real genomic inbreeding degree using genomic information. In this study, utilizing high-density SNP chip data, we analyzed the fre-quency and distribution of runs of homozygosity（ROH） in 2107 Chinese Holstein cattle in Beijing area, and calculated 2 genomic inbreeding coefficients, i.e., 1） the proportion of ROH length in the total length of autosomal genome（Froh）, and 2） the percentage of homozygous SNPs（Fhom）. Then we analyzed the correlation between 2 genomic inbreeding coefficients and the correlation between genomic and pedigree inbreeding coefficients. We totally detected 44 676 ROHs that mainly ranged from 1 to 10 Mb. Various lengths of ROHs existed in the genome. There were more short ROHs than long ROHs. ROHs aren＇t evenly distributed in chromosomes. The area with most ROHs is in the middle part of chromosome 10. Strong correlation（r〉0.90） existed between 2 kinds of genomic inbreeding coefficients, but the correlation between pedigree and genomic inbreeding coefficients were much lower（r 0.50）. Our finding suggests that pedigree completeness influences the correlation between genomic and pedigree inbreeding. Genomic inbreeding measures may reflect individuals＇ real inbreeding, which could be a useful tool to evaluate population inbreeding.