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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 pedigree breeding, pedigree information has been traditionally used to assess the degree of inbreeding. In recent years, with the low cost of single nucleotide polymorphism (SNP) detection, genomic information was used to analyze the actual degree of inbreeding Is possible? In this study, the frequency and distribution of runs of homozygosity (ROH) in 2107 Holstein cattle genomes in Beijing were calculated using the data of bovine 54 K SNP chip. The inbred coefficient of two genotypes The ratio of the length of chromosome ROH to the total length of the genome (Froh) and the proportion of homozygotes in all the marker genotypes of the individuals, namely, the genomic homozygosity (Fhom), and then the correlation between the two genomic inbreeding coefficients and Correlation between genomic inbreeding and pedigree inbreeding coefficient The results showed that a total of 44 676 ROH fragments were detected and their length mainly distributed between 1 and 10 Mb. ROHs of different length were scattered in the genome of individuals. Short ROH The longer ROH is more common. ROH is not uniformly distributed on the chromosome, and the region with the highest ROH frequency is the middle of chromosome 10. The correlation between the two genomic inbreeding coefficients is high (91%), but the base The correlation between inbreeding and pedigree inbreeding was low (less than 50%). Pedigree integrity was an important factor that affected genomic inbreeding and pedigree inbreeding results. Genomic inbreeding coefficients were able to reflect the true inbreeding of individuals This study provides a powerful tool for assessing the level of inbreeding in populations.