a ICAR- National Dairy Research Institute , Karnal , Haryana , India.
b ICAR- National Bureau of Animal Genetic Resources , Karnal , Haryana , India.
Anim Biotechnol. 2018 Apr 3;29(2):129-135. doi: 10.1080/10495398.2017.1329150. Epub 2017 Jun 21.
In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0.007, and 0.242 ± 0.009 in Sahiwal, Tharparkar and Gir, respectively, while that for 54K SNPs was on lower side. The average Reynold's genetic distance between breeds ranged from 0.042 to 0.055 based on BovineHD Beadchip, and from 0.052 to 0.084 based on 54K SNP Chip. The estimates of genetic diversity based on HD and 54K chips were almost same and, hence, low density chip seems to be good enough to decipher genetic diversity of these cattle breeds. The linkage disequilibrium started decaying (r < 0.2) at 140 kb inter-marker distance and, hence, a 20K low density customized SNP array from HD chip could be designed for genomic selection in these cattle else the 54K Bead Chip as such will be useful.
总计对 52 份萨希瓦尔牛（19 份）、塔尔帕卡尔牛（17 份）和吉尔牛（16 份）样本进行了基因型分析，使用 BovineHD SNP 芯片来分析这些牛种的次要等位基因频率（MAF）、遗传多样性和连锁不平衡。还提取了 BovineHD 和 54K SNP 芯片的常见 SNP，并评估了它们的性能。这些牛种中只有 40%-50%的 SNP 芯片信息对遗传分析有用。BovineHD SNPChip 的 SNP 平均 MAF 分别为 0.248±0.006、0.241±0.007 和 0.242±0.009，而 54K SNP 的平均 MAF 较低。基于 BovineHD Beadchip，品种间平均 Reynold 遗传距离为 0.042-0.055，基于 54K SNP Chip 为 0.052-0.084。基于 HD 和 54K 芯片的遗传多样性估计值几乎相同，因此，低密度芯片似乎足以破译这些牛种的遗传多样性。连锁不平衡在 140kb 标记间距离开始衰减（r<0.2），因此，可以从 HD 芯片设计一个 20K 低密度定制 SNP 芯片用于这些牛的基因组选择，否则 54K Bead Chip 本身就会有用。
