College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
Shanghai Animal Disease Control Center, Shanghai, 201103, China.
Sci Rep. 2017 Aug 30;7(1):10063. doi: 10.1038/s41598-017-09969-6.
As typical Chinese indigenous pig breeds, Erhualian and Meishan have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics of these pig breeds is still limited. Moreover, considering cost and output of sequencing, it is necessary to further develop cost-effective method for pig genome screening. To contribute on this issue, we developed a SLAF-seq (specific-locus amplified fragment sequencing) method for pigs and applied it to analyze the genetic difference among Landrace, Erhualian, and Meishan pigs. A total of 453.75 million reads were produced by SLAF-seq. After quality-control, 165,670 SNPs (single nucleotide polymorphisms) were used in further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian (F = 0.5480) and Meishan (F = 0.5800), respectively, while Erhualian and Meishan held the relatively close genetic relationship (F = 0.2335). Furthermore, a genome-wide scanning revealed 268 differentially selected regions (DSRs) with 855 genes and 256 DSRs with 347 genes between Landrace and the two Chinese indigenous pig breeds and between Erhualian and Meishan, respectively. This study provides a new cost-effective method for pig genome study and might contribute to a better understanding on the formation mechanism of genetic difference among pigs with different geographical origins.
作为中国典型的本土猪种，二花脸猪和梅山猪被广泛用于培育世界各地的新品系或品种。然而，这些猪种特征的遗传基础仍然有限。此外，考虑到测序的成本和产量，有必要进一步开发具有成本效益的猪基因组筛选方法。为解决这一问题，我们开发了一种用于猪的 SLAF-seq（特异位点扩增片段测序）方法，并应用该方法分析了长白猪、二花脸猪和梅山猪之间的遗传差异。通过 SLAF-seq 共产生了 4.5375 亿个reads，经过质量控制后，有 165670 个 SNP（单核苷酸多态性）用于进一步分析。结果表明，长白猪与二花脸猪（F=0.5480）和梅山猪（F=0.5800）的遗传关系明显不同，而二花脸猪和梅山猪的遗传关系较为密切（F=0.2335）。此外，全基因组扫描发现，长白猪与两个中国本土猪种之间有 268 个差异选择区域（DSR），包含 855 个基因；二花脸猪和梅山猪之间有 256 个 DSR，包含 347 个基因。本研究为猪基因组研究提供了一种新的成本效益方法，有助于更好地理解具有不同地理起源的猪种遗传差异的形成机制。
