Abstract：Shanghai white pig (Sus scrofa) has many outstanding economic traits, such as high prolific, high disease resistance, high resistance to crude feed and heterosis. Revaling the molecular genetic architechture of these complex traits is an important issue for genetic study. With the development of genetic study and biotechnologies as well as upgarating of study methods, the requirement to reveal the genetic mechanism of these complex traits in the genome level rathter than in the single or several genes level is becoming more intense. However, up to date, no studies performed genetic variation analysis for Shanghai white pig on the genome-wide. What's more, the genetic mechanism for their outstanding traits is still unclear. Therefore, this study will be performed as follows: 1)Next generation sequencing technology was used to detect the genome-wide of genetic variations using . The genetic variants of 99 Shanghai white pigs, 252 pigs from Taihu pig breeds (Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black) and 156 foreign pigs were genotyped according to the genotyping by genome reducing and sequencing (GGRS) protocol (http://klab.sjtu.edu.cn/GGRS/). Briefly, high molecular weight genomic DNA samples were extracted from ear tissue, digested with Ava Ⅱ, and then ligated with a unique adapter-barcode. Next, the samples were pooled and enriched to construct a sequencing library. Finally, the sequence libraries (fragments ranging from 300~400 bp, including the adapter-barcode sequence) were sequenced on an Illumina Hiseq2000 (the sequencing process is given in detail by the manufacturer, Illumina) instrument with a paired-end (2×100 bp) pattern. The SNPs of more than 75 (30% ) samples were genotyped and an average sequencing depth greater than 5× was achieved. In total, 100 120 SNP were identified in the genomes of the current pig population. These results were helpful to know the genome information of the Shanghai white pig and enrich the databse of genetic markers in the Chinese pig breeds. 2) Applied the detected genetic markers for conducting the genetic diversity and population structure analysis to provide suggestions for breeds classification and future conservation. Genetic diversity and population structure were analysised. The breed or sub-type classification of a population can bring a large effect for its protection and conservation. The genetic diversity and population structure of these pig breeds were investigated using whole-genome SNP data. Firstly, the allelic richness (AR), proportion of polymorphic markers (PN) and expected heterozygosity (He) were used to investigate the genome-wide genetic variability within these pig breeds. As a result, Shanghai white pigs exhibited the highest level of genetic diversity within population compared(PN=0.731, AR=1.709, He=0.221) to Taihu pig breeds and western pig breeds. Additionally, the genetic differentiation between Shanghai white and Taihu pig breeds (0.237±0.007) was greater than the one between Shanghai white and western pig breeds(0.219±0.008). What's more, (Neighbor Joining, NJ)-tree, principal components analysis(PCA) and STRUCTURE analysis showed that all the populations could be well distinguished from each other. In conclusion, The rationality of the current breed classification for Shanghai white pig were confirmed based on genome-wide genetic markers. The study results also lay a necessary theoretical basis for effectively conserving and utilizing the special genetic resource.
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