Oyelami Favour Oluwapelumi, Zhao Qingbo, Xu Zhong, Zhang Zhe, Sun Hao, Zhang Zhenyang, Ma Peipei, Wang Qishan, Pan Yuchun
Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, China.
Front Genet. 2020 Sep 4;11:752. doi: 10.3389/fgene.2020.00752. eCollection 2020.
The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average > 0.2 at SNPs distances 10-20 kb and concluded that about 120,000-240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched ( ≤ 0.05). These genes were significantly enriched in 2 GO terms ( < 0.01), and 2 KEGG pathways ( < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.
姜曲海（JQ）猪品种因其独特且显著的特征，是中国最广为人知的猪种群之一。在本研究中，我们检测了姜曲海猪品种的连锁不平衡（LD）程度和单倍型块结构，并扫描这些块以寻找可能位于重要数量性状基因座（QTL）之下的基因，这些基因可能与这些猪的某些适应性特征有关，或者可能经历了一些选择压力。我们将部分结果与其他中国和西方猪品种进行了比较。结果表明，姜曲海品种的总块长度最长（349.73 Mb≈其基因组的15%），除第4号染色体（SSC4）、SSC6、SSC7、SSC8、SSC10、SSC12、SSC13、SSC14、SSC17、SSC18和X染色体外，其大多数染色体上的块覆盖率大于其他品种。此外，与本研究中检测的其他品种相比，姜曲海品种有更多单核苷酸多态性（SNP）聚集成单倍型块。我们的共享和独特单倍型块分析表明，红灯笼（HD）品种的共享单倍型块百分比最低，而山猪（SZ）品种的最高。我们发现，在10 - 20 kb的SNP距离处，姜曲海品种的平均[此处原文缺失具体数值] > 0.2，并得出结论，在该品种中成功进行全基因组关联研究（GWAS）大约需要120,000 - 240,000个SNP。最后，我们在姜曲海品种中检测到选定单倍型块中共含88个基因，其中只有4个显著富集（[此处原文缺失具体数值]≤0.05）。这些基因在2个基因本体（GO）术语（[此处原文缺失具体数值]<0.01）和2条京都基因与基因组百科全书（KEGG）通路（[此处原文缺失具体数值]<0.02）中显著富集。这些富集基因大多与健康相关。此外，在单倍型块中检测到的大多数重叠QTL与肉质和胴体品质以及健康有关，其中少数与繁殖和生产有关。这些结果为姜曲海猪品种中观察到的一些适应性和肉质性状的遗传结构提供了见解，也揭示了猪基因组中的LD模式。我们的结果为提高GWAS的统计效力和优化该姜曲海猪品种的保护策略提供了重要指导。
