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Journal of Integrative Agriculture
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The development of a porcine 50K SNP panel using genotyping by target sequencing and its application
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摘要  

靶向捕获测序(GBTS)基因分型技术同时具备固相芯片技术(高稳定性和可靠性)和测序技术(高灵活性和低成本)的优点。然而, GBTS技术尚未应用于猪SNP芯片上。在本研究中,我们基于GBTS技术开发了猪首款50K液相芯片——GBTS50K,包含52000个SNP位点。我们选取来自10个种猪场的6032头大白、长白和杜洛克猪对GBTS50K的性能进行评估。结果表明,GBTS50K获得了较好的基因分型性能,其SNP检出率和个体检出率0.997~0.998,重复样本的基因分型一致性和相关系数分别为0.997和0.993。我们还评估了GBTS50K在群体遗传结构、选择信号检测、全基因组关联分析、基因型填充和基因组选择等方面的应用效果。结果表明,GBTS50K在遗传分析和分子育种上表现优异。例如,对于达100公斤体重日龄和100公斤活体背膘厚两个重要经济性状,使用GBTS50K的基因组选择准确性高于目前使用广泛GGP-Porcine固相芯片。并且,由于GBTS技术能够检测到多聚SNP位点GBTS50K在不增加基因分型成本的情况下能够获得更多高质量SNP位点(~100K)。利用这些SNP位点进行单倍型基因组选择,生长和繁殖性状基因组选择的准确性可以进一步提高2-6%。我们的研究表明,GBTS50K可以成为猪遗传分析和分子育种的有力工具,同时,也能够给其它畜禽液相芯片开发提供借鉴。



Abstract  

Genotyping by target sequencing (GBTS) integrates the advantages of silicon-based technology (high stability and reliability) and genotyping by sequencing (high flexibility and cost-effectiveness). However, GBTS panels are not currently available in pigs. In this study, based on GBTS technology, we first developed a 50K panel, including 52000 SNPs, in pigs, designated GBTS50K. A total of 6032 individuals of Large White, Landrace, and Duroc pigs from ten breeding farms were used to assess the newly developed GBTS50K. Our results showed that GBTS50K obtained a high genotyping ability, the SNP and individual call rates of GBTS50K were 0.997~0.998, and the average consistency rate and genotyping correlation coefficient were 0.997 and 0.993, respectively, in replicate samples. We also evaluated the efficiencies of GBTS50K in the application of population genetic structure analysis, selection signature detection, genome-wide association studies (GWAS), genotyped imputation, genetic selection (GS), etc. The results indicate that GBTS50K is plausible and powerful in genetic analysis and molecular breeding. For example, GBTS50K could gain higher accuracies than the current popular GGP-Porcine bead chip in genomic selection on two important traits of backfat thickness at 100 kg and days to 100 kg in pigs. Particularly, due to the multiple single-nucleotide polymorphisms (mSNPs), GBTS50K generated 100K qualified SNPs without increasing genotyping cost, and our results showed that the haplotype-based method can further improve the accuracies of genomic selection on growth and reproduction traits by 2 to 6%. Our study showed that GBTS50K could be a powerful tool for underlying genetic architecture and molecular breeding in pigs, and it is also helpful for developing SNP panels for other farm animals.

Keywords:  Genotyping by target sequencing              GBTS50K              pig  
Online: 26 July 2023  
Fund: 

This work was supported by grants from Key R&D Program of Shandong Province (2022LZGC003), China Agriculture Research System of MOF and MARA (CARS-35), National Key Research and Development Project (2019YFE0106800).

About author:  ZHANG Zi-peng, E-mail: zzp13226665505@126.com; #Correspondence DING-Xiangdong, Tel: +86-10-62734277, E-mail: xding@cau.edu.cn

Cite this article: 

ZHANG Zi-peng, XING Si-yuan, QIU Ao, ZHANG Ning, WANG Wen-wen, QIAN Chang-song, ZHANG Jia-nan, WANG Chu-duan, ZHANG Qin, DING Xiang-dong. 2023. The development of a porcine 50K SNP panel using genotyping by target sequencing and its application. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2023.07.033

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