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

doi:10.1016/j.jia.2023.07.033

Journal of Integrative Agriculture

2025, Vol. 24

Issue (5): 1930-1943 DOI: 10.1016/j.jia.2023.07.033

Animal Science · Veterinary Medicine

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

Zipeng Zhang¹, Siyuan Xing², Ao Qiu¹, Ning Zhang³, Wenwen Wang⁴, Changsong Qian², Jia’nan Zhang², Chuduan Wang¹, Qin Zhang⁴, Xiangdong Ding^1#

¹ State Key Laboratory of Animal Biotech Breeding/National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

² MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China

³Henan Institute of Pig Biological Breeding, College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China

Highlights
● Developed the inaugural porcine 50K liquid chip (GBTS50K) based on genotyping by target sequencing, comprising 52,000 single-nucleotide polymorphisms (SNPs) with 8.8K loci strategically located in QTL regions linked to economically importanttraits.
● GBTS50K demonstrates superior genotyping capability with key metrics exceeding 99% and exhibits robust utility in genetic analyses and molecular breeding.
● The multiple SNPs (mSNPs) of GBTS50K enable haplotype-enhanced genomic selection (GS) without increasing genotyping costs, significantly improving prediction accuracy.

Abstract
References

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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为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的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 52,000 single-nucleotide polymorphisms (SNPs), in pigs, designated GBTS50K. A total of 6,032 individuals of Large White, Landrace, and Duroc pigs from 10 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 2 important traits of backfat thickness at 100 kg and days to 100 kg in pigs. Particularly, due to the multiple SNPs (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

Received: 03 March 2023 Online: 26 July 2023 Accepted: 19 June 2023

Fund:

This work was supported by the grants from the Key R&D Program of Shandong Province, China (2022LZGC003), the China Agriculture Research System of MOF and MARA (CARS-35), the National Key Research and Development Project of China (2019YFE0106800), and the 2115 Talent Development Program of China Agricultural University.

About author: Zipeng Zhang, E-mail: zzp13226665505@126.com; #Correspondence Xiangdong Ding, Tel: +86-10-62734277, E-mail: xding@cau.edu.cn

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Zipeng Zhang, Siyuan Xing, Ao Qiu, Ning Zhang, Wenwen Wang, Changsong Qian, Jia’nan Zhang, Chuduan Wang, Qin Zhang, Xiangdong Ding. 2025. The development of a porcine 50K SNP panel using genotyping by target sequencing and its application. Journal of Integrative Agriculture, 24(5): 1930-1943.

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