iBP-seq: An efficient and low-cost multiplex targeted genotyping and epigenotyping system

IF 6 1区 农林科学 Q1 AGRONOMY
Juan Li , Rui Han , Ruonan Li , Qiang Xu , Mingzhu Li , Yue Tang , Jixiang Li , Xi Wang , Zhao Li , Qing Li , Zaiwen Feng , Lin Li
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引用次数: 0

Abstract

Inter- and intra-specific variations in phenotype are common and can be associated with genomic mutations as well as epigenomic variation. Profiling both genomic and epigenomic variants is at the core of dissecting phenotypic variation. However, an efficient targeted genotyping and epigenotyping system is lacking. We describe a new multiplex targeted genotyping and epigenotyping system called improved bulked-PCR sequencing (iBP-seq). We employed iBP-seq for the detection of genotypes and methylation levels of dozens of target regions in mixed DNA samples. iBP-seq can be adapted for the construction of linkage maps, fine mapping of quantitative-trait loci, and detection of genome editing mutations at a cost as low as $0.016 per site per sample. We developed an automated bioinformatics pipeline, including primer design, a series of bioinformatic analyses for genotyping and epigenotyping, and visualization of results. iBP-seq and its bioinformatics pipeline, available at http://zeasystemsbio.hzau.edu.cn/tools/ibp/, can be adapted to a wide variety of species.

iBP-seq:一种高效、低成本的多重靶向基因分型和表观基因分型系统
表型的特异性间和特异性内变异很常见,可能与基因组突变以及表观基因组变异有关。分析基因组和表观基因组变异是分析表型变异的核心。然而,缺乏有效的靶向基因分型和表观基因分型系统。我们描述了一种新的多重靶向基因分型和表观基因分型系统,称为改进的批量PCR测序(iBP-seq)。我们使用iBP-seq检测混合DNA样本中数十个靶区的基因型和甲基化水平。iBP-seq可以用于构建连锁图谱、精细定位定量性状基因座和检测基因组编辑突变,每个位点每个样本的成本低至0.016美元。我们开发了一个自动化的生物信息学管道,包括引物设计、基因分型和表观基因分型的一系列生物信息学分析,以及结果的可视化。iBP-seq及其生物信息学管道,可在http://zeasystemsbio.hzau.edu.cn/tools/ibp/,可以适应各种各样的物种。
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来源期刊
Crop Journal
Crop Journal Agricultural and Biological Sciences-Agronomy and Crop Science
CiteScore
9.90
自引率
3.00%
发文量
638
审稿时长
41 days
期刊介绍: The major aims of The Crop Journal are to report recent progresses in crop sciences including crop genetics, breeding, agronomy, crop physiology, germplasm resources, grain chemistry, grain storage and processing, crop management practices, crop biotechnology, and biomathematics. The regular columns of the journal are Original Research Articles, Reviews, and Research Notes. The strict peer-review procedure will guarantee the academic level and raise the reputation of the journal. The readership of the journal is for crop science researchers, students of agricultural colleges and universities, and persons with similar academic levels.
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