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.
Crop JournalAgricultural 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.