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

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.

The CropGPT project:Call for a global,coordinated effort in precision design breeding driven by Al using biological big data

Since the beginning of humanity,people have been seeking practical solutions to meet their most basic need:food.The advent of agriculture greatly increased the food supply and led to a rapid increase in the human population.Enhanced food production via agriculture can be attributed to both improved crop management practices and crop breeding through genetics.Plant(crop)breeding has been categorized into four major stages based on the techniques employed(Wallace et al.,2018).