Developing a pipeline for identification,characterization and molecular editing of cis-regulatory elements:a case study in potatoOA
Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene pleiotropy.The molecular manipulation of genes can effectively improve target traits,but this may not reduce gene pleiotropy,potentially leading to undesirable traits or even lethal conditions.However,molecular editing of cis-regulatory elements(CREs)of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene expression.In this study,we developed a pipeline,in potato,which employs open chromatin to predict candidate CREs,along with both transient and genetic assays to validate the function of CREs and CRISPR/Cas9 to edit candidate CREs.We used StCDF1 as an example,a key gene for potato tuberization and identified a 288 bp-core promoter region,which showed photoperiodic inducibility.A homozygous CRISPR/Cas9-editing line was established,with two deletions in the core promoter,which displayed a reduced expression level,resulting in late tuberization under both longday and short-day conditions.This pipeline provides an alternative pathway to improve a specific trait with limited downside on other phenotypes.
Min Wan;Handan Xie;Hongwei Guo;Shenglin Jing;Deying Zeng;Bing Li;Bo Zhu;Zixian Zeng
Department of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,China Plant Functional Genomics and Bioinformatics Research Center,Sichuan Normal University,Chengdu 610101,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,China Plant Functional Genomics and Bioinformatics Research Center,Sichuan Normal University,Chengdu 610101,ChinaCrop Research Institute,Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province,Sichuan Academy of Agricultural Sciences,Chengdu 610066,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,China Plant Functional Genomics and Bioinformatics Research Center,Sichuan Normal University,Chengdu 610101,ChinaDepartment of Biological Science,College of Life Sciences,Sichuan Normal University,Chengdu 610101,China Plant Functional Genomics and Bioinformatics Research Center,Sichuan Normal University,Chengdu 610101,China
农业科技
Cis-regulatory elementPotatoCRISPRGenome-editing
《aBIOTECH》 2025 (1)
P.91-96,6
supported by grants from the National Natural Science Foundation of China(32170573)Sichuan Science and Technology Program(2021YFYZ0019,2023ZYD0056).
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