Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae  

作　　者：Fei Zhao Shilong Tian Qiuhong Wu Zijuan Li Luhuan Ye Yili Zhuang Meiyue Wang Yilin Xie Shenghao Zou Wan Teng Yiping Tong Dingzhong Tang Ajay Kumar Mahato Moussa Benhamed Zhiyong Liu Yijing Zhang 

机构地区：[1]National Key Laboratory of Plant Molecular Genetics,CAS Center for Excellence in Molecular Plant Sciences,Shanghai Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai 200032,China [2]University of the Chinese Academy of Sciences,Beijing 100049,China [3]State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,The Innovative Academy of Seed Design,Chinese Academy of Sciences,Beijing 100101,China [4]State Key Laboratory of Genetic Engineering,Collaborative Innovation Center of Genetics and Development,Department of Biochemistry,Institute of Plant Biology,School of Life Sciences,Fudan University,Shanghai 200438,China [5]State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests,Fujian Agriculture and Forestry University,Fuzhou 350002 China [6]Key Laboratory of Ministry of Education for Genetics,Breeding and Multiple Utilization of Crops,Plant Immunity Center,Fujian Agriculture and Forestry University,Fuzhou 350002 China [7]Laboratory of Genome Informatics(LGI)In-charge Bioinformatics Wing-A,First Floor Center for DNA Fingerprinting and Diagnostics Inner Ring Road,Uppal,Hyderabad 500039,India [8]Institute of Plant Sciences Paris-Saclay(IPS2),Universite´Paris-Saclay,CNRS,INRAE,Univ Evry,Orsay 91405,France

出　　处：《Plant Communications》2022年第4期25-36,共12页植物通讯（英文）

基　　金：supported by the National Science Fund for Excellent Young Scholars(32022012).

摘　　要：Triticeae species,including wheat,barley,and rye,are critical for global food security.Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops.However,Triticeae includes many wild relatives with desirable agronomic traits,and frequent introgressions occurred during Triticeae evolution and domestication.Thus,Triticeae genomes are generally large and complex,making the localization of genes or functional elements that control agronomic traits challenging.Here,we developed Triti-Map,which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae,as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits.The Triti-Map pipeline accepts bothDNA and RNAbulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions.We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process.We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.

关 键 词：agronomic gene mapping TRITICEAE wheat bulk-segregated ChIP-seq Triti-Map 

分 类 号：S51[农业科学—作物学]