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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State Key Laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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Simultaneous gene editing of three homoeoalleles in self-incompatible allohexaploid grasses

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Journal of Integrative Plant Biology 2021年第8期63卷 1410-1415页

作者： Liang Zhang Tao Wang Guangyang Wang Aoyue Bi Misganaw Wassie Yan Xie Liwen Cao Huawei Xu Jinmin Fu Liang Chen Yang Zhao Tao Hu CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenThe Innovative Academy of Seed DesignThe Chinese Academy of SciencesWuhan430074 China Center of Economic Botany Core Botanical GardensThe Chinese Academy of SciencesWuhan430074 China University of Chinese Academy of Sciences Beijing100049 China Shanghai Center for Plant Stress Biology and CAS Center of Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai200032 China College of Agriculture Henan University of Science and TechnologyLuoyang471023 China School of Resources and Environmental Engineering Ludong UniversityYantai264011 China

Clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)system has been widely used for precise gene editing in plants.However,simultaneous gene editing of multiple homoeoalleles remains challenging,especially in self-incompatible polyploid plants.Here,we simultaneously introduced targeted mutations in all three homoeoalleles of two genes in the self-incompatible allohexaploid tall fescue,using both CRISPR/Cas9 and LbCas12a(LbCpf1)systems.Loss-of-function mutants of FaPDS exhibited albino leaves,while knockout of FaHSP17.9 resulted in impaired heat resistance in T0 generation of tall fescue.Moreover,these mutations were inheritable.Our findings demonstrate the feasibility of generating loss-of-function mutants in T0 generation polyploid perennial grasses using CRISPR/Cas systems.

关键词： allohexaploid Cas12a(Cpf1) CRISPR/Cas9 self-incompatible tall fescue

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