The Innovation Program of Oil Crops Genomics & Disease Resistance Improvement is one of 11 programs at Oil Crops Research Institute of Chinese Academy of Agricultural Sciences. In recent ten years, we have 38 to 46 people working on four interconnected areas, polyploid genome evolution, breeding by genome design, Brassica napus disease resistance, and their application to integrated disease control.

i. Polyploid Genome Evolution. Almost all higher plants experienced one or more cycles of whole genome duplications (WGD). However, why recurrent WGDs occur and how diploidization after polyploidization links to biodiversity and speciation are unclear. We use the family Brassicaceae plants as a model to address the questions by comparing sequence variation of individual genomes with different age WGDs and population genomics of Arabidopsis and Brassica species. To this end, we have completed de novo genome assembling of a dozen of B. napus accessions and constructed a consensus pangenome of Brassica genus, part of which were in collaboration with other research groups in the world. We also generated population phenome, metabolome, transcriptome and spliceome of a B. napus oilseed rape diverse accession panel.

ii. Breeding by Genome Design (BGD). The BGD objective is to conduct both fore- and back-ground selection in B. napus, not only for expected traits, but also more preferentially for shortening breeding period and designing elite cultivars. We developed a large association population and multiple bi-parental segregation populations, and by integrating multi-omics data of thousands of B. napus accessions, we mapped thousand loci controlling important traits and some of regulatory networks of traits-genes. Meanwhile, we have been investigating genome evolution of a large number of accessions and pedigrees. These together enable us to conduct BGD.

iii. Brassica Disease Resistance. With an aim to breeding disease resistance varieties, we conduct studies on gene mapping, cloning and molecular mechanisms of disease resistance in B. napus. Currently we are mainly working on three major diseases in Brassicaor oilseed crops: molecular mechanisms of broad-spectrum resistance conferred by a dominant and two recessive genes and breeding for sustainable resistant Brassica varieties against parasitic pathogen Plasmodiophora brassicae causing destructive clubroot; QTL and genes conferring resistance to necrotrophic pathogen Sclerotinia sclerotiorum causing devastating tissue rot, its co-evolution with flowering time, and breeding for resistance and earliness varieties; and gene mapping and mechanism of broad-spectrum resistance to Xanthomonas campestris causing black rot in Brassica crops, and its application to breeding.

iv. Green and Sustainable integrated Control of Oilseed Crop Diseases. In the integrated control, we use resistant varieties as a major measure and incorporate chemical pesticide by developing cost-saving and higher efficient spray technology (i.e. remote drone) for S. sclerotiorum disease control; for clubroot control, we aim to combine broad-spectrum resistance variety with crop rotation management.

（1）湖北省“楚天英才-青年拔尖人才培养计划”：60万元，2025.01-2027.01，主持

（2）安徽省生物育种专项子课题：油菜抗根肿病优异基因发掘与种质创制，40万元，2026.01-2028.12，参与

（3）湖北省博士后“揭榜领题”项目：新型高效农作物生防菌剂的研制与应用，20万元，2024年，主持，已结题

（4）国家自然科学基金青年科学基金项目：油菜株高遗传结构解析和优异株型半矮杆基因克隆（32101813），30万元，2022.01-2024.12，主持，已结题

（5）国家自然科学基金区域创新联合发展基金：油菜对根肿病和菌核病隐性广谱抗病基因及相关基因簇基因的作用机制研究（U20A2034），258万元，2021.01-2024.12，参与，已结题

（6）国家自然科学基金面上项目：小RNA介导的甘蓝型油菜亚基因组间反式调控的全基因组模式研究（31770250），60万元，2018.01-2021.12，参与，已结题

（7）国家自然科学基金面上项目：控制油菜菌核病抗性和早开花的主效QTL精细定位与基因克隆（31471536），80万元，2015.01-2018.12，参与，已结题

（1）湖北省“楚天英才-青年拔尖人才培养计划”：60万元，2025.01-2027.01，主持

（2）安徽省生物育种专项子课题：油菜抗根肿病优异基因发掘与种质创制，40万元，2026.01-2028.12，参与

（3）湖北省博士后“揭榜领题”项目：新型高效农作物生防菌剂的研制与应用，20万元，2024年，主持，已结题

（4）国家自然科学基金青年科学基金项目：油菜株高遗传结构解析和优异株型半矮杆基因克隆（32101813），30万元，2022.01-2024.12，主持，已结题

（5）国家自然科学基金区域创新联合发展基金：油菜对根肿病和菌核病隐性广谱抗病基因及相关基因簇基因的作用机制研究（U20A2034），258万元，2021.01-2024.12，参与，已结题

（6）国家自然科学基金面上项目：小RNA介导的甘蓝型油菜亚基因组间反式调控的全基因组模式研究（31770250），60万元，2018.01-2021.12，参与，已结题

（7）国家自然科学基金面上项目：控制油菜菌核病抗性和早开花的主效QTL精细定位与基因克隆（31471536），80万元，2015.01-2018.12，参与，已结题

发表论文情况（#共同第一作者，*通讯作者）

1. Yupo Wu#, Chuanji Zhao#, Yi Zhang#, Cuicui Shen#, Yuanyuan Zhang, Xiong Zhang, Lixia Gao, Lingyi Zeng, Qinglin Ke, Li Qin, Fan Liu, Junyan Huang, Li Ren, Yueying Liu, Hongtao Cheng, Chaobo Tong, Qiong Hu, Xiaohui Cheng, Yangdou Wei, Shengyi Liu*, Lijiang Liu*. Inactivation of β-1,3-glucan synthase-like 5 confers broad-spectrum resistance to Plasmodiophora brassicae pathotypes in cruciferous plants. (2025) Nature Genetics, 57 (9), 2302-2323. (IF=37.4) 中科院1区

2. Chuanji Zhao#, Yi Zhang#, Lixia Gao, Meili Xie, Xiong Zhang, Lingyi Zeng, Jie Liu, Yueying Liu, Yuanyuan Zhang, Chaobo Tong, Qiong Hu, Xiaohui Cheng*, Lijiang Liu*, Shengyi Liu. Genome editing of RECEPTOR-LIKE KINASE 902 confers resistance to necrotrophic fungal pathogens in Brassica napus without growth penalties. (2024) Plant Biotechnology Journal, 22 (3), 538-540. (IF2024=12.4) 中科院1区

3. Chuanji Zhao#, Xiaobo Cui#, Meili Xie#, Yi Zhang, Lingyi Zeng, Yueying Liu, Junyan Huang, Xiong Zhang, Chaobo Tong, Qiong Hu, Lijiang Liu, Shengyi Liu. Chromosome-scale genome assembly-assisted identification of Brassica napus BnDCPA1 for improvement of plant architecture and yield heterosis. (2024) Plant Communications, 5, 100854. (IF2024=11.8) 中科院1区

4. Chuanji Zhao, Luqman Bin Safdar, Meili Xie, Meijuan Shi, Zhixue Dong, Li Yang, Xiaohui Cheng, Yueying Liu, Zetao Bai, Yang Xiang, Chaobo Tong, Junyan Huang*, Lijiang Liu*, Shengyi Liu. Mutation of the PHYTOENE DESATURASE 3 gene causes yellowish-white petals in Brassica napus. (2021) The Crop Journal, 9 (5), 1124 – 1134. (IF2021=4.65) 中科院1区

5. Chuanji Zhao#, Meili Xie#, Longbing Liang, Li Yang, Hongshi Han, Xinrong Qin, Jixian Zhao, Yan Hou, Wendong Dai, Caifu Du, Yang Xiang*, Shengyi Liu*, Xianqun Huang. Genome-Wide Association Analysis Combined With Quantitative Trait Loci Mapping and Dynamic Transcriptome Unveil the Genetic Control of Seed Oil Content in Brassica napus L. (2022) Frontiers in Plant Science, 13, 929197. (IF2022=5.6) 中科院2区

6. Chuanji Zhao#, Li Yang#, Minqiang Tang, Lijiang Liu, Junyan Huang, Chaobo Tong, Yang Xiang, Shengyi Liu, Xiaohui Cheng*, Meili Xie*. Genome-wide association study reveals a GLYCOGEN SYNTHASE KINASE 3 gene regulating plant height in Brassica napus. (2022) Frontiers in Plant Science, 13, 1061196. (IF2022=5.6) 中科院2区

7. Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yang Xiang, Chaobo Tong, Jinxing Tu*, Junyan Huang*, Shengyi Liu. Characterization and fine Mapping of a yellow-virescent gene regulating chlorophyll biosynthesis and early stage chloroplast development in Brassica napus. (2020) G3: Genes, Genomes, Genetics, 10 (9), 3201 – 3211. (IF2020=3.15) 中科院3区

8. Meili Xie#, Chuanji Zhao#, Min Song#, Yang Xiang*, Chaobo Tong. Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors. (2022) Frontiers in Plant Science, 13, 998082. (IF2022=5.6) 中科院2区

9. Xiaohui Cheng#, Chuanji Zhao#, Lixia Gao, Lingyi Zeng, Yu Xu, Fan Liu, Junyan Huang, Lijiang Liu, Shengyi Liu, Xiong Zhang*. Alternative splicing reprogramming in fungal pathogen Sclerotinia sclerotiorum at different infection stages on Brassica napus. (2022) Frontiers in Plant Science, 13, 1008665. (IF2022=5.6) 中科院2区

10. Li Yang#, Meili Xie#, Yupo Wu, Xiaobo Cui, Minqiang Tang, Lingli Yang, Yang Xiang, Yan Li, Zetao Bai, Junyan Huang, Xiaohui Cheng, Chaobo Tong, Lijiang Liu, Shengyi Liu, Chuanji Zhao*. Genetic mapping and regional association analysis revealed a CYTOKININ RESPONSE FACTOR 10 gene controlling flowering time in Brassica napus L. (2023) Industrial Crops and Products, 193, 116239. (IF2023=5.6) 中科院1区

11. Zhixue Dong#, Muhammad Khorshed Alam#, Meili Xie, Li Yang, Jie Liu, MMU Helal, Junyan Huang, Xiaohui Cheng, Yueying Liu, Chaobo Tong, Chuanji Zhao*, Shengyi Liu. Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus. (2021) G3: Genes, Genomes, Genetics, 11 (7), jkab118. (IF2021=3.54) 中科院3区

12. Yang Xiang#*, M.M.U. Helal#, Longbing Liang, Minqin Zhang, Hongshi Han, Xianglai Dai, Jixian Zhao, Dalun Chen, Xianping Wang, Min Li, Chuanji Zhao*. Genome-wide association study exposed the pleiotropic genes for yield-related and oil quality traits in Brassica napus L. (2023) Oil Crop Science, 8 (3), 156-164.

发明专利：

1. 甘蓝型油菜油菜早花性状的分子标记及其获得方法和应用。完成人排名1/7，2024年授权

2. 甘蓝型油菜BnaA08.PDS3基因在甘蓝型油菜花瓣颜色性状育种中的应用。完成人排名1/7，2022年授权

3. 敲除BnaA05.RLK902基因在提高植物抗菌核病和灰霉病中的应用和分子标记。完成人排名2/7，2024年授权

4. 甘蓝型油菜种子含油量性状的主效QTL位点的SNP分子标记相关检测引物或探针及应用。完成人排名2/5，2024年授权

5. 甘蓝型油菜千粒重性状的主效QTL位点的SNP分子标记、相关检测引物或探针、及应用。完成人排名2/5，2025年授权

6. 十字花科作物GSL5基因在根肿病抗性改良中的应用及产品开发。完成人排名5/9，2024年授权

7. 十字花科作物GSL5基因在根肿病抗性改良中的应用。完成人排名5/9，2025年授权

8. 一种油菜黑腐病的分子标记及其获得方法和应用。完成人排名4/9，2025年授权

9. 根肿菌Pb034基因及其在防控十字花科作物根肿病中的应用。完成人排名5/6，2025年授权

10. 根肿菌Pb035基因在防控十字花科作物根肿病中的应用。完成人排名5/6，2025年授权

11. 根肿菌侵染早期几丁质在防控十字花科根肿病中的应用。完成人排名6/6，2025年授权

12. USE OF β-1,3-GLUCAN SYNTHASELIKE 5 IN IMPROVING CLUBROOT DISEASE RESISTANCE AND RELATED PRODUCT DEVELOPMENT IN CRUCIFEROUS CROPS.完成人排名5/10，2026年授权，美国专利