The Innovation Program of Oil Crops Genomics & Disease Resistance Improvement (油料作物基因组学与抗病性改良创新团队) 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.

1）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.

2）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.

3）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 Brassica or 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.

4）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.

中国农业科学院油料作物研究所油料作物基因组学与抗病性改良创新团队（2022年）

团队网站： https://www.ocri-genomics.net

1）甘蓝型油菜叶片高硫苷种子低硫苷的调控机制解析及种质创制，国家自然科学基金面上项目，32370681，50万元，2024-2027，主持；

2）油菜籽营养品质形成机理与全产业链质量控制，湖北洪山实验室重大项目课题资助，2022hszd002，440万元，2022-2026，课题主持；

3）芸臺属近缘种 DNA 渐渗入 A 基因组的热点区研究，华北作物改良与调控国家重点实验室 2021 年度开放研究课题，NCCIR2021KF-6，10万元，2021-2024，主持；

4）基于代谢组的关联分析发掘油菜菌核病抗性相关基因资源，自家自然科学基金青年基金，31801730，23万元，2019-2021，主持；

5）基于代谢组的关联分析发掘油菜菌核病抗性相关基因资源，中国博士后科学基金特别资助，2018T110166，15万元，2018-2019，主持；

6）基于代谢组的关联分析解析油菜抗菌核病的分子机理，中国博士后科学基金面上资助，2016M601188，5万元，2016-2017，主持；

7）小麦等作物规模化基因鉴定与基因组育种技术平台建设，国家重点研发计划课题，2016YFD0101001，36万元，2016-2020，课题主持。

1）甘蓝型油菜叶片高硫苷种子低硫苷的调控机制解析及种质创制，国家自然科学基金面上项目，32370681，50万元，2024-2027，主持；

2）油菜籽营养品质形成机理与全产业链质量控制，湖北洪山实验室重大项目课题资助，2022hszd002，440万元，2022-2026，课题主持；

3）芸臺属近缘种 DNA 渐渗入 A 基因组的热点区研究，华北作物改良与调控国家重点实验室 2021 年度开放研究课题，NCCIR2021KF-6，10万元，2021-2024，主持；

4）基于代谢组的关联分析发掘油菜菌核病抗性相关基因资源，自家自然科学基金青年基金，31801730，23万元，2019-2021，主持；

5）基于代谢组的关联分析发掘油菜菌核病抗性相关基因资源，中国博士后科学基金特别资助，2018T110166，15万元，2018-2019，主持；

6）基于代谢组的关联分析解析油菜抗菌核病的分子机理，中国博士后科学基金面上资助，2016M601188，5万元，2016-2017，主持；

7）小麦等作物规模化基因鉴定与基因组育种技术平台建设，国家重点研发计划课题，2016YFD0101001，36万元，2016-2020，课题主持。

 1）Yuanyuan Zhang, ZhiquanYang, Yizhou He, Dongxu Liu, Yueying Liu, Congyuan Liang, Meili Xie, YupengJia, Qinglin Ke, Yongming Zhou, Xiaohui Cheng, Junyan Huang, Lijiang Liu, YangXiang, Harsh Raman, Daniel J. Kliebenstein, Shengyi Liu, and Qing-Yong Yang."Structural Variation Reshapes Population Gene Expression and TraitVariation in 2,105 Brassica napus Accessions." Nature Genetics 56, no. 11 (2024): 2538-50. https://dx.doi.org/10.1038/s41588-024-01957-7.（2023IF=31.8，第一作者；全面解析基因组结构变异调控基因表达和表型变异的分子机制）

2）Aixia Gu, Xiaomin Li, Zengfeng Wang, Yanhua Wang, Shuxin Xuan, WeiMa, Yalei Zhao, Xueping Chen, Shuangxia Luo, Yuanming Liu, Shengyi Liu, Yuanyuan Zhang*, Jianjun Zhao, and ShuxingShen. "A Triploid-mediated Geneticsystem of Generating Extremely High Genomic Segment Introgression From Brassica oleracea to B. rapa."Plant Biotechnology Journal, no. 1 (2025) https://onlinelibrary.wiley.com/doi/10.1111/pbi.14564（2023 IF=11.2，通讯作者；创建了由异源三倍体介导的白菜–甘蓝高频渐渗平台，实现了跨物种的大规模渐渗育种）

3) Yizhou He, Zhiquan Yang, Minqiang Tang, Qing-Yong Yang, Yuanyuan Zhang*, and Shengyi Liu."Enhancing Canola Breeding by Editing a Glucosinolate Transporter GeneLacking Natural Variation." Plant Physiology 188, no. 4 (2022): 1848-51. https://dx.doi.org/10.1093/plphys/kiac021.（2022IF=8.005，通讯作者；开发了多拷贝基因功能鉴定的新思路/方法，创制了油菜育种上可直接利用的种子低硫苷、营养组织高硫苷的种质资源）

4）Raman, Harsh, Rosy Raman, RamethaaPirathiban, Brett McVittie, Niharika Sharma, Shengyi Liu, Yu Qiu, Anyu Zhu,Andrzej Kilian, Brian Cullis, Graham D. Farquhar, Hilary Stuart-Williams,Rosemary White, David Tabah, Andrew Easton, and Yuanyuan Zhang*. "Multienvironment QTL AnalysisDelineates a Major Locus Associated with Homoeologous Exchanges for Water-UseEfficiency and Seed Yield in Canola." Plant, Cell & Environment 45, no. 7 (2022): 2019-36. https://dx.doi.org/https://doi.org/10.1111/pce.14337.（2022IF=7.947，通讯作者；鉴定并解析了由非同源重组交换(HE)引起的一个调控油菜水分利用率和产量相关性状的QTL位点）

5) Xueyan Wang, Min Liu, Ruinan Yang, Xiaobo Cui, Jie Liu, Yu Zhang,Yizhou He, Li Yu, Fei Ma, Xiong Zhang, YuanyuanZhang*, Shengyi Liu, Peiwu Li, and Liangxiao Zhang. "Metabolome and Transcriptome Analysis Reveal the Effect of Methyl Jasmonate on Phytosterol Biosynthesis in Brassica napus." Food Frontiers 5, no. 5 (2024): 2319-32. https://dx.doi.org/https://doi.org/10.1002/fft2.420.（2023IF=9.9，通讯作者；阐述了茉莉酸甲酯对油菜甾醇合成的调控机制）

6) Yizhou He, Yan Li, Zetao Bai, Meili Xie, Rong Zuo, Jie Liu, JingXia, Xiaohui Cheng, Yueying Liu, Chaobo Tong, Yuanyuan Zhang*, and Shengyi Liu."Genome-Wide Identification and Functional Analysis of Cupin_1Domain-Containing Members Involved in the Responses to Sclerotinia Sclerotiorum and Abiotic Stress in Brassica napus." Frontiers in Plant Science 13:983786 (2022). https://dx.doi.org/10.3389/fpls.2022.983786. （2022IF=6.627，通讯作者；解析了BnCDPs基因对油菜菌核病和非生物胁迫的调控机制）

7) MMU Helal, Rafaqat Ali Gill, Minqiang Tang, Li Yang, Ming Hu,Lingli Yang, Meili Xie, Chuanji Zhao, Xiaohui Cheng, Yuanyuan Zhang*, XiongZhang, and Shengyi Liu. "Snp- and Haplotype-Based Gwas of Flowering-RelatedTraits in Brassica napus." Plants 10, no. 11 (2021): 2475. https://www.mdpi.com/2223-7747/10/11/2475. （通讯作者；利用Haplotype-GWAS相较于SNP-GWAS的优势剖析了油菜开花调控的遗传结构）

8)  Minqiang Tang, Juanling Li, Xu Hu, Lu Sun, MMU Helal, Jianguo Chen,and Yuanyuan Zhang*. "Asymmetric Divergence in Transmitted Snps of DNAReplication/Transcription and Their Impact on Gene Expression in Polyploid Brassica napus." Frontiers in genetics 12:756172, no.2182 (2021). https://dx.doi.org/10.3389/fgene.2021.756172. （通讯作者；解析了多倍体油菜中DNA复制和RNA转录突变的亚基因组不对称性）

9）Yuanyuan Zhang, Baohua Li, Dongxin Huai, Yongming Zhou, and Daniel J. Kliebenstein."The Conserved Transcription Factors, Myb115 and Myb118, ControlExpression of the Newly Evolved Benzoyloxy Glucosinolate Pathway in Arabidopsis Thaliana." Frontiers in Plant Science 6 (2015): 343. https://dx.doi.org/10.3389/fpls.2015.00343. （第一作者；报道了调控硫苷合成代谢的两个MYB转录因子）

10）Yuanyuan Zhang, Dongxin Huai, Qingyong Yang, Yang Cheng, Ming Ma, Daniel J. Kliebenstein,and Yongming Zhou. "Overexpression of Three Glucosinolate Biosynthesis Genes in Brassica napus Identifies Enhanced Resistanceto Sclerotinia sclerotiorum and Botrytis cinerea." PloS One 10, no. 10 (2015): e0140491. https://dx.doi.org/10.1371/journal.pone.0140491. （第一作者；通过调控硫苷合成基因增强对油菜菌核病的抗病性）

11）Baohua Li, Yuanyuan Zhang, SA. Mohammadi, Dongxin Huai, Yongming Zhou, and Daniel J.Kliebenstein. "An Integrative Genetic Study of Rice Metabolism, Growth and Stochastic Variation Reveals Potential C/N Partitioning Loci." Scientific Reports 6 (2016):30143. https://dx.doi.org/10.1038/srep30143. （并列第一作者；群体代谢组水平阐述了植物碳/氮分配的调控机制）

1）甘蓝型油菜种子硫苷性状的主效QTL位点、SNP分子标记开发及应用，ZL 2019 1 0804728.2（第一完成人）

2）硫苷转运相关的甘蓝型油菜BnaA06.GTR2基因及其应用，ZL 2021 1 0363245.0 （第一完成人）

3）硫苷转运相关的甘蓝型油菜BnaA09.GTR2基因及其应用，ZL 2021 1 0361987.X （第一完成人）

4）一个甘蓝型油菜开花期性状的主效QTL位点、SNP分子标记开发及应用，ZL 2019 1 0521681.9 （第二完成人）

5）一个甘蓝型油菜主花序角果数性状的主效QTL位点、SNP分子标记开发及应用，ZL 2019 1 0521682.3 （第二完成人）

6）甘蓝型油菜种子油酸性状的主效QTL位点、SNP分子标记开发及应用，ZL 2019 1 0804722.5  （第二完成人）

7）调控甘蓝型油菜菌核病抗性的BnTLP1基因及其应用，ZL 2020 1 0905281.0 （第六完成人）

8）真菌病害相关的甘蓝型油菜BnTLK1基因及其应用，ZL 2020 1 0948698.5  （第六完成人）

9）一种鉴定油菜硫苷含量的单倍体型BnHapGLU及其应用，ZL 2016 1 0325474.2 （第八完成人）

10）一种与油菜脂肪酸性状相关的单体型BnHapFatty及其应用，ZL 2016 1 0362173.7 （第八完成人）

11）与甘蓝型油菜第一分枝高度性状紧密相关的主效QTL位点及SNP分子标记及应用，ZL 2020 1 0515090.3 （第九完成人）