商连光课题组

	姓名：		商连光
	职称：		研究员，博士生导师
	电话/传真：
	电子邮件：		shanglianguang@caas.cn
	课题组微信公众号：		iBreeding
	地址：		深圳市大鹏新区布新路97号

 简历介绍：

商连光，研究员，博士生导师。

长期从事全球野生稻及栽培水稻种质资源的收集和创制、并利用水稻大规模种质资源群体集合多组学大数据挖掘野生稻和栽培水稻中耐盐等抗逆、产量等性状具有育种重大价值的优异等位基因，解析其分子机制，及全基因组设计育种和大数据智慧育种等前沿研究。他以第一或通讯作者在Cell Research（2022，封面文章）、The Plant Cell (2024)、Molecular Plant （2020，2021，2023）、Nucleic Acids Research (2023)、Science Bulletin （2024，封面文章）、National Science Review （2024a，2024b）、Trends in Plant Science（2022）、New Phytologist （2020，2024）、Plant Biotechnology Journal （2021，2024）、Plant Communications （2023）、Journal of Integrative Plant Biology （2019，2023，2024a，2024b）、Plant Physiology （2023）等高水平杂志上共发表50余篇SCI论文。获软件著作权5项，专利5项，审定新品种5个。广东省杰出青年基金获得者、入选中国农科院青年创新人才支持计划、人社部首批“博新计划”，并获深圳市高层次人才。担任《Rice》、《New Crops》等期刊编委，获得国家自然科学基金面上项目、广东省自然科学基金、深圳市科技计划、中国博士后科学基金一等资助等多个项目资助。担任Nature Communications、Molecular Plant等多个高水平SCI期刊审稿人。

工作经历：

2021.12 - 至今       中国农业科学院（深圳）农业基因组研究所  研究员, PI

2019.6 - 2021.11   中国农业科学院（深圳）农业基因组研究所  副研究员

2016.7 - 2019.5     中国农业科学院（深圳）农业基因组研究所  助理研究员

教育经历：

2016.7-2019.7    中国农业科学院（深圳）农业基因组研究所 博士后

2010.9-2016.6    中国农业大学 获博士学位

 团队招聘：

常年招访问学者、博士后和客座研究生，欢迎对水稻群体多组学数据挖掘、优异基因克隆和功能组学研究方向感兴趣的优秀科研人员和同学申请。

欢迎各高校和研究单位同学来本课题组实习，欢迎报考本实验室博士和硕士研究生。

团队前期研究中与多个国内外顶尖研究机构和大学建立了良好的合作关系，积累了丰富的包含全球野生稻和栽培稻的稻属核心种质资源、3000余份栽培稻和野生稻不同等遗传背景的大规模遗传渗入系群体、并结合三代基因组测序绘制了群体规模最大的超级泛基因组图谱和多组学图谱，利用超级泛基因组和群体多组学图谱挖掘到了大量有育种价值的基因位点，具有良好的材料、大数据和功能基因组及育种研究基础。

 代表论著（近五年）：

2024年

1. Hong Zhang#, Wu Chen#, De Zhu#, Bintao Zhang#, Qiang Xu#, Huiying He, Xiaofan Dai, Yilin Li, Wenchuang He, Yang Lv, Longbo Yang, Xinglan Cao, Yan Cui, Yue Leng, Hua Wei, Xiangpei Liu, Bin Zhang, Chuanlin Shi, Xianmeng Wang, Mingliang Guo, Zhipeng Zhang, Xiaoxia Li, Congcong Liu, Qiaoling Yuan, Tianyi Wang, Xiaoman Yu, Hongge Qian, Qianqian Zhang, Dandan Chen, Guanjing Hu*, Qian Qian*, Lianguang Shang*. Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice. The Plant Cell, 2024. (IF 11.6)

2. Xiaoxia Li#, Xiaofan Dai#, Huiying He#, Yang Lv#, Longbo Yang#, Wenchuang He, Congcong Liu, Hua Wei, Xiangpei Liu, Qiaoling Yuan, Xianmeng Wang, Tianyi Wang, Bintao Zhang, Hong Zhang, Wu Chen, Yue Leng, Xiaoman Yu, Hongge Qian, Bin Zhang, Mingliang Guo, Zhipeng Zhang, Chuanlin Shi, Qianqian Zhang, Yan Cui, Qiang Xu, Xinglan Cao, Dandan Chen, Yongfeng Zhou*, Qian Qian*, Lianguang Shang*. A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice. National Science Review, 2024. doi:10.1093/nsr/nwae188. (IF 20.6)

3. Hua Wei#, Xianmeng Wang#, Zhipeng Zhang#, Longbo Yang#, Qianqian Zhang#, Yilin Li, Huiying He, Dandan Chen, Bin Zhang, Chongke Zheng, Yue Leng, Xinglan Cao, Yan Cui, Chuanlin Shi, Yifan Liu, Yang Lv, Jie Ma, Wenchuang He, Xiangpei Liu, Qiang Xu, Qiaoling Yuan, Xiaoman Yu, Tianyi Wang, Hongge Qian, Xiaoxia Li, Bintao Zhang, Hong Zhang, Wu Chen, Mingliang Guo, Xiaofan Dai, Yuexing Wang, Xiaoming Zheng, Longbiao Guo, Xianzhi Xie*, Qian Qian*, Lianguang Shang*. Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice. National Science Review, 2024, 11(4): nwae043. doi: 10.1093/nsr/nwae043. (IF 20.6)

4. Yuchao Cui#, Yarong Lin#, Hua Wei#, Yuehan Pan#, Huiying He, Hongge Qian, Longbo Yang, Xinglan Cao, Zhipeng Zhang, Xiaosi Zeng, Tianyi Wang, Wenchuang He, Xiangpei Liu, Chuanlin Shi, Qiaoling Yuan, Xiaoman Yu, Liang Chen, Feng Wang, Yiwang Zhu*, Qian Qian*, Lianguang Shang*. Identification of salt tolerance-associated presence-absence variations in the OsMADS56 gene through the integration of DEGs dataset and eQTL analysis. New Phytologist, 2024. doi: 10.1111/nph.19887. (IF 9.4)

5. Wenchuang He^#, Huiying He^#, Qiaoling Yuan^#, Hai Zhang^#, Xiaoxia Li, Tianyi Wang, Yingxue Yang，Longbo Yang, Yuting Yang, Xiangpei Liu, Hua Wei, Hong Zhang, Bin Zhang, Mingliang Guo, Yue Leng, Chuanlin Shi, Yang Lv, Wu Chen, Xianmeng Wang, Zhipeng Zhang, Bohui Yu, Bintao Zhang, Qiang Xu, Hongge Qian, Yongfeng Zhou, Shaokui Wang*, Qian Qian*, Lianguang Shang*. Widespread inversions shape the genetic and phenotypic diversity in rice. Science Bulletin, 2024. doi: 10.1016/j.scib.2023.12.048 (封面文章，IF 18.9)

6. Yang Lv^#, Congcong Liu^#, Xiaoxia Li^#, Yueying Wang^#, Huiying He, Wenchuang He, Wu Chen, Longbo Yang, Xiaofan Dai, Xinglan Cao, Xiaoman Yu, Jiajia Liu, Bin Zhang, Hua Wei, Hong Zhang, Hongge Qian, Chuanlin Shi, Yue Leng, Xiangpei Liu, Mingliang Guo, Xianmeng Wang, Zhipeng Zhang, Tianyi Wang, Bintao Zhang, Qiang Xu, Yan Cui, Qianqian Zhang, Qiaoling Yuan, Noushin Jahan, Jie Ma, Xiaoming Zheng, Yongfeng Zhou, Qian Qian*, Longbiao Guo*, Lianguang Shang*. A centromere map based on super pan-genome highlights the structure and function of rice centromeres. Journal of Integrative Plant Biology, 2024, 00:1-12. doi:10.1111/jipb.13607. (IF 11.4)

7. Chuanlin Shi#, Wenli Zou#, Xiangpei Liu#, Hong Zhang#, Xiaofang Li, Guiling Fu, Qili Fei*, Qian Qian*, Lianguang Shang*. Programmable RNA N6-methyladenosine editing with CRISPR/dCas13a in plants. Plant Biotechnology Journal, 2024. doi: 10.1111/pbi.14307. (IF 13.2)

8. Zhen Li#, Junhua Ye#, Qiaoling Yuan#, Mengchen Zhang, Xingyu Wang, Jing Wang, Tianyi Wang, Hongge Qian, Xinghua Wei, Yaolong Yang, Lianguang Shang*, Yue Feng*. BTA2 controls tiller angle and the shoot gravity response through regulating auxin content and distribution in rice. Journal of Integrative Plant Biology, 2024. (IF 11.4)

2023年

1. Lianguang Shang^#*, Wenchuang He^#, Tianyi Wang^#, Yingxue Yang^#, Qiang Xu^#, Xianjia Zhao^#, Longbo Yang, Hong Zhang, Xiaoxia Li, Yang Lv, Wu Chen, Shuo Cao, Xianmeng Wang, Bin Zhang, Xiangpei Liu, Xiaoman Yu, Huiying He, Hua Wei, Yue Leng, Chuanlin Shi, Mingliang Guo, Zhipeng Zhang, Bintao Zhang, Qiaoling Yuan, Hongge Qian, Xinglan Cao, Yan Cui, Qianqian Zhang, Xiaofan Dai, Congcong Liu, Longbiao Guo, Yongfeng Zhou, Xiaoming Zheng, Jue Ruan, Zhukuan Cheng, Weihua Pan*, Qian Qian*. A complete assembly of the rice Nipponbare reference genome. Molecular Plant, 2023, 16:1232-1236. doi: 10.1016/j.molp.2023.08.003. (IF 27.5)

2. Tianyi Wang#, Wenchuang He#, Xiaoxia Li#, Chao Zhang#, Huiying He, Qiaoling Yuan, Bin Zhang, Hong Zhang, Yue Leng, Hua Wei, Qiang Xu, Chuanlin Shi, Xiangpei Liu, Mingliang Guo, Xianmeng Wang, Wu Chen, Zhipeng Zhang, Longbo Yang, Yang Lv, Hongge Qian, Bintao Zhang, Xiaoman Yu, Congcong Liu, Xinglan Cao, Yan Cui, Qianqian Zhang, Xiaofan Dai, Longbiao Guo, Yuexing Wang, Yongfeng Zhou, Jue Ruan, Qian Qian*, Lianguang Shang*. A rice variation map derived from 10548 rice accessions reveals the importance of rare variants. Nucleic Acids Research, 2023, 51(20):10924-10933. doi: 10.1093/nar/gkad840. (IF 14.9)

3. Yarong Lin^#, Yiwang Zhu^#, Yuchao Cui^#, Hongge Qian^#, Qiaoling Yuan^#, Rui Chen, Yan Lin, Jianmin Chen, Xishi Zhou, Chuanlin Shi, Huiying He, Taijiao Hu, Chenbo Gu, XiaomanYu, Xiying Zhu, Yuexing Wang, Qian Qian, Cuijun Zhang*, Feng Wang*, Lianguang Shang*. Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome. Journal of Integrative Plant Biology, 2023, 65(12):2541-2551. doi: 10.1111/jipb.13568. (IF 11.4)

4. Zhan Xu^#*, Mingnan Qu^#, Chuanlin Shi^#, Hong Zhang, Wu Chen, Hongge Qian, Zhipeng Zhang , Jiehua Qiu , Qian Qian*, Lianguang Shang*. The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae. Plant Communications, 2023.5(4):100789 doi: 10.1016/j.xplc.2023.100789.（IF 10.5）

5. Chuanlin Shi#, Wenli Zou#, Yiwang Zhu#, Jie Zhang#, Chong Teng, Hua Wei, Huiying He, Wenchuang He, Xiangpei Liu, Bin Zhang, Hong Zhang, Yue Leng, Mingliang Guo, Xianmeng Wang, Wu Chen, Zhipeng Zhang, Hongge Qian, Yan Cui, Hongshuang Jiang, Ying Chen, Qili Fei, Blake C. Meyers, Wanqi Liang*, Qian Qian*, Lianguang Shang*. mRNA cleavage by 21-nucleotide phasiRNAs determines temperature-sensitive male sterility in rice. Plant Physiology, 2023,194(4):2354-2371 doi: 10.1093/plphys/kiad654. (IF 7.4)

6. Weixia Chang, Wei Wang, Zhangsheng Shi, Guodong Cao, Xingchen Zhao, Xiuli Su, Yi Chen, Jiabin Wu, Zhu Yang, Chaolei Liu, Lianguang Shang*, and Zongwei Cai*. Comparative metabolomics combined with physiological analysis revealed cadmium tolerance mechanism in indica rice (Oryza sativa L.). Journal of Agricultural and Food Chemistry, 2023, 71(20):7669-7678. doi:10.1021/acs.jafc.3c00850. (IF 6.1)

2022年

1. Lianguang Shang#*, Xiaoxia Li#, Huiying He#, Qiaoling Yuan#, Yanni Song#, Zhaoran Wei#, Hai Lin#, Min Hu#, Fengli Zhao#, Chao Zhang, Yuhua Li, Hongsheng Gao, Tianyi Wang, Xiangpei Liu, Hong Zhang, Ya Zhang, Shuaimin Cao, Xiaoman Yu, Bintao Zhang, Yong Zhang, Yiqing Tan, Mao Qin, Cheng Ai, Yingxue Yang, Bin Zhang, Zhiqiang Hu, Hongru Wang, Yang Lv, Yuexing Wang, Jie Ma, Quan Wang, Hongwei Lu, Zhe Wu, Shanlin Liu, Zongyi Sun, Hongliang Zhang, Longbiao Guo, Zichao Li, Yongfeng Zhou, Jiayang Li, Zuofeng Zhu*, Guosheng Xiong*, Jue Ruan*, Qian Qian*. A super pan-genomic landscape of rice. Cell Research, 2022. doi.org/10.1038/s41422-022-00685-z (IF 46.297) 封面文章

2. Yanqing Sun#, Lianguang Shang#, QianHao Zhu, Longjiang Fan*, Longbiao Guo*. Twenty years of plant genome sequencing: achievements and challenges. Trends in Plant Science, 2022, 27(4):391-401. doi: 10.1016/j.tplants.2021.10.006. (IF 22.012)

3. Ning Yan#*, Ting Yang#, Xiu-Ting Yu#, Lianguang Shang#, Deping Guo, Yu Zhang, Lin Meng, Qianqian Qi, Yali Li, Yongmei Du, Xinmin Liu, Xiaolong Yuan, Peng Qin, Jie Qiu, Qian Qian*, Zhongfeng Zhang*. Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. Communications Biology, 2022, 5(1):36. doi.org/10.1038/s42003-021-02993-3. (IF 6.548)

4. Shaobo Wei#, Xia Li#, Zefu Lu, Hui Zhang, Xiangyuan Ye, Yujie Zhou, Jing Li, Yanyan Yan, Hongcui Pei, Fengying Duan, Danying Wang, Song Chen, Peng Wang, Chao Zhang, Lianguang Shang, Yue Zhou, Peng Yan, Ming Zhao, Jirong Huang, Ralph Bock, Qian Qian, Wenbin Zhou*, A transcriptional regulator that boosts grain yields and shortens the growth duration of rice. Science, 2022, 377(6604):eabi8455. (IF 63.714)

2021年

1. Jing Xu#, Lianguang Shang#, Jiajia Wang#, Minmin Chen, Xue Fu, Huiying He, Zian Wang, Dali Zeng, Li Zhu, Jiang Hu, Chao Zhang, Guang Chen, Zhenyu Gao, Weiwei Zou, Deyong Ren, Guojun Dong, Lan Shen, Qiang Zhang, Longbiao Guo, Qian Qian*, and Guangheng Zhang*, The SEEDLING BIOMASS 1 allele from indica rice enhances yield performance under low-nitrogen environments. Plant Biotechnology Journal, 2021, 19(9):1681-1683. doi: 10.1111/pbi.13642. (IF 13.263)

2. Jiyue Qiao#, Hongzhen Jiang#, Yuqing Lin#, Lianguang Shang#, Mei Wang, Dongming Li, Xiangdong Fu, Markus Geisler, Yanhua Qi*, Zhenyu Gao*, Qian Qian*, A Novel miR167a-ARF6-AUX3 Pathway Regulates Grain Length and Weight in Rice. Molecular Plant, 2021, 14(10):1683-1698. doi: 10.1016/j.molp.2021.06.023. (IF 21.949)

3. Yang Lv#, Jie Ma#, Yueying Wang#, Quan Wang, Xueli Lu, Haitao Hu, Qian Qian, Longbiao Guo*, and Lianguang Shang*, Loci and natural alleles for low-nitrogen-induced growth response revealed by GWAS analysis in rice (Oryza sativa L.). Frontiers in Plant Science, 2021, 12:770736. doi: 10.3389/fpls.2021.770736. (IF 6.627)

4. Zhaoran Wei#, Qiaoling Yuan#, Hai Lin#, Xiaoxia Li, Chao Zhang, Hongsheng Gao, Bin Zhang, Huiying He, Tianjiao Liu, Zhang Jie, Xu Gao, Shandang Shi, Bo Wang, Zhenyu Gao, Lingrang Kong, Qian Qian*, Lianguang Shang*. Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress. BMC Plant Biology, 2021, 21(1):85. doi: 10.1186/s12870-021-02857-2. (IF 5.26)

5. Jianping Yu#, Chaolei Liu#, Hai Lin#, Bin Zhang, Xiaoxia Li, Qiaoling Yuan, Tianjiao Liu, Huiying He, Zhaoran Wei, Shilin Ding, Chao Zhang, Hongsheng Gao, Longbiao Guo, Quan Wang, Qian Qian*, Lianguang Shang*. Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice. BMC Plant Biology, 2021, 21(1):374. doi: 10.1186/s12870-021-03145-9. (IF 5.26)

6. Jiangfan Guo#, Wei Li#, Lianguang Shang, Yuguang Wang, Peng Yan, Youhuang Bai, Xiaowen Da, kai Wang, Qian Qian, Ruirui Jiang, Chuanzao Mao*, Xiaorong Mo*, OsbHLH98 regulates leaf angle in rice through transcriptional repression of OsBUL1. New Phytologist, 2021, 230(5):1953-1966. doi: 10.1111/nph.17303. (IF 10.323)

2020年

1. Yuexing Wang#, Lianguang Shang#, Hong Yu#, Longjun Zeng#, Jiang Hu, Shen Ni, Yuchun Rao, Sanfeng Li, Jinfang Chu, Xiangbing Meng, Lei Wang, Ping Hu, Shujing Kang, Minghao Qu, Hai Lin, Xingming Hu, Hongqi Chen, Bing Wang, Zhenyu Gao, Dali Zeng, Xudong Zhu, Guosheng Xiong*, Jiayang Li*, Qian Qian*, A strigolactones biosynthesis gene contributed to the Green Revolution in rice. Molecular Plant, 2020, 13(6): 923-932. doi: 10.1016/j.molp.2020.03.009. (IF 13.164)

2. Banpu Ruan#, Lianguang Shang#, Bin Zhang, Jiang Hu, Yuexing Wang, Anpeng Zhang, Chaolei Liu, Youlin Peng, Li Zhu, Deyong Ren, Guojun Dong, Guangheng Zhang, Dali Zeng, Longbiao Guo, Zhenyu Gao* and Qian Qian*, Natural variation in the promoter of TGW2 determines grain width and weight in rice. New Phytologist, 2020, 227(2):629-640. doi: 10.1111/nph.16540. (IF 10.152)

3. Sanfeng Li#, Lan Shen#, Ping Hu, Xianmei Wu, Qiaoling Yuan, Yuchun Rao, Qian Qian, Kejian Wang, Xudong Zhu, Lianguang Shang*, Yuexing Wang*, A Method for Effectively Overcoming Tight Functional Linkage Between Genes in Rice by CRISPR/Cas9 System. Rice Science, 2020, 27(3): 180-183. doi:10.1016/j.rsci.2020.04.002. (IF 3.333)

4. Jun Lv#, Lianguang Shang#, Yun Chen#, Yao Han, Xiaoyan Yang, Shuzhang Xie, Wenqin Bai, Mingyu Hu, Hong Wu, Kairong Lei, Yanan Yang, Shengzhen Ge, Hai Phuong Trinh, Yi Zhang, Longbiao Guo*, Zhongwei Wang, OsSLC1 encodes a pentatricopeptide repeat protein essential for early chloroplast development and seedling survival. Rice, 2020, 13(1):25. doi: 10.1186/s12284-020-00385-5. (IF 4.783)

5. Hongsheng Gao#, Chao Zhang#, Huiying He#, Tianjiao Liu, Bin Zhang, Hai Lin, Xiaoxia Li, Zhaoran Wei, Qiaoling Yuan, Quan Wang, Chunyan Yu*, Lianguang Shang*. Loci and alleles for submergence responses revealed by GWAS and transcriptional analysis in rice. Molecular Breeding, 2020, 40:75. doi: 10.1007/s11032-020-01160-6. (IF 2.589)

2019年

1. Bin Zhang#, Lianguang Shang#, Banpu Ruan, Anpeng Zhang, Shenglong Yang, Hongzhen Jiang, Chaolei Liu, Kai Hong, Hai Lin, Zhenyu Gao, Jiang Hu, Dali Zeng, Longbiao Guo, Qian Qian*, Development of three sets of high-throughput genotyped rice chromosome segment substitution lines and QTL mapping for eleven traits. Rice, 2019, 12(33):1-15. doi: 10.1186/s12284-019-0293-y. (IF 3.912)

2. Chaolei Liu#, Zhenyu Gao#, Lianguang Shang#, Changhong Yang, Banpu Ruan, Dali Zeng, Longbiao Guo, Fangjie Zhao, Chaofeng Huang*, Qian Qian*, Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice. Journal of Integrative Plant Biology, 2019, 62(3):314-329. doi: 10.1111/jipb.12794. (IF 4.885)

3. Yang Lv#, Yueying Wang#, Jahan Noushin, Haitao Hu, Ping Chen, Lianguang Shang, Haiyan Lin, Guojun Dong, Jiang Hu, Li Zhu, Qian Qian, Yu Zhang*, Longbiao Guo*, Genome-wide association analysis and allelic mining of grain.shape related traits in rice. Rice Science, 2019, 26(5): 2. doi:10.1016/j.rsci.2018.09.002. (IF 3.162)

4. Zhenyu Gao#, Yufeng Wang#, Guang Chen#, Anpeng Zhang, Shenglong Yang, Lianguang Shang, Danying Wang, Banpu Ruan, Chaolei Liu, Hongzhen Jiang, Guojun Dong, Li Zhu, Jiang Hu, Guangheng Zhang, Dali Zeng, Longbiao Guo, Guohua Xu, Sheng Teng, Nicholas P Harberd*, Qian Qian*, The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency. Nature Communications, 2019, 10(1):5207. doi: 10.1038/s41467-019-13110-8. (IF 12.121)

2018年

1. Shikai Hu, Xingming Hu, Jiang Hu, Lianguang Shang, Guojun Dong, Dali Zeng, Longbiao Guo, Qian Qian*, Xiaowei, a new rice germplasm for large-scale indoor research. Molecular Plant, 2018, 11(11):1418-1420. doi: 10.1016/j.molp.2018.08.003. (IF 10.812)

商连光课题组更新于2024年6月