发布人:     发布日期: 2021-03-25    浏览次数:

   教授 博士生导师

   办公地址：南京农业大学理科楼 A622   

   联系电话：025-84395702  

   电子邮箱：qxsong@njau.edu.cn

个人简介：

      2006年本科毕业于沈阳农业大学，2006-2013 年在中国科学院遗传与发育生物学研究所攻读博士学位，期间主要研究种子油脂合成调控的分子机理。2013年-2018 年，在美国德克萨斯大学奥斯汀分校从事博士后研究，主要从表观遗传修饰和转录调控网络两个角度研究杂种优势和多倍体化形成的遗传机制。2018 年9 月作为南京农业大学高层次引进人才到农学院任教授。研究论文主要发表在《Nature Genetics》、《Plant Cell》、《PNAS》、《Genome Biology》、《Molecular Plant》、《Nature Communications》等国际主流期刊。

      入选国家青年人才、江苏双创团队领军人才和江苏特聘教授；主持国家重点研发计划青年科学家项目和国家自然科学基金委面上项目等；获得中国农学会青年科技奖和中科院遗传发育所“20年20人”等荣誉；担任Industrial Crops & Products杂志副主编、 Genome Biology和Frontiers in Plant Science等杂志编委；

研究方向：

      在自然进化和人工驯化过程中，作物的形态发生巨大变化。实验室主要以大豆为材料，综合利用生物信息学、群体遗传学和基因编辑等手段，研究表观遗传在多倍体作物进化和驯化中的作用以及鉴定与作物重要农艺性状相关的遗传和表观遗传位点，进一步通过人工设计对农作物进行改良并探索创制多倍体新物种。

      课题组热烈欢迎对生物信息学和表观遗传学感兴趣的同学加入，希望帮助学生在生物学的多个维度得到全方位的锻炼，鼓励学生提出并开展自己感兴趣的科研项目，欢迎感兴趣的学生和我联系。

发表论文(#: co-first author, *: corresponding author)：

Wang L, Zhang M, Li M, Jiang X, Jiao W, Song Q*. (2023) A telomere-to-telomere gap-free assembly of soybean genome. Molecular Plant, 16:1711-1714

Cao S, Chen K, Lu K, Chen S, Zhang X, Shen C, Zhu S, Niu Y, Fan L, Chen, ZJ*, Xu J*,Song Q*. (2023) Asymmetric variation in DNA methylation during domestication and de-domestication of rice. The Plant Cell, 35:3429-3443

Zhang M, Zhang X, Jiang X, Qiu L, Jia G, Wang L, Ye W, Song Q*. (2022) iSoybean: a database for the mutational fingerprints of soybean. Plant Biotechnology Journal, 20:1435-1437

Cao S, Wang L, Han T, Ye W, Liu Y, Sun Y, Moose SP, Song Q*, Chen ZJ*. (2022) Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize. Genome Biology, 23:53

Yuan J, Sun H, Wang Y, Li L, Chen S, Jiao W, Jia G, Wang L, Mao J, Ni Z, Wang X, Song Q*. (2022) Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution. Genome Biology, 23:34

Wang L, Jia G, Jiang X, Cao S, Chen ZJ, Song Q*. (2021) Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. The Plant Cell. 33: 1430-1446

Liu Y, Yuan J*, Jia G, Ye W, Chen ZJ*, Song Q*. (2021) Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization. Plant Journal. 105:678-690

Yuan J, Jiao W, Liu Y, Ye W, Wang X, Liu B, Song Q*, Chen ZJ*. (2020) Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat. BMC Biology. 18:171

Chen ZJ^#*, Sreedasyam A^#, Ando A^#, Song Q^#, De Santiago LM^#, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J* and Schmutz J. (2020) Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics. 52:525-533

Song Q^#, Ando A^#, Jiang N, Ikeda Y and Chen ZJ*. (2020) Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biology. 21:178

Yin D^#*, Ji C^#, Song Q^#, Zhang W^#, Zhang X, Zhao K, Chen CY, Wang C, He G, Liang Z, Ma X, Li Z, Tang Y, Wang Y, Li K, Ning L, Zhang H, Zhao K, Li X, Yu H, Lei Y, Wang M, Ma L, Zheng H, Zhang Y, Zhang J*, Hu W* and Chen ZJ*. (2020) Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. Advanced Science. 7:1901672

Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ*. (2021) An epigenetic basis of inbreeding depression in maize. Science Advances. 7 : eabg5442

Jiang X, Song Q, Ye W, Chen ZJ*. (2021) Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids. Nature Ecology & Evolution. 5:1382-1393

Wang L, Cao S, Wang P, Lu K, Song Q, Zhao FJ, Chen ZJ* (2021) DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance. PNAS. 118:e2023981118

2019年之前

Song Q^#, Huang TY^#, Yu HH, Ando A, Mas P, Ha M, Chen ZJ*. (2019) Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biology. 20:170

Song Q, Ando A, Xu D, Fang L, Zhang T, Huq E, Qiao H, Deng XW*, Chen ZJ*. (2018) Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis. PNAS. 115: 5606-5611.

Song Q, Zhang T, Stelly D and Chen ZJ*. (2017) Epigenomic and functional analyses revealed roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biology. 18:99.

Song Q, Guan X and Chen ZJ*. (2015) Dynamic Roles for Small RNAs and DNA Methylation during Ovule and Fiber Development in Allotetraploid Cotton. PLoS Genetics 11:e1005724.

Miller M^#, Song Q^#, Shi X, Juenger TE and Chen, ZJ*. (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nature Communications 6:7453.

Song Q and Chen, ZJ*. (2015) Epigenetic and developmental regulation in plant polyploids. Current Opinion Plant Biology 24:101-109.

Song QX^#, Li QT^#, Liu YF, Zhang FX, Ma B, Zhang WK, Man WQ, Du WG, Wang GD, Chen SY* and Zhang JS*. (2013) Soybean GmbZIP123 gene enhances lipid content in the seeds of transgenic Arabidopsis plants. Journal of Experimental Botany 64:4329-4341.

Song QX, Lu X, Li QT, Chen H, Hu XY, Ma B, Zhang WK, Chen SY* and Zhang JS*. (2013) Genome-wide analysis of DNA methylation in soybean. Molecular Plant 6:1961-1974.

Song QX, Liu YF, Hu XY, Zhang WK, Ma B, Chen SY* and Zhang JS*. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biology 11:5.

Li QT, Lu X, Song QX, Chen HW, Wei W, Tao JJ, Bian XH, Shen M, Ma B, Zhang WK, Bi YD, Li W, Lai YC, Lam SM, Shui GH, Chen SY* and Zhang JS*. (2017) Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication. Plant Physiology 173:2208-2224.

Saski CA*, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J and Chen ZJ. (2017) Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Scientific Reports 7:15274.

Zheng D, Ye W, Song Q, Han F, Zhang T and Chen ZJ*. (2016) Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton. Plant Physiology 172:1760-1771.

Ko DK, Rohozinski D, Song Q, Taylor SH, Juenger TE, Harmon FG and Chen ZJ*. (2016) Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids. PLoS Genetics 12:e1006197.

Zhang T*, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG0, Thaxton P, Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X, Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W*, Li R* and Chen ZJ*. (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33:531-537.

Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE and Haigler CH*. (2015) Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 16:477.

Guan X, Song Q and Chen ZJ*. (2014) Polyploidy and small RNA regulation of cotton fiber development. Trends Plant Science 19:516-528.

Guan X, Nah G, Song Q, Udall JA, Stelly DM and Chen ZJ*. (2014) Transcriptome analysis of extant cotton progenitors revealed tetraploidization and identified genome-specific single nucleotide polymorphism in diploid and allotetraploid cotton. BMC Research Notes 7:493.

Liu YF, Li QT, Lu X, Song QX, Lam SM, Zhang WK, Ma B, Lin Q, Man WQ, Du WG, Shui GH, Chen SY* and Zhang JS*. (2014) Soybean GmMYB73 promotes lipid accumulation in transgenic plants. BMC Plant Biolology 14:73.

Zou HF, Zhang YQ, Wei W, Chen HW, Song QX, Liu YF, Zhao MY, Wang F, Zhang BC, Lin Q, Zhang WK, Ma B, Zhou YH, Zhang JS* and Chen SY*. (2013) The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis. Biochemical Journal 449:373-378.

Ma B, He SJ, Duan KX, Yin CC, Chen H, Yang C, Xiong Q, Song QX, Lu X, Chen HW, Zhang WK, Lu TG, Chen SY* and Zhang JS*. (2013) Identification of rice ethylene-response mutants and characterization of MHZ7/OsEIN2 in distinct ethylene response and yield trait regulation. Molecular Plant 6:1830-1848.

Hao YJ, Wei W, Song QX, Chen HW, Zhang YQ, Wang F, Zou HF, Lei G, Tian AG, Zhang WK, Ma B, Zhang JS* and Chen SY*. (2011) Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants. Plant Journal 68:302-313.

Hao YJ, Song QX, Chen HW, Zou HF, Wei W, Kang XS, Ma B, Zhang WK, Zhang JS* and Chen SY*. (2010) Plant NAC-type transcription factor proteins contain a NARD domain for repression of transcriptional activation. Planta 232:1033-1043.