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  2021      
  Yu H.*, Lin T.*, Meng X.*, Du H.*, Zhang J.*, Liu G., Chen M., Jing Y., Kou L., Li X., Gao Q., Liang Y., Liu X., Fan Z., Liang Y., Cheng Z., Chen M., Tian Z., Wang Y., Chu C., Zuo J., Wan J., Qian Q., Han B., Zuccolo A., Wing R., Gao C., Liang C., and Li J.. 2021. A route to de novo domestication of wild allotetraploid rice. Cell 184: 1156-1170.e14.      
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  Wang C., Ji W., Liu Y., Zhou P., Meng Y., Zhang P., Wen J., Mysore K., Zhai J., Young N., Tian Z., Niu L., Lin H.. 2021. The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula. New Phytol 229: 3330-3344.      
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  Liu Q., Jiao X., Meng X., Wang C., Xu C., Tian Z., Xie C., Li G., Li J., Yu H., Wang K.. 2021. FED: a web tool for foreign element detection of genome-edited organism. Sci China Life Sci 64: 167-170.      
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  Li X., Wang P., Zhang K., Liu S., Qi Z., Fang Y., Wang Y., Tian X., Song J., Wang J., Yang C., Sun X., Tian Z., Li W., Ning H.. 2021. Fine mapping QTL and mining genes for protein content in soybean by the combination of linkage and association analysis. Theor Appl Genet 134: 1095-1122.      
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  2020      
  Tian Z.*, Wang J.*, Li J., and Han B.. 2020. Designing future crops: challenges and strategies for sustainable agriculture. Plant J      
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  Liu Y., and Tian Z.2020. From one linear genome to a graph-based pan-genome: a new era for genomics. Sci China Life Sci. 63      
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Liu S.*, Fan L., Liu Z., Yang X., Zhang Z., Duan Z., Liang Q., Imran M., Zhang M., and Tian Z.†. 2020. A Pd1-Ps-P1 Feedback Loop Controls Pubescence Density in Soybean. Mol Plant 13: 1-16.

     
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  Liu Y.*, Du H.*, Li P., Shen Y., Peng H., Liu S., Zhou GA., Zhang H., Liu Z., Shi M., Huang X., Li Y., Zhang M., Wang Z., Zhu B., Han B., Liang C.†, and Tian Z.†2020. Pan-genome of wild and cultivated soybeans. Cell 182:1–15.      
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  Wang S.*, Liu S.*, Wang J.*, Yokosho K., Zhou B., Yu Y.C., Liu Z., Frommer W.B., Ma J.F., Chen L.Q.†, Guan Y.†, Shou H.†, and Tian Z.†2020. Simultaneous changes in seed size, oil content, and protein content driven by selection of SWEET homologues during soybean domestication. Natl Sci Rev 7: 1776–1786.      
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  Liu S., Zhang M., Feng F., and Tian Z.†2020. Toward a “green revolution” for soybean. Mol Plant 13: 688-697.      
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  Lu S.*, Dong L.*, Fang C.*, Liu S.*, Kong L.*, Cheng Q.*, Chen L.*, Su T., Nan H., Zhang D., Zhang L., Wang Z., Yang Y., Yu D., Liu X., Yang Q., Lin X., Tang Y., Zhao X., Yang X., Tian C., Xie Q., Li X., Yuan X.Tian Z.†, Liu B., Weller J., and Kong F.2020. Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication. Nat Genet 52:428-436.      
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  Dong X.*, Wang Z.*, Tian L., Zhang Y., Qi D., Huo H., Xu Ji., Li Z., Liao R., Shi M., Wahocho S-A., Liu C., Zhang S., Tian Z., and Cao Y.2020De novo assembly of a wild pear (Pyrus betuleafolia) genome. Plant Biotechnol J 1:1-15.      
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  Zhu X., Pan Y., Liu Z., Liu Y., Zhong D., Duan Z., Tian Z., Zhu B., and Zhou G.. 2020. Mutation of YL results in a yellow leaf with chloroplast RNA editing defect in soybean. Int J Mol Sci 21: E4275.      
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  Tian X.*, Zhang K.*, Liu S., Sun X., Li X., Song J., Qi Z., Wang Y., Fang Y., Wang J., Jiang S., Yang C., Tian Z., Li W., and Ning H.. 2020. Quantitative trait locus analysis of protein and oil content in response to planting density in soybean (Glycine max [L.] Merri.) seeds based on SNP linkage mapping. Front Genet 11: 563.      
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  Qi Z., Song J., Zhang K., Liu S., Tian X., Wang Y., Fang Y., Li X., Wang J., Yang C., Jiang S., Sun X., Tian Z., Li WX., Ning H.. 2020. Identification of QTNs controlling 100-seed weight in soybean using multi-locus genome-wide association studies. Front Genet 11: 689.      
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  Fang Y.*, Liu S., Dong Q., Zhang K., Tian Z., Li X., Li W., Qi Z., Wang Y., Tian X., Song J., Wang J., Yang C., Jiang S., Li WX., Ning H.2020. Linkage analysis and multi-locus genome-wide association studies identify QTNs controlling soybean plant height. Front Plant Sci 11:9.      
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  2019      
  Shen Y.*, Du H.*, Liu Y., Ni L., Wang Z., Liang C., and Tian Z.2019. Update soybean Zhonghuang 13 genome to a golden reference. Sci China Life Sci. 62:1257-1260      
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  Chen E., Huang X.†, Tian Z., Wing RA., Han B.. 2019. The genomics of Oryza species provides insights into rice domestication and heterosis. Annu Rev Plant Biol. 70:639-665      
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  Liu W.*, Chen L.*, Zhang S.*, Hu F., Wang Z., Lyu J., Wang B., Xiang H., Zhao R., Tian Z., Ge S.†, and Wang W.. 2019. Decrease of gene expression diversity during domestication of animals and plants. BMC Evol Biol. 19:19      
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  2018      
  Zhang K.*, Liu S.*, Li W., Liu S., Li X., Fang Y., Zhang J., Wang Y., Xu S., Zhang J., Song J., Qi Z., Tian X., Tian Z., Li W-X.†, and Ning H.†. 2018 Identification of QTNs controlling seed protein content in soybean using multi-locus genome-wide association studies. Front. Plant Sci. 9:1690      
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  Wang M.*, Li W.*, Fang C.*, Xu F.*, Liu Y.*, Wang Z., Yang R., Zhang M., Liu S., Lu S., Lin T., Tang J., Wang Y., Wang H., Lin H., Zhu B., Chen M., Kong F., Liu B., Zeng D., Jackson S., Chu C., and Tian Z.. 2018. Parallel domestication selection of a dormancy gene in crops from multiple families. Nat Genet 50:14351441      
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  Shen Y.*, Zhang J., Liu Y., Liu S., Liu Z., Duan Z., Wang Z., Zhu B., Guo YL., and Tian Z.. 2018. DNA methylation footprints during soybean domestication and improvement. Genome Biol 19:128      
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  Shen Y.*, Liu J., Geng H., Zhang J., Liu Y., Zhang H., Xing S., Du J., Ma S., and Tian Z.. 2018. De novo assembly of a Chinese soybean genome. Sci China Life Sci 61: 871-884      
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  Xu R.*, Duan P., Yu H., Zhou Z., Zhang B., Wang R., Li J., Zhang G., Zhuang S., Lyu J., Li N., Chai T., Tian Z., Yao S., and Li Y.. 2018. Control of grain size and weight by the OsMKKK10-OsMKK4-OsMAPK6 signaling pathway in rice. Mol Plant 11: 860-873      
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  Zhang D.*, Sun L.*, Li S.*, Wang W.*, Ding Y., Swarm S., Li L., Wang X., Tang X., Zhang Z., Tian Z., J. Brown P., Cai C., Nelson R., Ma J.. 2018. Elevation of soybean seed oil content through selection for seed coat shininess. Nat Plants 4: 30-35      
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  2017      
  Zou Y.*, Hou X.*, Wu Q., Chen J., Li Z., Han T., Niu X., Yang L., Xu Y., Zhang J., Zhang F., Tan D., Tian Z., Gu H. and Guo Y.. 2017. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol 18:239      
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  Fang C.*, Ma Y.*, Wu S.*, Liu Z., Wang Z., Yang R., Hu G., Zhou Z., Yu H., Zhang M., Pan Y., Zhou G., Ren H., Du W., Yan H., Wang Y., Han D., Shen Y., Liu S., Liu T., Zhang J., Qin H., Yuan J., Yuan X., Kong F., Liu B., Li J., Zhang Z., Wang G., Zhu B., and Tian Z.†. 2017. Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean. Genome Biol 18:161      
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  Chu S.*, Wang J.*, Zhu Y.*, Liu S., Zhou X., Zhang H., Wang C., Yang W., Tian Z., Cheng H., Yu D.. 2017. A R2R3-type MYB transcription factor GmMYB29 regulates isoflavonoid biosynthesis in soybean. PLoS Genet 13: e1006770      
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  Lu S.*, Zhao X.*, Hu Y., * Liu S.*, Nan H., Li X., Fang C., Cao D., Shi X., Kong L., Su T., Zhang F., Li S., Wang Z., Yuan X., Cober E., Weller J., Liu B., Hou X., Tian Z.†, and Kong F.†. 2017. Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield. Nat Genet 49(5):773-779      
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  Zeng D.*, Tian Z.*, Rao Y., Dong G., Yang Y., Huang L., Leng Y., Xu J., Sun C., Zhang G., Hu J., Zhu L., Gao Z., Hu X., Guo L., Xiong G., Wang Y., Li J.†, Qian Q.†. 2017. Rational design of high-yield and superior-quality rice. Nat Plants 3:17031      
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  2016      
  Cao, K.*, Zhou, Z.*, Wang, Q., Guo, J., Zhao, P., Zhu, G., Fang, W., Chen, C., Wang, X., Wang, X., Tian, Z.†, and Wang, L.†. 2016. Genome-wide association study of 12 agronomic traits in peach. Nat Commun 7:13246      
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  Li, Q.*, Fang, C., Duan, Z., Liu, Y., Qin, H., Zhang, J., Sun, P., Li, W., Wang, G., Tian, Z.† 2016. Functional conservation and divergence of GmCHLI genes in polyploid soybean.Plant J 88:584-596      
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  Takeshima, R.*, Hayashi, T., Zhu, J., Zhao, C., Xu, M., Yamaguchi, N., Sayama, T., Ishimoto, M., Kong, L., Shi, X., Liu, B., Tian, Z., Yamada, T., Kong, F.†, and Abe, J.†. 2016. A soybean quantitative trait locus that promotes flowering under long days is identified as FT5a, a FLOWERING LOCUS T ortholog. J Exp Bot 67: 5247-5258      
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  Fang, C.*, Ma, Y., Yuan, L., Wang, Z., Yang, R., Zhou, Z., Liu, T., and Tian, Z.† 2016. Chloroplasts DNA underwent independent selection from nuclear genes during soybean domestication and improvement. J Genet Genomics 43:217-221      
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  Liu, T.*, Fang, C., Ma, Y., Shen, Y., Li, C.,Li, Q., Wang, M., Liu, S., Zhang, J., Zhou, Z., Yang, R., Wang, Z., Tian, Z. 2016.Global investigation of the coevolution of MIRNA genes and microRNA targets during soybean domestication.Plant J 85: 396-409      
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  2015      
  Yang, K.*, Tian, Z.*, Chen, C.*, Luo, L.*, Zhao, B., Wang, Z., Yu, L., Li, Y., Sun, Y., Li, W., Chen, Y., Li, Y., Zhang, Y., Ai, D., Zhao, J., Shang, C., Ma, Y., Wu, B., Wang, M., Gao, L., Sun, D., Zhang, P., Guo, F., Wang, W., Li, Y., Wang, J., Varshney RK., Wang, J.†, Ling, H.†, and Wan, P.†2015. Genome sequencing of adzuki bean (Vigna angularis) provides insight into high starch and low fat accumulation and domestication. Proc Natl Acad Sci USA 112: 13213-8      
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  Wang, Z.*, and Tian, Z. 2015. Genomics progress will facilitate molecular breeding in soybean. Sci China Life Sci 58: 813-815      
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  Bai, C.*, Guo, P.*, Zhao, Q., Lv, Z., Zhang, S., Gao, F., Gao, L., Wang, Y., Tian, Z., Wang, J., Yang, F., Liu, C. 2015. Protomer roles in chloroplast chaperonin assembly and function. Mol Plant 8: 1478-92      
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  Wang, Z.*, Zhou, Z.*, Liu, Y.*, Liu, T., Li, Q., Ji, Y., Li, C., Fang, C., Wang, M., Wu, M., Shen, Y., Tang, T., Ma, J.†, and Tian, Z. 2015. Functional evolution of phosphatidylethanolamine-binding proteins in soybean and Arabidopsis.  Plant Cell 27: 323-336      
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  Zhou, Z.*, Jiang, Y.*, Wang Z.*, Gou Z.*, Lyu J.*, Li W.*, Yu Y., Shu L., Zhao Y., Ma Y., Fang C., Shen Y., Liu T., Li C., Li Q., Wu M., Wang M., Wu Y., Dong Y., Wan W., Wang X., Ding Z., Gao Y., Xiang H., Zhu B., Lee SH., Wang W..†, and Tian Z. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature Biotechnol 33: 408–414      
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2014
  Ping, J., Liu, Y. Sun, L., Zhao, M., Li, Y., She, M., Sui, Y., Lin, F., Liu, X., Tang, Z., Nguyen, H., Tian, Z., Qiu, L., Nelson, RL., Clemente, TE., Specht, JE., and Ma, J.† 2014. Dt2 is a gain-of-function MADS-domain factor gene that specifies semideterminacy in soybean. Plant Cell 26: 2831-2842    
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  Shen, Y.*, Zhou, Z.*, Wang, Z., Li, W., Fang, C., Wu, M., Ma, Y., Liu, T., Kong, L.A., Peng, D.L., and Tian, Z.† 2014. Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell 26: 996–1008    
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  Zhang, F.*, Shen,Y.*, Sun, S.*, Guo, J., Li, C., Wu, C., Li, Q., Nian, H., Huang, X., Tian, Z., and Han, T.† 2014. Genome-wide gene expression analysis in a dwarf soybean mutant. Plant Genetic Resources: Characterization and Utilization 12(S1):S70-S73    
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Fang, C.*, Li, C.*, Li, W., Wang, Z., Zhou, Z., Shen, Y., Wu, M., Wu, Y., Li, G., Kong, L.A., Liu, C., Jackson, S.A. †, and Tian, Z.† 2014. Concerted evolution of D1 and D2 to regulate chlorophyll degradation in soybean. Plant J 77: 700–712
   
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2013
 
Zhou, Z.*, Wang, Z.*, Li, W.*, Fang, C., Shen, Y., Li, C., Wu, Y., and Tian, Z† 2013. Comprehensive analyses of microRNA genes evolution in paleopolyploid soybean genome. Plant J 76: 332-344
   
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Fang, C.*, Li, W.*, Li, G., Wang, Z., Zhou, Z., Ma, Y., Shen, Y., Li, C., Wu, Y., Zhu, B., Yang, W., and Tian, Z.† 2013. Cloning of Ln gene through combined approach of map-based cloning and association study in soybean. J. Genet. Genomics 40: 93-96
   
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2012
 
Tian, Z., Zhao, M., She, M., Du, J., Cannon, S., Liu, X., Xu, X., Qi, X., Li, M., Lam, H., and Ma, J.† 2012. Genome-wide characterization of non-reference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell 24: 4422-4436
   
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Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P., and Ma, J.† 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean.Plant Cell 24:21-32
   
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Before 2012
  Gao, Z., Zeng, D., Cheng, F., Tian, Z., Guo, L., Su,Y., Yan, M., Jiang, H., Dong, G., Huang, Y., Han, H., Li, J., and Qian, Q.† 2011. ALK, the key gene for gelatinization temperature, is a modifier gene for gel consistency in rice (Oryza sativa L.).J Integr Plant Biol.10:756
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Tian, Z., Yu, Y., Lin, F., Yu, YS., SanMiguel, JP., Wing, AR., McCouch, RS., Ma, J.†, and Jackson, AS.† 2011. Exceptional lability of a genomic complex in rice and its close relatives. BMC Genomics.12:124
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Yan, C.*, Tian, Z.*, Fang, Y., Yang, Y., Li, J., Zeng, S., Gu, S., Xu, C., T, and Gu, M.† 2011. Genetic dissection of starch paste viscosity characteristics in glutinous rice (Oryza sativa L.). Theor Appl Genet 122: 63-76 (*Co-first author)
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Tian, Z.*, Yan, C.*, Qian, Q., Yan, S., Xie, H., Wang, F., Xu, J., Liu, G., Wang, Y., Liu, Q., Tang, S., Li, J. #, and Gu, M.† 2010. Development of gene-tagged molecular markers for starch synthesis-related genes in rice. Chinese Sci Bull 55: 2591-2601
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Du, J., Tian, Z., Hans, C., Laten, H., Jackson, S., Cannon, S., Shoemaker, R.†, and Ma, J.† 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63: 584-598
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Tian, Z.*, Wang, X.*, Lee, R., Li, Y., Specht, J., Nelson, R., McClean, P.†, Qiu, L.†, and Ma, J.† 2010. Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107: 8563-8568
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  Du, J., Grant, D., Tian, Z., Nelson, R.T., Zhu, L., Shoemaker, R.C.†, and Ma, J.† 2010. SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11: 113
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Du, J., Tian, Z., Schmutz, J., Bowen, N.J., Shoemaker, R.C., and Ma, J.† 2010. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. Plant Cell 22: 48-61
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Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., ... Du, J., Tian, Z., Zhu, L.…, Rokhsar, D., Shoemaker, R.C., Jackson, S.A.† 2010. Genome sequence of the paleopolyploid soybean. Nature 463: 178-183
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Tian, Z.*, Qian, Q.*, Liu, Q.*, Yan, M., Liu, X., Yan, C., Liu, G., Gao, Z., Tang, S., Zeng, D., Wang, Y., Yu, J.†, Gu, M.† and Li, J.† 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106: 21760-21765.
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Tian, Z.*, Rizzon, C.*, Du, J., Liu, Z., Bennetzen, J. L., Gaut, B. #, Jackson, S. A.†, and Ma, J.† 2009. Do genetic recombination and gene density shape the pattern of DNA elimination in rice LTR-retrotransposons? Genome Res 19:2221-2230.
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  Wu, J.*, Fujisawa, M.*, Tian, Z.*, Yamagata, H., Kamiya, K., Shibata, M., Hosokawa, S., Ito, Y., Hamada, M., Katagiri, S., Kurita, K., Yamamoto, M., Kikuta, A., Machita, K., Karasawa, W., Kanamori, H., Namiki, N., Mizuno, H., Ma, J., Sasaki, T., and Matsumoto, T.† 2009. Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure. Plant J 60:805-819
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