Jianxin Ma Publications cont.

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Zhao, M., Du, J., Lin, F., Tong, C., Yu, J., Huang, S. Wang, X. Liu, S., Ma, J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous retrotransposons and relics of a whole genome triplication. Plant J. 76: 211-222.​

Zhao, M., Du, J., Lin, F., Tong, C., Yu, J., Huang, S. Wang, X. Liu, S. Ma, J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous retrotransposons and relics of a whole genome triplication. Plant J. 10.1111/tpj.12291.

Zhao, M., Zhang, B., Liu, S.-Y., and Ma, J. 2013Transposon expression and potential effect on gene regulation in the Brassica rapa and Brassica oleracea genomes. Hereditas 35: 1014-1022.

Zhao, M., and Ma, J. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein Cell 4: 493-501.

Motamayor. J.C., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone, D. 3rd, Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Stack, J.C., Feltus, F.A., Mustiga, G.M., Amores, F., Phillips, W., Marelli, J.P., May, G.D., Shapiro, H., Ma, J., Bustamante, C.D., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol.14: R53.

Lin, F., Zhao, M., Ping, J., Johnson, A., Zhang, B., Abney, T.S., Hughes, T.J., and Ma, J. 2013. Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B. Theor. Appl. Genet. 126: 2177-2185.

Li, Y.H., Zhao, S.C., Ma, J.X., Li, D., Yan, L., Li, J., Qi, X.T., Guo, X.S., Zhang, L., He, W.M., Chang, R.Z., Liang, Q.S., Guo, Y., Ye, C., Wang, X.B., Tao, Y., Guan, R.X., Wang, J.Y., Liu, Y.L., Jin, L.G., Zhang, X.Q., Liu, Z.X., Zhang, L.J., Chen, J., Wang, K.J., Nielsen, R., Li, R.Q., Chen, P.Y., Li, W.B., Reif, J.C., Purugganan, M., Wang, J., Zhang, M.C., Wang, J., Qiu, L.J. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14: 579.

Ma, J., 2013. Retrotransposons. In: Stanley, M., and Kelly, H., (eds). Brenner’s Encyclopedia of Genetics, 2nd edition, Vol. 6., San Diego, Academic Press, p. 208-210.

Yin, H., Liu, J., Xu, Y., Liu, X., Zhang, S., Ma, J., Du, J. 2013. TARE1, a mutated copia-Like LTR retrotransposon followed by recent massive amplification in tomato. PLoS One 8: e68587.

Tian, Z., Zhao, M., She, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Qi, X., Li, M.W., Lam, H.M., and Ma, J. 2012. Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell. 24: 4422-4436.

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 palaeopolyploid soybean (Glycine max (L.). Plant Cell 24: 21-32 

Zhuang, X., Köllner, T., Zhao, N., Li, G., Jiang, Y., Zhu, L., Ma, J. Degenhardt, J. Chen, F.  2012. Dynamic evolution of herbivore-induced sesquiterpene biosynthesis in sorghum and related grass crops. Plant J. 69: 70-80

Li, X., Zhu, C., Lin, Z., Wu, Y., Zhang, D., Ma, J., Song, W., Bai., G., Muehlbauer, G., Scanlon, M., Zhang., M., and Yu,, J. 2011. Conservative boundaries of chromosome size variation in Eukaryotes. Mol. Bio. Evol. 28: 1901-1911

Tian, Z., Yu.Y., Lin, F., Yu, Y.-S., SanMiguel, P., Wing, R.A., McCouch, S., Ma, J.*, and Jackson, S.A.* 2011. Exceptional lability of a genomic complex of rice and its close relatives. BMC Genomics, 12: 142 (*co-corresponding)

Kim, M.Y., Lee, S., Van, K., Kim, T.-H., Jeong, S.-C., Choi, I.-Y., Kim. D.-S., Lee, Y.-S., Park, D., Ma, J., Kim, W.-Y., Kim., B., Park, S., Lee, K.-A., Kim, D.-H., Kim, K.-H., Shin, J.-H., Jang, T.-E., Kim, K.D., Liu, W.X., Chaisan, T., Kang, Y.J., Lee, Y.-H., Kim, K.-H., Moon, J.-K., Schmutz, J., Jackson, S., Bhak, J., and Lee., S.-H. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl. Acad. Sci. USA 107: 22032-22037

Sanyal, A., Jetty, A.S.S., Lu, F., Yu, Y. Rambo, T., Currie, J., Kollura, K., Kim, H.R., Chen, J., Ma, J..SanMiguel, P., Chen, M., Wing, R.A., Jackson, S.A. 2010. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryzaspecies and Ddsruptions to microsynteny in sorghum Mol. Bio. Evol. 27: 2487-2506

Du, J., Tian, Z., Christian, H., Laten, H., Jackson, S., Cannon, S., Shoemaker, R.C., and Ma, J. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: new insights from genome-wide analysis and multi-specific comparison. The Plant Journal 63: 584-598

Findley, S.D., Cannon, S., Varala, K., Du, J., Ma, J., Hudson, M., Birchler, J., and Stacey, G. 2010. A soybean paint-by-numbers kit: a fluorescence in situ hybridization karyotyping system. Genetics 185: 727-744.

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.

The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyonNature 463: 763-768

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

Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J. ... Du, J., Tian, Z., Zhu. L. ... (many others), Rokhsar, D., R.C. Shoemaker, R.C., Jackson, S.A.. 2010. Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature 463: 178-183.

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. The Plant Cell. 22: 48-61

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.

Ma, J. Jackson, S.A., Cannon, S. and Shoemaker, R.C., 2009. Comparative genomics of soybean. In, Bilyeu, K., Ratnaparkhe, M.B., and Kole, C. (ed.), Genetics, Genomics and Breeding in Soybean, Science Publisher, Inc. pp395-410.

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., 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.

Joseph, B., Schlueter, J.A., Du, J., Graham, M.A., Ma, J. and Shoemaker, R.C. 2009. Retrotransposons in the intergenic regions of syntenic blocks between soybean and medicago truncatula and their contribution to local genome evolution. The Plant Genome2:211-223.

Gill, N., Findley, S., Walling, J.G., Ma, J., Stacey, G, Doyle, J.J., and Jackson, S.A. 2009. Molecular and chromosomal evidence for allopolyploidy in soybean, Glycine max (L.) Merr. Plant Physiol. 151:1167-1174.

Gao, D., Gill, N., Kim, H-R., Walling, J., Zhang, W., Fan, C., Yu, Y., Ma, J. SanMiguel, P, Jiang, N., Cheng, Z., Wing, R., Jiang, J., Jackson, S.A. 2009. A lineage-specific centromere retrotransposon in Oryza brachyanthaPlant J.  60:820-831.

Nelson, W.*, Luo, M.*, Ma, J.*, Estep, M,, Estill, J., He, R., Talag, J., Sisneros, N., Kudrna, D., Kim, H., Ammiraju, J.S., Collura, K., Bharti, A.K., Messing, J., Wing, R.A., SanMiguel, P., Bennetzen, J.L., Soderlund, C. 2008. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics 9:621 (*equal contribution)

Ma, J., Wing, R.A., Bennetzen, J.L., and Jackson, S.A. 2007. Evolutionary history and positional shift of a rice centromere. Genetics, 177: 1217-1220.

Jetty, S.S.A., Zuccolo, A., Yu, Y., Song, X., Peigu, B., Chevalier, F., Walling, J.G., Ma., J., Talag, J., Brar, D.S., SanMiguel, P.J., Jinag, N., Jackson, S.A., Panaud, O., and Wing, R.A. 2007. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52: 342-351.

Liu, R., Vitte, C., Ma, J., Mahama, A., Dhliwayo, T., Lee M., and Bennetzen, J.L. 2007. A GeneTrek analysis of the maize genome. Proc. Natl. Acad. Sci. USA 104:11844-11849 

Ma, J., Wing, R.A., Bennetzen, J.L. and Jackson, S.A. 2007. Plant centromere organization:  conserved functions within a dynamic structure. Trends Genet. 23: 134-139

Wing, R.A., Kim, H.R., Goicoechea, J.L., Yu, Y., Kudrna, D.,  Zuccolo, A., Jetty, S.S.A., Luo, M., Nelson, W., Ma, J., SanMiguel, P., Hurwitz, B., Ware, D., Brar, D., Mackill, D., Soderlund, C., Stein, L., and Jackson, S.A. 2006. Resource for comparative genome studies within Oryza. In Upadhyaya, N.M. (ed.) Rice Functional Genomics. Springer (395-410)

Ma, J., and Jackson, S.A. 2006. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res. 16: 251-259

Ma, J., and Bennetzen, J.L. 2006. Recombination, rearrangement, reshuffling and divergence in a centromeric region of rice.  Proc. Natl. Acad. Sci. USA 103: 383-388

Bennetzen, J.L., Liu, R., Ma, J., and Pontaroli, A. 2005. Maize genome structure and rearrangement. Maydica 50: 387-392

Devos, K.M., Ma, J., Pontaroli, A., Pratt, L., and Bennetzen, J.L. 2005. Analysis and physical mapping of randomly chosen BAC clones from hexaploid bread wheat.  Proc. Natl. Acad. Sci. USA 102: 19243-19248

Ma, J., SanMiguel, P.J., Lai, J., Messing, J., and Bennetzen, J.L. 2005. DNA rearrangements in the orthologous Orp regions of the maize, rice and sorghum genomes. Genetics, 170: 1209-1220

Emberton, J.*, Ma, J.*, Yuan, Y., and Bennetzen, J.L. 2005. Consrtuction of HypoMethylated Partial Restriction (HMPR) librariy and it application in sequencing maize genes. Genome Res. 15: 1441-1446 (*co-first authorship)

Bennetzen, J.L., Ma, J., and Devos, K.M. 2005. Mechanisms of recent genome size variation in flowering plants. Annals Bot. 95: 127-132

Ma, J., and Bennetzen, J.L. 2004. Recent rapid growth and divergence of the rice nucleotide genomes. Proc. Natl. Acad. Sci. USA 101: 12404-12410

Ma, J., Devos, K.M., and Bennetzen, J.L. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res.14: 860-869

Swigonova, Z., Lai, J., Ma, J., Ramakrishna, R., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. Close split of the maize and sorghum progenitors. Genome Res. 14: 1916-1923

Lai, J., Ma, J., Swigonova, Z., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. Gene loss and movement in the maize genome. Genome Res. 14: 1924-1931

Bennetzen, J.L., Coleman, C., Liu, R., Ma, J., and Ramakrishna, W. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736

Swigonova, Z., Lai, J., Ma, J., Ramakrishna, R., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. On the tetraploid origin of maize genome. Comp. Funct. Genomics. 5: 281-284

Bennetzen, J.L., and Ma, J. 2003. The genetic colinearity of rice and other cereals based on gnomic sequence analysis. Curr. Opin. Plant Biol., 6:  128-133

Wang, L., Ma, J., Zhou, R., Wang, X., and Jia, J. 2002. Molecular tagging of the yellow rust resistance gene Yr10 in common wheat, P.I.178383 (Triticum aestivum L.). Euphytica 124: 71-73

Ramakrishna, W., Ma, J., SanMiguel, P., Emberton, J., Dubcovsky, J., Shiloff, B.A., Jiang, Z., Rostoks N., Busso, C.S., Matthew, O., Linton, E., Kleinhofs, A., Devos, K.M., Messing, J., and Bennetzen, J.L. 2002. Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. Comp. Funct. Genomics, 3:165-166

Rostoks, N., Park, Y.-J., Ramakrishna, W., Ma, J., Druka, A., Shiloff, B.A., SanMiguel, P.J., Jiang, Z., Brueggeman, R., Sandhu, D., Gill, K., Bennetzen, J.L., and Kleinhofs, A. 2002. Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct. Integr. Genomics, 10: 1007-1014

Ma, J., Zhou, R., Dong, Y., and Jia J.  2001. Chromosomal location and detection of a yellow rust resistance gene in common wheat transferred from Triticum tugidum L. using microsatellite markers. Euphytica, 120: 219-226

Ma, J., Zhou, R., Dong, Y., and Jia J. 2000. Control and inheritance of resistance to yellow rust in Triticum aestivum-Lophopyrum elongatum chromosomal substitution lines. Euphytica, 111:57-60

Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Chromosomal location of yellow rust resistance gene in Triticum aestivum-Lophopyrum elongatum substitution lines. Chn. Sci. Bull., 44: 65-69

Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Molecular mapping of yellow rust resistance genes of wheat. Biotech. Bull., 24: 1-6

Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Genetic stability and transmission of chromosome 6V from H. villosa through gametes in wheat background. Chn. J. Genetics, 26: 384-390

Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Molecular mapping of a novel yellow rust resistance gene of wheat using microsatellite markers. Chn. Sci. Bull., 44: 1513-1517

Ma, J., Zhou, R., and Jia, J. 1997. Identification of wheat-Haynaldia villosa substitution line conferring resistance to powdery mildew using GISH and RFLP markers. Chn. J. Genetics 24: 309-314