References
- Almeida, G. D., D. Makumbi, C. Magorokosho, S. Nair, A. Borem, J.-M. Ribaut, M. Banziger, B. M. Prasanna, J. Crossa, and R. Babu. 2013. QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance. Theor. Appl. Genet. 126(3) : 583-600. https://doi.org/10.1007/s00122-012-2003-7
- Baker, M. 2012. De novo genome assembly: what every biologist should know. Nat. Methods. 9 : 333. https://doi.org/10.1038/nmeth.1935
- Banzinger, M., G. O. Edmeades, D. L. Beck, and M. Bellon. 2000. Breeding for drought and N stress tolerance in maize: from theory to practice. CIMMYT, Mexico, D. F.
- Banzinger, M., P. S. Setimela, D. Hodson, and B. Vivek. 2006. Breeding for improved abiotic stress tolerance in maize adapted to southern Africa. Agr. Water Manage. 80 : 1-3 https://doi.org/10.1016/j.agwat.2005.07.002
- Bassetti, P. and M. E. Westgate. 1993. Water deficit affects receptivity of maize silks. Crop Sci. 33 : 279-282. https://doi.org/10.2135/cropsci1993.0011183X003300020013x
- Bawa, A., I. K. Addai, and J. X. Kugbe. 2015. Evaluation of some genotypes of maize (Zea mays L.) for tolerance to drought in Northern Ghana. Plant Biol. 5(6) : 19-29.
- Birol, I., S. D. Jackman, C. B. Nielsen, J. Q. Qian, R. Varhol, G. Stazyk, R. D. Morin, Y. Zhao, M. Hirst, J. E. Schein, D. E. Horsman, J. M. Connors, R. D. Gascoyne, M. A. Marra, and S. J. M. Jones. 2009. De novo transcriptome assembly with ABySS. Bioinformatics. 25(21) : 2872-7. https://doi.org/10.1093/bioinformatics/btp367
- Bohnert, H. J., D. E. Nelson, and R. G. Jensen. 1995. Adaptations to environmental stresses. The plant cell. 7(7) : 1099-1111. https://doi.org/10.2307/3870060
- Bolanos, J. and G. O. Edmeades. 1993. Eight cycle of selection for drought tolerance in lowland tropical maize. II. Responses in reproductive behavior. Field Crops Res. 31 : 269-289. https://doi.org/10.1016/0378-4290(93)90066-V
- Bolanos, J. and G. O. Edmeades. 1996. The importance of the anthesis-silking interval in breeding for drought tolerance in tropical maize. Field Crops Research. 48 : 65-80. https://doi.org/10.1016/0378-4290(96)00036-6
- Bradnam, K. R., J. N. Fass, A. Alexandrov, P. Baranay, M. Bechner, I. Birol, S. Boisvert, J. A. Chapman, G. Chapuis, R. Chikhi, H. Chitsaz, W. C. Chou, J. Corbeil, C. Del Fabbro, T. R. Docking, R. Durbin, D. Earl, S. Emrich, P. Fedotov, N. A. Fonseca, G. Ganapathy, R. A. Gibbs, S. Gnerre, E. Godzaridis, S. Goldstein, M. Haimel, G. Hall, D. Haussler, J. B. Hiatt, I. Y. Ho, J. Howard, M. Hunt, S. D. Jackman, D. B. Jaffe, E. D. Jarvis, H. Jiang, S. Kazakov, P. J. Kersey, J. O. Kitzman, J. R. Knight, S. Koren, T. W. Lam, D. Lavenier, F. Laviolette, Y. Li, Z. Li, B. Liu, Y. Liu, R. Luo, I. Maccallum, M. D. Macmanes, N. Maillet, S. Melnikov, D. Naquin, Z. Ning, T. D. Otto, B. Paten, O. S. Paulo, A. M. Phillippy, F. Pina-Martins, M. Place, D. Przybylski, X. Qin, C. Qu, F. J. Ribeiro, S. Richards, D. S. Rokhsar, J. G. Ruby, S. Scalabrin, M. C. Schatz, D. C. Schwartz, A. Sergushichev, T. Sharpe, T. I. Shaw, J. Shendure, Y. Shi, J. T. Simpson, H. Song, F. Tsarev, F. Vezzi, R. Vicedomini, B. M. Vieira, J. Wang, K. C. Worley, S. Yin, S. M. Yiu, J. Yuan, G. Zhang, H. Zhang, S. Zhou, and I. F. Korf. 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2 : 1-31. https://doi.org/10.1186/2047-217X-2-1
- Bray, E. A. 1993. Molecular responses to water deficit. Plant Physiol. 103(4) : 1035-1040. https://doi.org/10.1104/pp.103.4.1035
- Briskine, R. V. and K. K. Shimizu. 2017. Positional bias in variant calls against draft reference assemblies. BMC Genomics. 18 : 1. https://doi.org/10.1186/s12864-016-3406-7
- Buckler, E. S., J. B. Holland, P. J. Bradbury, C. Acharya, P. J. Brown, C. Browne, E. Ersoz, S. Flint-Garcia, A. Garcia, J. C. Glaubitz, M. M. Goodman, C. Harjes, K. Guill, D. E. Kroon, S. Larsson, N. K. Lepak, H. Li, S. E. Mitchell, G. Pressoir, J. A. Peiffer, M. O. Rosas, T. R. Rocheford, M. C. Romay, S. Romero, S. Salvo, V. H. Sanchez, H. S. da Silva, Q. Sun, F. Tian, N. Upadyayula, D. Ware, H. Yates, J. Yu, Z. Zhang, S. Kresovich, and M. D. McMullen. 2009. The genetic architecture of maize flowering time. Science. 325 : 714-718. https://doi.org/10.1126/science.1174276
- Byrne, P. F., J. Bolanos, G. O. Edmeades, and D. L. Eaton. 1995. Gains from selection under drought versus multilocation testing in related tropical maize populations. Crop Science. 35 : 63. https://doi.org/10.2135/cropsci1995.0011183X003500010011x
- Chapman, S. C. and G. O. Edmeades. 1999. Selection improves drought tolerance in tropical maize populations : II. Direct and correlated responses among secondary traits. Crop Science. 39 : 1315-1324. https://doi.org/10.2135/cropsci1999.3951315x
- Duan, J., C. Xia, G. Zhao, J. Jia, and X. Kong. 2012. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics. 13(1) : 392. https://doi.org/10.1186/1471-2164-13-392
- Edmeades, G. O., M. Banziger, A. Elings, S. C. Chapman, and J. M. Ribaut. 1997. Recent advances in breeding for drought tolerance in maize. Applications of Systems Approaches at the Field Level. 63-78.
- Edmeades, G. O., J. Bolanos, A. Elings, J. M. Ribaut, M. Banziger, and M. E. Westgate. 2000. The role and regulation of the anthesis-silking interval in maize. In: Westgate, M. E. and K. J. Boote. (eds). Physiology and Modeling Kernel Set in Maize. CSSA, Madison, WI, CSSA Special Publication No. 29. pp. 43-73.
- Fan, H., Y. Xiao, Y. Yang, W. Xia, A. S. Mason, Z. H. Xia, F. Qiao, S. L. Zhao, and H. R. Tang. 2013. RNA-Seq analysis of Cocos nucifera : transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. PloS one. 8(3) : e59997. https://doi.org/10.1371/journal.pone.0059997
- Fuad-Hassan, A., F. Tardieu, and O. Turc. 2008. Drought-induced changes in anthesis-silking interval are related to silk expansion: a spatio-temporal growth analysis in maize plants subjected to soil water deficit. Plant, Cell and Environ. 31 : 1349-1360. https://doi.org/10.1111/j.1365-3040.2008.01839.x
- Grabherr, M. G., B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng, Z. Chen, E. Mauceli, N. Hacohen, A. Gnirke, N. Rhind, F. di Palma, B. W. Birren, C. Nusbaum, K. Lindblad-Toh, N. Friedman, and A. Regev. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29(7) : 644-52. https://doi.org/10.1038/nbt.1883
- Gong, F., L. Yang, F. Tai, X. Hu, and W. Wang. 2014. "Omics" of maize stress response for sustainable food production: opportunities and challenges. Omics 18(12) : 714-732. https://doi.org/10.1089/omi.2014.0125
- Hall, A. J., J. H. Lemcoff, and N. Trapani. 1981. Water stress before and during flowering in maize and its effects on yield, its components, and their determinants. Maydica. 26 : 19-38.
- Harder, H. J., R. E. Carlson, and R. H. Shaw. 1982. Yield, yield components, and nutrient content of corn grains as influenced by post-silking moisture stress. Agronomy J. 74(2) : 275-278. https://doi.org/10.2134/agronj1982.00021962007400020005x
- Kim, H. C., J.-C. Moon, J. Y. Kim, K. Song, K.-H. Kim, and B.-M. Lee. 2017. Evaluation of drought tolerance using anthesissilking interval in maize. Korean J. Crop Sci. 62(1) : 24-31. https://doi.org/10.7740/kjcs.2016.62.1.024
- Lehtimaki, N., M. Lintala, Y. Allahverdiyeva, E. M. Aro, and P. Mulo. 2010. Drought stress-induced upregulation of components involved in ferredoxin-dependent cyclic electron transfer. J Plant Physiol. 167 : 1018-1022. https://doi.org/10.1016/j.jplph.2010.02.006
- Li, R., C. Yu, Y. Li, T. W. Lam, S. M. Yiu, K. Kristiansen, and J. Wang. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 25(15) : 1966-1997. https://doi.org/10.1093/bioinformatics/btp336
- Li, Y. X., C. Li, P. J. Bradbury, X. Liu, F. Lu, C. M. Romay, J. C. Glaubitz, X. Wu1, B. Peng, Y. Shi, Y. Song, D. Zhang, E. S. Buckler, Z. Zhang, Y. Li, and T. Wang. 2016. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population. Plant J. 86 : 391-402. https://doi.org/10.1111/tpj.13174
- Lischer, H. E. L. and K. K. Shimizu. 2017. Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC Bioinformatics. 18 : 474. https://doi.org/10.1186/s12859-017-1911-6
-
Livak, K. J. and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the
$2^{-{\Delta}{\Delta}CT}$ Method. Methods. 25 : 402-408. https://doi.org/10.1006/meth.2001.1262 - Lu, Y., Z. Hao, C. Xie, J. Crossa, J. L. Arus, S. Gao, B. S. Vivek, C. Magorokosho, S. Mugo, D. Makumbi, S. Taba, G. Pan, X. Li, T. Rong, S. Zhang, and Y. Xu. 2011. Large-scale screening for maize drought resistance using multiple selection criteria evaluated under water-stressed and well-watered environments. Field Crops Res. 124(1) : 37-45. https://doi.org/10.1016/j.fcr.2011.06.003
- Manoli, A., A. Sturaro, S. Trevisan, S. Quaggiotti, and A. Nonis. 2012. Evaluation of candidate reference genes for qPCR in maize. J. Plant Physiol. 169 : 807-815. https://doi.org/10.1016/j.jplph.2012.01.019
- Moon, J.-C., S. Shin, H. C. Kim, K. Song, J. Y. Kim, K.-H. Kim, and B.-M. Lee. 2018. Assessment of the candidate genes of expression marker associated with drought stress in maize seedling. Korean J. Breed. Sci. 50(3) : 229-240.
- Moss, G. I. and L. A. Downey. 1971. Influence of drought stress on female gametophyte development in corn (Zea mays L.) and subsequent grain yield. Crop Sci. 11(3) : 368-372. https://doi.org/10.2135/cropsci1971.0011183X001100030017x
- Mulo, P. 2011. Chloroplast-targeted ferredoxin-NADP+oxidoreductase (FNR): Structure, function and location. Biochim Biophys Acta. 1807 : 927-934. https://doi.org/10.1016/j.bbabio.2010.10.001
- Shendure, J. and H. Ji. 2008. Next-generation DNA sequencing. Nat Biotechnol. 26 : 1135-1145. https://doi.org/10.1038/nbt1486
- Schulz, M. H., D. R. Zerbino, M. Vingron, and E. Birney. 2012. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8) : 1086-1092. https://doi.org/10.1093/bioinformatics/bts094
- Shin, S. H., J. S. Lee, S. G. Kim, T. H. Go, J. Y. Shon, S. G. Kang, J.-S. Lee, H. H. Bae, J.-T. Kim, K.-B. Shim, W. Yang, and M.-O. Woo. 2015. Yield of maize (Zea mays L.) logistically declined with increasing length of the consecutive visible wilting days during flowering. J. Crop Sci. Biotech. 18(4) : 237-248. https://doi.org/10.1007/s12892-015-0112-y
- Song, K., K.-H. Kim, H. C. Kim, J.-C. Moon, J. Y. Kim, S.-B. Baek, Y. U. Kwon, and B.-M. Lee. 2015. Evaluation of drought tolerance in maize seedling using leaf rolling. Korean J. Crop sci. 60(1) : 8-16. https://doi.org/10.7740/kjcs.2014.60.1.008
- Song, K., H. C. Kim, K.-H. Kim, J.-C. Moon, J. Y. Kim, S.-K. Lee, and B.-M. Lee. 2018. Gene Expression Analysis and Polymorphism Discovery to Investigate Drought Responsive System in Tropical Maize. Plant Breeding and Biotechnology. 6(4) : 354-362. https://doi.org/10.9787/PBB.2018.6.4.354
- Treangen, T. J. and S. L. Salzberg. 2012. Repetitive DNA and nextgeneration sequencing: computational challenges and solutions. Nat. Rev. Genet. 13(1) : 36-46. https://doi.org/10.1038/nrg3117
- Udomprasert, N., J. Kijjanon, K. C. Iam, and A. Machuay. 2005. Effects of water deficit at tasseling on photosynthesis, development, and yield of corn. Kastsart J. (Nat. Sci.). 39 : 546-551.
- Westgate, M. E. and J. S. Boyer. 1985. Carbohydrate re-serves and reproductive development at low leaf water potentials in maize. Crop Sci. 25(5) : 762-769. https://doi.org/10.2135/cropsci1985.0011183X0025000500010x
- Xia, Z., H. Xu, J. Zhai, D. Li, H. Luo, C. He, and X. Huang. 2011. RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Molecular Biology. 77(3) : 299. https://doi.org/10.1007/s11103-011-9811-z
- Zhao, Q. T., Y. Wang, Y. M. Kong, D. Luo, X. Li, and P. Hao. 2011. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics. 12 (suppl. 14) : S2.
- Ziyomo, C. and R. Bernardo. 2013. Drought tolerance in maize: indirect selection through secondary traits versus genomewide selection. Crop Science. 53 : 1269. https://doi.org/10.2135/cropsci2012.11.0651