Aya K, Suzuki G, Suwabe K, Hobo T, Takahashi H, Shiono K, Yano K, Tsutsumi N, Nakazono M, Nagamura Y (2011). Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays. PLoS One 6: e26162.
Bei XJ, Shahid MQ, Wu JW, Chen ZX, Wang L, Liu XD (2019) Re-sequencing and transcriptome analysis reveal rich DNA variations and differential expressions of fertility-related genes in neo-tetraploid rice. PLOS One 14: e0214953. doi.org/10.1371/journal.pone.0214953.
Bingham ET, Groose RW, Woodfield DR, Kidwell KK (1994) Complementary gene interactions in alfalfa are greater in autotetraploids than diploids. Crop Sci 34:823–829.
Comai L (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6: 836–846.
Chen L, Shahid MQ, Wu JW, Chen ZX, Liu XD, (2018) Cytological and transcriptome analyses reveal abrupt gene expression for meiosis and saccharide metabolisms that associated with pollen abortion in autotetraploid rice. Mol Genet Genomics 3: 1-14.
Chen L, Yuan Y, Wu JW, Chen ZX, Wang L, Shahid MQ, Liu XD (2019) Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes. Rice 12:34.
Deveshwar P, Bovill WD, Sharma R, Able JA, Kapoor S (2011) Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice. BMC Plant Biol 11:78.
Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008) Evolutionary genetics of genome merger and doubling in plants. Genetics 42:443–461.
Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) AgriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:64-70.
Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N (2010) Rice expression atlas in reproductive development. Plant Cell Physiol 51:2060-2081.
Ghaleb MAA, Li C, Shahid, MQ, Yu H, Liang JH, Chen RX, Wu JW, Liu XD (2020) Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles. BMC Plant Biol 20:83.
Guo HB, Mendrikahy JN, Xie L, Deng J, Lu ZJ, Wu JW, Li X, Shahid MQ, Liu XD, (2017) Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis. Sci Rep-UK 7:40139.
He JH, Shahid MQ, Chen ZX, Chen XA, Liu XD, Lu YG (2011a) Abnormal PMC microtubule distribution pattern and chromosome behavior resulted in low pollen fertility of an intersubspecific autotetraploid rice hybrid. Plant Syst and Evol 291:257-265. doi:10.1007/s00606-010-0386-y
He JH, Shahid MQ, Li YJ, Guo HB, Cheng XA, Liu XD, Lu YG (2011b) Allelic interaction of F1 pollen sterility loci and abnormal chromosome behavior caused pollen sterility in intersubspecific autotetraploid rice hybrids. J Exp Bot 62:4433-4445. doi:10.1093/jxb/err098
Hollister JD, Arnold BJ, Svedin E, Xue KS, Dilkes BP, Bomblies K (2012) Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genet 8:e1003093.
Huang XH, Lu TT, Han B (2013) Resequencing rice genomes: an emerging new era of rice genomics.
Trends Genet 29:225–232. doi:10.1016/j.tig.2012.12.001
Li X, Yu H. Jiao YM, Shahid MQ, Wu JW, Liu XD (2018) Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice. PLoS One 13:e0201854. doi.org/10.1371/journal.
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408.
Masterson J (1994) Stomatal size in fossil plants: Evidence for polyploidy in majority of angiosperms. Science 264:421-424.
Marhold K, Lihová J (2006) Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae. Plant Syst Evol 259:143-174.
Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytol 186:5-17.
Qi YB, Liu QL, Zhang L, Mao BZ, Yan DW, Jin QS, He ZH (2014) Fine mapping and candidate gene analysis of the novel thermo-sensitive genic male sterility tms9-1 gene in rice. Theor Appl Genet 127:1173-1182.
Shahid MQ, Sun JF, Wei CM, Zhang P, Liu XD (2010) Studies on the abnormality of embryo sac and pollen fertlity in autoterploid rice during different growing seasons. Pak J Bot 42:7-19.
Shahid MQ, Liu GF, Li JQ, Naeem M, Liu XD (2011) Heterosis and gene action study of agronomic traits in diploid and autotetraploid rice. Acta Agriculturae Scandinavica Section B–Soil and Plant Science 61: 23-32.
Shahid MQ, Li YJ, Saleem MF, Naeem M, Wei CM, Liu XD (2013) Yield and yield components in autotetraploid and diploid rice genotypes (indica and japonica) sown in early and late seasons. J Crop Sci 7:632-641.
Tu SB, Luan L, Liu YH, Long WB, Kong FL, He T, Xu QF, Yan WG, Yu MQ (2007) Production and heterosis analysis of rice autotetraploid hybrids. Crop Sci 47: 2356-2363.
Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522-530. doi:10.1016/j.tibtech.2009.05.006
Wright KM, Arnold B, Xue K, Šurinová M, O'Connell J, Bomblies K (2015) Selection on meiosis genes in diploid and tetraploid Arabidopsis arenosa. Mol Biol and Evol 32:944-955. doi:10.1186/1471-2164-11-338
Wu JW, Hu CY, Shahid MQ, Guo HB, Zeng YX, Liu XD, Lu YG (2013) Analysis on genetic diversification and heterosis in autotetraploid rice. SpringerPlus 2:1-12. doi:10.1186/2193-1801-2-439
Wu JW, Shahid MQ, Guo HB, Yin W, Chen ZX, Wang L, Liu XD, Lu YG (2014) Comparative
cytological and transcriptomic analysis of pollen development in autotetraploid and diploid rice.
Plant Reprod 27:181-196. doi:10.1007/s00497-014-0250-2
Wu JW, Shahid MQ, Chen L, Chen ZX, Wang L, Liu XD, Lu YG (2015) Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice. Plant Physiol 169:2700-2717. doi:10.1104/pp.15.00791
Wu JW, Chen L, Shahid MQ, Chen MY, Dong QL, Li JR, Xu XX, Liu XD (2017) Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice. Rice 10:49.
Wu JW, Shahid MQ, Chen MY, Li X, Li JR, Xu XS, Du SS, Liu XD (2019) Cytological and transcriptome analysis reveal that interaction at Sb pollen sterility locus cause down-regulation of important meiosis-related genes associated with high pollen sterility in autotetraploid rice hybrids. Plant Physiology and Biochemistry 141:73-82
Yant L, Hollister JD, Wright KM, Arnold BJ, Higgins JD, Franklin FCH, Bomblies K (2013) Meiotic
adaptation to genome duplication in Arabidopsis arenosa. Curr Biol 23:2151.
Yu H, Shahid MQ, Li QH, Li YD, Li C, Lu ZJ, Wu JW, Zhang ZM, Liu XD (2020) Production assessment and genome comparison revealed high yield potential and novel specific alleles associated with fertility and yield in neo-tetraploid rice. Rice 13:32.
Yu Z, Haage K, Streit VE, Gierl A, Ruiz RA (2009) A large number of tetraploid Arabidopsis thaliana
lines, generated by a rapid strategy, reveal high stability of neo-tetraploids during consecutive
generations. Theor Appl Genet 118:1107-1119.
Zeng YX, Hu CY, Lu YG, Li JQ, Liu XD (2007) Diversity of abnormal embryo sacs in indica/japonica hybrids in rice demonstrated by confocal microscopy of ovaries. Plant Breeding 126:574-580
Zhang H, Liang WQ, Yang XJ, Luo X, Jiang N, Ma H, Zhang DB (2010) Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development. The Plant Cell 22: 672-689
Zhou H, He M, Li J, Chen L, Huang ZF, Zheng SY, Zhu LY, Ni ED, Jiang DG, Zhao BR, Zhuang CX (2016) Development of commercial thermo-sensitive genic male sterile rice accelerates hybrid rice breeding using the CRISPR/Cas9-mediated TMS5 editing system. Sci Rep 6:37395.
Zhou H, Zhou M, Yang YZ, Li J, Zhu LY, Jiang DG, Dong JF, Liu QJ, Gu LF, Zhou LY, Feng MJ, Qin P, Hu X C, Song CL, Shi JF, Song XW, Ni ED, Wu XJ, Deng QY, Liu ZL, Chen MS, Liu YG, Cao XF, Zhuang CX (2014) RNase ZS1 processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice. Nature Communications 5:4884.