1.R. F. Sage, T. L. Sage, F. Kocacinar, Photorespiration and the evolution of C4 photosynthesis. Annu. Rev. Plant Biol., 63(2012), pp. 19–47.
2.R. F. Sage, The evolution of C4 photosynthesis. New Phytol., 161(2004), pp. 341–370.
3.E. J. Edwards, S. A. Smith, Phylogenetic analyses reveal the shady history of C4 grasses. Proc. Natl. Acad. Sci. USA, 107(2010), pp. 2532–2537.
4.J. M. Hibberd, S. Covshoff, The regulation of gene expression required for C4 photosynthesis. Annu. Rev. Plant Biol., 61(2010), pp. 181–207.
5.S. von Caemmerer, R. T. Furbank, The C4 pathway: an efficient CO2 pump. Photosynth. Res., 77(2003), pp. 191.
6.J. M. Hibberd, J. E. Sheehy, J. A. Langdale, Using C4 photosynthesis to increase the yield of rice-rationale and feasibility. Curr. Opin. Plant Biol., 11(2008), pp. 228–231.
7.J. A. Langdale, C4 cycles: past, present, and future research on C4 photosynthesis. Plant Cell, 23(2011), pp. 3879–3892.
8.S. von Caemmerer, R. T. Furbank, Strategies for improving C4 photosynthesis. Curr. Opin. Plant Biol., 31(2016), pp. 125–134.
9.C. J. Still, J. A. Berry, G. J. Collatz, R. S. DeFries, Global distribution of C3 and C4 vegetation: carbon cycle implications. Global Biogeochem. Cy., 17(2003), pp. 1–14.
10.S. P. Long, X. G. Zhu, S. L. Naidu, D. R. Ort, Can improvement in photosynthesis increase crop yields? Plant Cell Environ., 29(2006), pp. 315–330.
11.X. G. Zhu, L. L. Shan, Y. Wang, W. P. Quick, C4 rice-an ideal arena for systems biology research. J. Integr. Plant Biol., 52(2010), pp. 762–770.
12.S. von Caemmerer, W. P. Quick, R. T. Furbank, The development of C4 rice: current progress and future challenges. Science, 336(2012), pp. 1671–1672.
13.S. Covshoff, M. Szecowka, T. E. Hughes, R. Smith-Unna, S. Kelly, K. J. Bailey, T. L. Sage, J. A. Pachebat, R. Leegood, J. M. Hibberd, C4 photosynthesis in the rice paddy: insights from the noxious weed echinochloa glabrescens. Plant Physiol., 170(2016), pp. 57–73.
14.M. D. Hatch, T. Kagawa, S. Craig, Subdivision of C4-pathway species based on differing C4 acid decarboxylating systems and ultrastructural features. Funct. Plant Biol., 2(1975), pp. 111–128.
15.A. Bräutigam, S. Schliesky, C. Külahoglu, C. P. Osborne, A. P.M. Weber, Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. J. Exp. Bot., 65(2014), pp. 3579–3593.
16.B. V. Sonawane, R. E. Sharwood, S. Whitney, O. Ghannoum, Shade compromises the photosynthetic efficiency of NADP-ME less than PEP-CK and NAD-ME C4 grasses. J. Exp. Bot. 69(2018), pp. 3053–3068.
17.G. Grass Phylogeny Working, II, New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytol., 193(2012), pp. 304–312.
18.S. P. Kidambi, D. R. Krieg, D. T. Rosenow, Genetic variation for gas exchange rates in grain sorghum. Plant Physiol., 92(1990), pp. 1211–1214.
19.S. B. Peng, D. R. Krieg, Gas exchange traits and their relationship to water-use efficiency of grain sorghum. Crop Sci., 32(1992), pp. 386–391.
20.S. Henderson, S. von Caemmerer, G. D. Farquhar, L. J. Wade, G. Hammer, Correlation between carbon isotope discrimination and transpiration efficiency in lines of the C4 species Sorghum bicolor in the glasshouse and the field. Aust. J. Plant Physiol., 25(1998), pp. 111–123.
21.M. Balota, W. A. Payne, W. Rooney, D. Rosenow, Gas exchange and transpiration ratio in sorghum. Crop Sci., 48(2008), pp. 2361–2371.
22.M. G. S. Fernandez, K. Strand, M. T. Hamblin, M. Westgate, E. Heaton, S. Kresovich, Genetic analysis and phenotypic characterization of leaf photosynthetic capacity in a sorghum (Sorghum spp.) diversity panel. Genet. Resour. Crop Ev., 62(2015), pp. 939–950.
23.L. Y. Zheng, X. S. Guo, B. He, L. J. Sun, Y. Peng, S. S. Dong, T. F. Liu, S. Y. Jiang, S. Ramachandran, C. M. Liu, H. C. Jing, Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol., 12(2011), pp. 1–14.
24.A. H. Paterson, J. E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. B. Tang, X. Y. Wang, T. Wicker, A. K. Bharti, J. Chapman, F. A. Feltus, U. Gowik, I. V. Grigoriev, E. Lyons, C. A. Maher, M. Martis, A. Narechania, R. P. Otillar, B. W. Penning, A. A. Salamov, Y. Wang, L. F. Zhang, N. C. Carpita, M. Freeling, A. R. Gingle, C. T. Hash, B. Keller, P. Klein, S. Kresovich, M. C. McCann, R. Ming, D. G. Peterson, Mehboob-ur-Rahman, D. Ware, P. Westhoff, K. F. X. Mayer, J. Messing, D. S. Rokhsar, The Sorghum bicolor genome and the diversification of grasses. Nature, 457(2009), pp. 551–556.
25.E. S. Mace, S. S. Tai, E. K. Gilding, Y. H. Li, P. J. Prentis, L. L. Bian, B.C. Campbell, W. S. Hu, D. J. Innes, X. L. Han, A. Cruickshank, C. M. Dai, C. Frere, H. K. Zhang, C. H. Hunt, X. Y. Wang, T. Shatte, M. Wang, Z. Su, J. Li, X. Z. Lin, I. D. Godwin, D. R. Jordan, J. Wang, Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nat. Commun., 4(2013), pp. 1–9.
26.N. Fankhauser, S. Aubry, Post-transcriptional regulation of photosynthetic genes is a key driver of C4 leaf ontogeny. J. Exp. Bot., 68(2017), pp. 137–146.
27.P. Huang, A. J. Studer, J. C. Schnable, E. A. Kellogg, T. P. Brutnell, Cross species selection scans identify components of C4 photosynthesis in the grasses. J. Exp. Bot., 68(2017), pp. 127–135.
28.S. J. Burgess, J. M. Hibberd, Insights into C4 metabolism from comparative deep sequencing. Curr. Opin. Plant Biol., 25(2015), pp. 138–144.
29.G. Reeves, M. J. Grangé-Guermente, J. M. Hibberd, Regulatory gateways for cell-specific gene expression in C4 leaves with Kranz anatomy. J. Exp. Bot., 68(2017), pp. 107–116.
30.P.-A. Christin, C. P. Osborne, D. S. Chatelet, J. T. Columbus, G. Besnard, T. R. Hodkinson, L. M. Garrison, M. S. Vorontsova, E. J. Edwards, Anatomical enablers and the evolution of C4 photosynthesis in grasses. Proc. Natl. Acad. Sci. USA, 110(2013), pp. 1381–1386.
31.J. J. Moreno-Villena, L. T. Dunning, C. P. Osborne, P.-A. Christin, Highly expressed genes are preferentially co-opted for C4 photosynthesis. Mol. Biol. Evol., 35(2018), pp. 94–106.
32.A. R. Borba, T. S. Serra, A. Gorska, P. Gouveia, A.M. Cordeiro, I. Reyna-Llorens, J. Knerova, P.M. Barros, I. A. Abreu, M. M. O. Oliveira, J. M. Hibberd, N. J. M. Saibo, Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state. Mol. Biol. Evol. 7(2018), pp. 1690–1705.
33.P. A. Christin, B. Petitpierre, N. Salamin, L. Büchi, G. Besnard, Evolution of C4 phospho enol pyruvate carboxykinase in grasses, from genotype to phenotype. Mol. Biol. Evol., 26(2008), pp. 357–365.
34.P. A. Christin, N. Salamin, A.M. Muasya, E. H. Roalson, F. Russier, G. Besnard, Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol. Biol. Evol., 25(2008), pp. 2361–2368.
35.J. R. Ehleringer, R. F. Sage, L. B. Flanagan, R. W. Pearcy, Climate change and the evolution of C4 photosynthesis. Trends Ecol. Evol., 6(1991), pp. 95–99.
36.P. A. Christin, N. Salamin, V. Savolainen, M. R. Duvall, G. Besnard, C4 photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr. Biol., 17(2007), pp. 1241–1247.
37.P. A. Christin, E. Samaritani, B. Petitpierre, N. Salamin, G. Besnard, Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics. Genome Biol. Evol., 1(2009), pp. 221–230.
38.J. D. Clark, A. Stemler, Early domesticated sorghum from central Sudan. Nature, 254(1975), pp. 588–591.
39.F. Wendorf, A. E. Close, R. Schild, K. Wasylikowa, R. A. Housley, J. R. Harlan, H. Królik, Saharan exploitation of plants 8,000 years BP. Nature, 359(1992), pp. 721–724.
40.Y. Tao, E. Mace, B. George-Jaeggli, C. Hunt, A. Cruickshank, R. Henzell, D. Jordan, Novel grain weight loci revealed in a cross between cultivated and wild sorghum. Plant Genome, 11(2018), pp. 1–10.
41.Y. Tao, E. S. Mace, S. Tai, A. Cruickshank, B.C. Campbell, X. Zhao, E. J. Van Oosterom, I. D. Godwin, J. R. Botella, D. R. Jordan, Whole-genome analysis of candidate genes associated with seed size and weight in Sorghum bicolor reveals signatures of artificial selection and insights into parallel domestication in cereal crops. Front. Plant Sci., 8(2017), pp. 1–14.
42.Y. Tao, X. Zhao, E. Mace, R. Henry, D. Jordan, Exploring and exploiting pan-genomics for crop improvement. Mol. Plant, 12(2019), pp. 156–169.
43.B. M. C. Kümpers, S. J. Burgess, I. Reyna-Llorens, R. Smith-Unna, C. Boursnell, J. M. Hibberd, Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria. J. Exp. Bot., 68(2017), pp. 177–189.
44.C. Külahoglu, A. K. Denton, M. Sommer, J. Maß, S. Schliesky, T. J. Wrobel, B. Berckmans, E. Gongora-Castillo, C. R. Buell, R. Simon, L. De Veylder, A. Bräutigam, A. P.M. Weber, Comparative transcriptome atlases reveal altered gene expression modules between two cleomaceae C3 and C4 plant species. Plant Cell, 26(2014), pp. 3243–3260.
45.S. J. Burgess, I. Reyna-Llorens, S. R. Stevenson, P. Singh, K. Jaeger, J. M. Hibberd, Genome-wide transcription factor binding in leaves from C3 and C4 grasses. bioRxiv (2019), pp. 165787.
46.K. Massel, B.C. Campbell, E. S. Mace, S. Tai, Y. Tao, B. G. Worland, D. R. Jordan, J. R. Botella, I. D. Godwin, Whole genome sequencing reveals potential new targets for improving nitrogen uptake and utilization in Sorghum bicolor. Front. Plant Sci., 7(2016), pp. 1544.
47.R. M. Riley, W. Jin, G. Gibson, Contrasting selection pressures on components of the Ras-mediated signal transduction pathway in Drosophila. Mol. Ecol., 12(2003), pp. 1315–1323.
48.B.C. Campbell, E. K. Gilding, E. S. Mace, S. Tai, Y. Tao, P. J. Prentis, P. Thomelin, D. R. Jordan, I. D. Godwin, Domestication and the storage starch biosynthesis pathway: Signatures of selection from a whole sorghum genome sequencing strategy. Plant Biotechnol. J. 14(2016), pp.2240–2253.
49.Y. Wang, W. Xu, L. Hu, L. Zhang, Y. Li, X. Du, Expression of maize gene encoding C4-pyruvate orthophosphate dikinase (PPDK) and C4-phosphoenolpyruvate carboxylase (PEPC) in transgenic Arabidopsis. Plant Mol. Biol. Rep., 30(2012), pp. 1367–1374.
50.D. Wang, A. R. Portis, S. P. Moose, S. P. Long, Cool C4 photosynthesis: pyruvate pi dikinase expression and activity corresponds to the exceptional cold tolerance of carbon assimilation in Miscanthus × giganteus. Plant Physiol., 148(2008), pp. 557–567.
51.S. L. Naidu, S. P. Moose, A. K. AL-Shoaibi, C. A. Raines, S. P. Long, Cold tolerance of C4 photosynthesis in Miscanthus × giganteus: adaptation in amounts and sequence of C4 photosynthetic enzymes. Plant Physiol., 132(2003), pp. 1688–1697.
52.C. J. Chastain, C. J. Failing, L. Manandhar, M. A. Zimmerman, M. M. Lakner, T. H. T. Nguyen, Functional evolution of C4 pyruvate, orthophosphate dikinase. J. Exp. Bot., 62(2011), pp. 3083–3091.
53.H. Bauwe, R. Chollet, Kinetic properties of phosphoenolpyruvate carboxylase from C3, C4, and C3-C4 intermediate species of Flaveria (Asteraceae). Plant Physiol., 82(1986), pp. 695–699.
54.S. von Caemmerer, G. E. Edwards, N. Koteyeva, A. B. Cousins, Single cell C4 photosynthesis in aquatic and terrestrial plants: a gas exchange perspective. Aquat. Bot., 118(2014), pp. 71–80.
55.R. A. Boyd, A. Gandin, A. B. Cousins, Temperature responses of C4 photosynthesis: biochemical analysis of rubisco, phosphoenolpyruvate carboxylase, and carbonic anhydrase in Setaria viridis. Plant Physiol., 169(2015), pp. 1850–1861.
56.M. D. Hatch, J. N. Burnell, Carbonic anhydrase activity in leaves and its role in the first step of C4 photosynthesis. Plant Physiol., 93(1990), pp. 825–828.
57.S. Von Caemmerer, V. Quinn, N. Hancock, G. D. Price, R. T. Furbank, M. Ludwig, Carbonic anhydrase and C4 photosynthesis: a transgenic analysis. Plant Cell Environ., 27(2004), pp. 697–703.
58.A. B. Cousins, M. R. Badger, S. von Caemmerer, Carbonic anhydrase and its influence on carbon isotope discrimination during C4 photosynthesis. Insights from antisense RNA in Flaveria bidentis. Plant Physiol., 141(2006), pp. 232–242.
59.H. L. Osborn, H. Alonso-Cantabrana, R. E. Sharwood, S. Covshoff, J. R. Evans, R. T. Furbank, S. von Caemmerer, Effects of reduced carbonic anhydrase activity on CO2 assimilation rates in Setaria viridis: a transgenic analysis. J. Exp. Bot., 68(2016), pp. 299–310.
60.N. Watanabe, J. R. Evans, W. S. Chow, Changes in the photosynthetic properties of Australian wheat cultivars over the last century. Aust. J. Plant Physiol., 21(1994), pp. 169–183.
61.X. Liu, X. Li, C. Zhang, C. Dai, J. Zhou, C. Ren, J. Zhang, Phosphoenolpyruvate carboxylase regulation in C4-PEPC-expressing transgenic rice during early responses to drought stress. Physiol. plant., 159(2017), pp. 178–200.
62.M. Jeanneau, D. Gerentes, X. Foueillassar, M. Zivy, J. Vidal, A. Toppan, P. Perez, Improvement of drought tolerance in maize: towards the functional validation of the Zm-Asr1 gene and increase of water use efficiency by over-expressing C4–PEPC. Biochimie, 84(2002), pp. 1127–1135.
63.B. P. Williams, S. Aubry, J. M. Hibberd, Molecular evolution of genes recruited into C4 photosynthesis. Trends Plant Sci., 17(2012), pp. 213–220.
64.X. Wang, U. Gowik, H. Tang, J. E. Bowers, P. Westhoff, A. H. Paterson, Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol., 10(2009), pp. R68.
65.M. Nei, W. Li, Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA, 76(1979), pp. 5269–5273.
66.F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(1989), pp. 585–595.
67.G. A. Watterson, On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol., 7(1975), pp. 256–276.
68.R. Hudson, D. D. Boos, N. Kaplan, A statistical test for detecting geographic subdivision. Mol. Biol. Evol., 9(1992), pp. 138–151.
69.B. Pfeifer, U. Wittelsbürger, S. E. R. Onsins, M. J. Lercher, PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol. Biol. Evol. (2014), pp. msu136.
70.E. Paradis, J. Claude, K. Strimmer, APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2004), pp. 289–290.
71.E. Paradis, pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics, 26(2010), pp. 419–420.