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Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex
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 Title & Authors
Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex
Choi, Sang Chul; Chung, Yong Suk; Kim, Changsoo;
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 Abstract
Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.
 Keywords
evolution;genomics-assisted breeding;panicoideae;poaceae;polyploidyzation;
 Language
English
 Cited by
 References
1.
Abrouk M, Murat F, Pont C, Messing J, Jackson S, Faraut T, Tannier E, Plomion C, Cooke R, Feuillet C et al. 2010. Palaeogenomics of plants: synteny-based modelling of extinct ancestors.

2.
Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815. crossref(new window)

3.
Bremer G. 1961. Problems in breeding and cytology of sugarcane. Euphytica 10:59-78. crossref(new window)

4.
D'Hont A, Ison D, Alix K, Roux C, Glaszmann J-C. 1998. Determination of basic choromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41:221-225. crossref(new window)

5.
Daniels J, Roach BT. 1987. Taxonomy and Evolution. in Sugarcane Improvement Through Breeding (ed. DJ Heinz), pp. 7-84. Elsevier Press, Amsterdam.

6.
Daniels J, Smith P, Panton N, Williams CA. 1975. The origin of the genus Saccharum. Sugarcane Breed Newsl 36:24-39.

7.
de Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GM, Del Bem LE, Vicentini R, Nogueira FT, Campos RA, Nunes SL, Turrini PC et al. 2014. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics 15:540. crossref(new window)

8.
Edwards GE, Franceschi VR, Voznesenskaya EV. 2004. Single-cell C(4) photosynthesis versus the dual-cell (Kranz) paradigm. Annual Rreview of Plant Biology 55:173-196. crossref(new window)

9.
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al. 2002. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica). Science 296:92-100. crossref(new window)

10.
Grass Phylogeny Working Group. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88:373-457. crossref(new window)

11.
Grivet L, Arruda P. 2001. Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5:122-127.

12.
Grivet L, Glaszmann J, D'Hont A. 2006. Molecular evidence of sugarcane evolution and domestication. in Darwin's harvest: New approaches to the origins, evolution and conservation of crops (ed. TJ Motley), pp. 49-66. Columbia University Press, New York.

13.
Ha S, Moore PH, Heinz DJ, Kato S, Ohmido N, Fukui K. 1999. Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and imaging methods. Plant Mol Biol 39:1165-1173. crossref(new window)

14.
Irvine JE. 1999. Saccharum species as horticultural classes. Theoretical and Applied Genetics 98:186-194. crossref(new window)

15.
Kellogg EA. 2000. The grasses: a case study of macroevolution. Annual review of ecology and systematics 31:217-238. crossref(new window)

16.
Kellogg. 2013. Phylogenetic Relationships of Saccharinae and Sorghinae. in Genomics of the Saccharinae (ed. AH Paterson), pp. 3-21. Springer, Springer New York.

17.
Kim C, Lee TH, Compton RO, Robertson JS, Pierce GJ, Paterson AH. 2013. A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin. Plant Molecular Biology 81:139-147. crossref(new window)

18.
Kim C, Lee TH, Guo H, Chung SJ, Paterson AH, Kim DS, Lee GJ. 2014a. Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships. BMC Plant Biology 14:134. crossref(new window)

19.
Kim C, Tang H, Paterson AH. 2009. Duplication and divergence of grass genomes: Integrating the Cloridoids. Tropical Plant Biol 2:51-62. crossref(new window)

20.
Kim C, Wang X, Lee TH, Jakob K, Lee GJ, Paterson AH. 2014b. Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates. The Plant cell 26:2420-2429. crossref(new window)

21.
Kim C, Zhang D, Auckland SA, Rainville LK, Jakob K, Kronmiller B, Sacks EJ, Deuter M, Paterson AH. 2012. SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. Theoretical and Applied Genetics 124:1325-1338. crossref(new window)

22.
Luo MC, Deal KR, Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ et al. 2009. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proceedings of the National Academy of Sciences of the United States of America 106:15780-15785. crossref(new window)

23.
Ma X-F, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T et al. 2012. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 7:e33821. crossref(new window)

24.
Ming R, Liu S-C, Lin Y-R, da Silva J, Wilson W, Braga D, Van Deynze A, Wenslaff TF, Wu KK, Moore PH et al. 1998. Detailed alignment of Saccharum and Sorghum chromosomes: comparative organization of closely related diploid and polyploidy genomes. Genetics 150:1663-1682.

25.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556. crossref(new window)

26.
Paterson AH, Bowers JE, Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101:9903-9908. crossref(new window)

27.
Pinto H, Sharwood RE, Tissue DT, Ghannoum O. 2014. Photosynthesis of C3, C3-C4, and C4 grasses at glacial CO2. Journal of Experimental Botany 65:3669-3681. crossref(new window)

28.
Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.

29.
Rayburn AL, Crawford J, Rayburn CM, Juvik JA. 2009. Genome size of Three Miscanthus species. Plant Molecular Biology Reporter 27:184-188. crossref(new window)

30.
Sacks EJ, Juvik JA, Lin Q, Stewart R, Yamada T. 2013. The gene pool of Miscanthus species and its improvement. in Genomics of the Saccharinae (ed. AH Paterson), pp. 73-101. Springer, New York.

31.
Schnable PS Ware D Fulton RS Stein JC Wei F Pasternak S Liang C Zhang J Fulton L Graves TA et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115. crossref(new window)

32.
Simon BK. 2007. Grass phylogeny and classification: Conflict of morphology and molecules. A Journal of Systematic and Evolutionary Botany 23:259-266.

33.
Souza GM, Berges H, Bocs S, Casu R, D'Hont A, Ferreira JE, Henry R, Ming R, Potier B, Sluys M-A et al. 2011. The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome. Tropical Plant Biology 4:145-156. crossref(new window)

34.
Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacha K, Hall M, Jezowski S, Ming R et al. 2012. A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. BMC Genomics 13:142. crossref(new window)

35.
Swigonova Z, Lai J, Ma J, Ramarkrishna W, Llaca V, Bennetzen JL, Messing J. 2004. Close split of sorghum and maize genome progenitors. Genome Research 14:1916-1923. crossref(new window)

36.
Taylor SH, Ripley BS, Martin T, De-Wet LA, Woodward FI, Osborne CP. 2014. Physiological advantages of C4 grasses in the field: a comparative experiment demonstrating the importance of drought. Global Change Biology 20:1992-2003. crossref(new window)

37.
Tomkins JP, Yu Y, Miller-Smith H, Frisch DA, Woo SS, Wing RA. 1999. A bacterial artificial chromosome library for sugarcane. Theor Appl Genet 99:419-424. crossref(new window)

38.
Varshney RK, Graner A, Sorrells ME. 2005. Genomics-assisted breeding for crop improvement. Trends in plant science 10:621-630. crossref(new window)

39.
Wei F, Coe E, Nelson W, Bharti A, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S et al. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLOS Genetics 3:e123. crossref(new window)

40.
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92. crossref(new window)