Relationships between Sorghum bicolor (Poaceae) and its closerelatives based on genomic in situ hybridization evidence

Relationships between Sorghum bicolor (Poaceae) and its closerelatives based on genomic in situ hybridization evidence

Sorghum bicolor (L.) Moench (sorghum) is a naturally well-established diploid species with 2n = 2x = 20. Here we provide evidence to identify the genomic relationships of S. bicolor and its extant relatives using genomic in situ hybridization. The genomic divergences between S. bicolor and its close relatives may be presented as: S. bicolor-S. × drummondii (Nees ex Steud.) Millsp. & Chase < S. bicolor-S. × almum Parodi < S. bicolor S. arundinaceum (Desv.) Stapf < S. bicolor-S. propinquum (Kunth) Hitchc. Sorghum arundinaceumprobe signals showed spotted or painted patterns on the S. bicolor chromosomes, indicating that the degree of genomic divergence between S. bicolor and S. arundinaceum is distinct. It is reasonable to infer that S. bicolor might have diverged from S. arundinaceum in the early diversification history of the subgenus. The probe signal intensity of S. arundinaceum and S. propinquum is greater on the 17 chromosomes than on the remaining 23 chromosomes of S. halepense (L.) Pers., whereas S. bicolor and S. propinquum probes produced spotted or patchy signals on the 40 S. halepense chromosomes. Therefore, the degree of genomic divergence may be presented as: S. halepense-S. bicolor < S.halepense-S. arundinaceum < S. halepense-S. propinquum.

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  • Biscotti MA, Olmo E, Heslop-Harrison JS (2015). Repetitive DNA in eukaryotic genomes. Chromosome Res 23: 415-420.
  • Carmona A, Friero E, de Bustos A, Jouve N, Cuadrado A (2013). The evolutionary history of sea barley (Hordeum marinum) revealed by comparative physical mapping of repetitive DNA. Ann Bot-London 112: 1845-1855.
  • Celarier RP (1958). Cytotaxonomic notes on the subsection Halepensia of the genus Sorghum. B Torrey Bot Club 85: 49-62.
  • Chen SL, Phillips SM (2006). Sorghum Moench. In: Wu ZY, Raven PH, editors. Flora of China, Vol. 22. Beijing, China: Science Press, pp. 602-604.
  • Clayton WD, Renvoize SA (1982). Gramineae (Part 3). In: Polhill RM, editor. Flora of Tropical East Africa. Rotterdam, the Netherlands: August Aimé Balkema, pp. 320-734.
  • Crow JF (1994). Anecdotal, historical and critical commentaries on genetics. Genetics 137: 891-894.
  • Dai F, Chen ZH, Wang XL, Li ZF, Jin GL, Wu DZ, Cai SG, Wang N, Wu FB, Nevo E et al. (2004). Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley. P Natl Acad Sci USA 111: 13403-13408.
  • De Wet JMJ (1978). Systematics and evolution of Sorghum sect. Sorghum (Gramineae). Am J Bot 65: 477-484.
  • Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, Piednoël M, Weiss-Schneeweiss H, Leitch AR (2015). Genomic repeat abundances contain phylogenetic signal. Syst Biol 64: 112-126.
  • Doggett J (1970). Sorghum. London, UK: Green and Company, Longmans.
  • Doggett H (1976). Sorghum. In: Simmonds NW, editor. Evolution of Crop Plants. London, UK: Longman Scientific and Technical, pp. 112-117.
  • Doyle JJ, Doyle JL (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
  • Hacker JB (1992). Sorghum × drummondii (Steud) Millsp. & Chase. In: Mannetje LT, Jones RM, editors. Plant Resources of South-East Asia. No. 4. Forages. Wageningen, Germany: Pudoc Scientific Publishers, pp. 206-208.
  • Hawkins JS, Ramachandran D, Henderson A, Freeman J, Carlise M, Harris A, Willison-Headley Z (2015). Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum. Ann Bot-London 116: 291-299.
  • He GM, Zhu XP, Elling AA, Chen LB, Wang XF, Guo L, Liang MZ, He H, Zhang HY, Chen FF et al. (2010). Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
  • Heslop-Harrison JS (2000). Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12: 617-636.
  • Heslop-Harrison JS, Leitch AR, Schwarzacher T, Anamthawat-Jónsson K (1990). Detection and characterization of IB/IR translocations in hexaploid wheat. Heredity 65: 385-392.
  • Hoffmann MH, Schneider J, Hase P, Röser M (2013). Rapid and recent world-wide diversification of bluegrasses (Poa, Poaceae) and related genera. PLoS One 8: e60061.
  • House LR (1985). A Guide to Sorghum Breeding. Andhra, India: Pradesh Institute for the Semi-Arid Tropics.Huang XH, Kurata N, Wei XH, Wang ZX, Wang AH, Zhao Q, Zhao Y, Liu KY, Lu HY, Li WJ et al. (2012). A map of rice genome variation reveals the origin of cultivated rice. Nature490: 497-503.
  • Hunt HV, Badakshi F, Romanova O, Howe CJ, Jones MK, Heslop-Harrison JSP (2014). Reticulate evolution in Panicum(Poaceae): the origin of tetraploid broomcorn millet, P. miliaceum. J Exp Bot 65: 3165-3175.
  • Iourov IY, Soloviev IV, Vorsanova SG, Monakhov VV, Yurov YB (2005). An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics. J Histochem Cytochem 53: 401-408.
  • Jiang B, Liu LQ, Hu XY, Liu Q (2012). Distribution of Eleusine indicaAA genome on finger millet (Poaceae) chromosomes identified by genomic in situ hybridization and optimization method of probe length. J Trop Subtrop Bot 20: 44-50.
  • Katsiotis A, Loukas M, Heslop-Harrison JS (2000). Repetitive DNA, genome and species relationships in Av e n a and Arrhenatherum(Poaceae). Ann Bot-London 86: 1135-1142.
  • Lazarides M, Hacker JB, Andrew MH (1991). Taxonomy, cytology and ecology of indigenous Australian sorghums (SorghumMoench, Andropogoneae, Poaceae). Aust Syst Bot 4: 591-635.
  • Li CB, Zhang DM, Ge S, Lu BR, Hong DY (2001a). Differentiation and inter-genomic relationships among C, E and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet 103: 197-203.
  • Li CB, Zhang DM, Ge S, Lu BR, Hong DY (2001b). Identification of genome constitution of Oryza malampuzhaensis, O. minuta, and O. punctata by multicolor genomic in situ hybridization. Theor Appl Genet 103: 204-211.
  • Liu H, Zeng FY, Liu Q (2014). Geographical distribution of SorghumMoench (Poaceae). J Trop Subtrop Bot 22: 1-11.
  • Liu Q (2015). Research progress on structure and evolution of plant centromeres. J Trop Subtrop Bot 23: 576-586.
  • Liu Q, Jiang B, Wen J, Peterson PM (2014a). Low-copy nuclear gene and McGISH resolves polyploidy history of Eleusine coracanaand morphological character evolution in Eleusine. Turk J Bot 38: 1-12.
  • Liu Q, Liu H, Wen J, Peterson PM (2014b). Infrageneric phylogeny and temporal divergence of Sorghum (Andropogoneae, Poaceae) based on low-copy nuclear and plastid sequences. PLoS One 9: e104933.
  • Liu Q, Triplett JM, Wen J, Peterson PM (2011). Allotetraploid origin and divergence in Eleusine (Chloridoideae, Poaceae): evidence from low-copy nuclear gene phylogenies and a plastid gene chronogram. Ann Bot-London 108: 1287-1298.
  • Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, The International Wheat Genome Sequencing Consortium, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KF et al. (2014). Ancient hybridizations among the ancestral genomes of bread wheat.Science 345: 1250092.
  • Messing J (2009). The polyploidy origin of maize. In: Bennetzen JL, Hake S, editors. Maize Handbook, Vol. II: Genetics and Genomics. New York, NY, USA: Springer, pp. 221-238.
  • Morden CW, Doebley J, Schertz KF (1990). Allozyme variation among the spontaneous species of Sorghum section Sorghum(Poaceae). Theor Appl Genet 80: 296-304.
  • Mutegi E, Sagnard F, Muraya M, Kanyenji B, Rono B, Mwongera C, Marangu C, Kamau J, Parzies H, De Villiers S et al. (2010). Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow. Genet Resour Crop Ev 57: 243-253.
  • Ng’uni D, Geleta M, Fatih M, Bryngelsson T (2010). Phylogenetic analysis of the genus Sorghum based on combined sequence data from cpDNA regions and ITS generate well-supported trees with two major lineages. Ann Bot-London 105: 471-480.
  • Nouzova M, Neumann P, Navratilova A, Galbraith DW, Macas J (2001). Microarray-based survey of repetitive genomic sequences in Vicia spp. Plant Mol Biol 45: 229-244.
  • 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.
  • Paterson AH, Bowers JE, Chapman BA (2004). Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. P Natl Acad Sci USA 101: 9903-9908.
  • Paterson AH, Schertz KF, Lin YR, Liu C, Chang YL (1995). The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of Johnsongrass, Sorghum halepense (L.) Pers. P Natl Acad Sci USA 92: 6127-6131.
  • Piednoël M, Carrete-Vega G, Renner SS (2013). Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species. Plant J 75: 699-709.
  • Price HJ, Dillon SL, Hodnett G, Rooney WL, Ross L, Johnston JS (2005). Genome evolution in the genus Sorghum (Poaceae). Ann Bot-London95: 219-227.
  • Schmidt T, Heslop-Harrison JS (1998). Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3: 195-199.
  • Schwarzacher T, Heslop-Harrison P (2000). Practical in situ Hybridization. Oxford, UK: BIOS Scientific Publishers.Spangler RE, Zaitchik B, Russo E, Kellogg EA (1999). Andropogoneae evolution and generic limits in Sorghum (Poaceae) using ndhF sequences. Syst Bot 24: 267-281.
  • Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006). All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. P Natl Acad Sci USA 103: 6805-6810.
  • Swigoňová Z, Lai JS, Ma JX, Ramakrishna W, Llaca V, Bennetzen JL, Messing J (2004). Close split of sorghum and maize genome progenitors. Genome Res 14: 1916-1923.
  • Tang H, Liang GH (1988). The genomic relationship between cultivated sorghum [Sorghum bicolor (L.) Moench] and Johnsongrass [S. halepense (L.) Pers.]: a re-evaluation. Theor Appl Genet 76: 277-284.
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  • ISSN: 1300-008X
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