Identification of Candidate Genes Related to Polyploidy and/or Apomixis in Eragrostis curvula

Juan-Pablo Selva, Silvina C. Pessino, Mauro S. Meier, Viviana C. Echenique

Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina.
Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Rosario, Argentina.

DOI: 10.4236/ajps.2012.33049                

Abstract

This work was aimed at identifying genes that show altered expression profiles in response to changes in ploidy and/or reproductive mode (from sexual to apomictic) in the African grass Eragrostis curvula. A differential display analysis was performed on leaf and flower transcriptomes from a series of genetically related euploid plants, including tetraploid apomictic, diploid sexual, and tetraploid sexual plants. More than 100 primer combinations were used to generate 11,864 total markers, yielding 1293 differential bands. Of these bands, 11.84% to 6.74% were related to ploidy and 0.71% to 2.17% to the reproductive mode, depending on the tissue. A small percentage of bands showed similar expressions between the tetraploid apomictic and the diploid sexual plants. Expression-based similarity dendrograms were constructed. Our data suggested that ploidy is more decisive than tissue type in defining the transcriptome structure. Out of 102 fragments sequenced, 50 showed strong homology to known genes. The differentially expressed genes were mapped in silico onto maize chromosomes. Several candidates mapped within the linkage group syntenic to the Tripsacum dactyloides diplospory-governing region. The evidence indicates that expression of genes located around the diplospory-associated region may be strongly influenced by ploidy and may be silenced in the apomictic genotype. These findings are discussed in the context of diplospory molecular control and its connection with ploidy.

Keywords

Differential Display; Diplosporous Apomixis; Eragrostis curvula; Gene Expression; Ploidy

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	G. Nogler, “Gametophytic Apomixis,” In: B. Johri, Ed., Embryology of Angiosperms, Springer Verlag, Berlin, 1984, pp. 475-518. doi:10.1007/978-3-642-69302-1_10
[2]	P. Ozias-Akins and P. van Dijk, “Mendelian Genetics of Apomixis in Plants,” Annual Review of Genetics, Vol. 41, No. 2, 2007, pp. 509-537. doi:10.1146/annurev.genet.40.110405.090511
[3]	A. J. Richards, “Apomixis in Flowering Plants: An Overview,” Philosophical Transaction of the Royal Society B, Vol. 358, No. 1434, 2003, pp. 1085-1093. doi:10.1098/rstb.2003.1294
[4]	U. Grossniklaus, “From Sexuality to Apomixis: Molecular and Genetic Approaches,” In: Y. Savidan, G. Carman, T. Dresselhaus, Eds., Flowering of Apomixis: From Mechanisms to Genetic Engineering, CIMMYT, Mexico City, 2001, pp. 168-211.
[5]	R. A. Bicknell and A. M. Koltunow, “Understanding Apomixis: Recent Advances and Remaining Conundrums,” The Plant Cell, Vol. 16, Suppl. 1, 2004, pp. S228-S245. doi:10.1105/tpc.017921
[6]	J. E. Bradley, G. C. Carman, M. S. Jamison and T. N. Naumova, “Heterochronic Features of the Female Germline among Several Sexual Diploid Tripsacum L. (Andropogoneae, Poaceae),” Sex Plant Reproduction, Vol. 20, No. 1, 2007, pp. 9-17. doi:10.1007/s00497-006-0038-0
[7]	D. Grimanelli, M. García, E. Kaszas, E. Perotti and O. Leblanc, “Heterochronic Expression of Sexual Reproductive Programs during Apomictic Development in Tripsacum,” Genetics, Vol. 165, No. 3, 2003, pp. 1521-1531.
[8]	T. F. Sharbel, M. L. Voigt, J. M. Corral, G. Galla, J. Kumlehn, C. Klukas, F. Schreiber, H. Vogel and B. Rotter, “Apomictic and Sexual Ovules of Boechera Display Heterochronic Global Gene Expression Patterns,” The Plan Cell, Vol. 22, No. 3, 2010, pp. 655-671. doi:10.1105/tpc.109.072223
[9]	M. R. Tucker, A. C. Araujo, N. A. Paech, V. Hecht, D. L. Schmidt, J. B. Rossell, S. C. de Vries and A. M. Koltunow, “Sexual and Apomictic Reproduction in Hieracium Subgenus Pilosella are Closely Interrelated Developmental Pathways,” The Plant Cell, Vol. 15, No. 7, 2003, pp. 1524-1537. doi:10.1105/tpc.011742
[10]	M. D. Bennett, “Nuclear DNA Content and Minimum Generation Time in Herbaceous Plants,” Philosophical Transaction of the Royal Society B, Vol. 181, No. 1063, 1972, pp. 109-135.
[11]	P. Voigt, N. Rethman and M. Poverene, “Lovegrasses,” In: Warm-Season (C4) Grass, American Society of Agronomy, Madison, 2004, pp. 1027-1056.
[12]	M. Poverene and P. Voigt, “Isozyme Variation and Germplasm Relationships in the Eragrostis curvula Complex,” Biochemical Systematics and Ecology, Vol. 25, No. 1, 1997, pp. 21-32. doi:10.1016/S0305-1978(96)00089-0
[13]	L. J. Streetman, “Reproduction of the Lovegrasses, the Genus Eragrostis: Eragrostis chloromelas Stend. E. Curvula (Schrad.) Nees., E. lehmanniana Nees. and E. superba Peyr. Wrightia,” A Botanical Journal, Vol. 3, 1963, pp. 41-51.
[14]	C. Crane, “Classification of Apomictic Mechanisms,” In: Y. Savidan, G. Carman and T. Dresselhaus, Eds., Flowering of Apomixis: From Mechanisms to Genetic Engineering, CIMMYT, Mexico City, 2001, pp. 168-211.
[15]	R. D. Noyes, “Inheritance of Apomeiosis (Diplospory) in Fleabanes (Erigeron, Asteraceae),” Heredity, Vol. 94, No. 2, 2005, pp. 193-198. doi:10.1038/sj.hdy.6800597
[16]	R. D. Noyes, “Apomixis via Recombination of Genome Regions for Apomeiosis (Diplospory) and Parthenogenesis in Erigeron (Daisy Fleabane, Asteraceae),” Sexual Plant Reproduction, Vol. 19, No. 1, 2006, pp. 7-18. doi:10.1007/s00497-005-0017-x
[17]	R. D. Noyes and L. H. Rieseberg, “Two Independent Loci Control Agamospermy (Apomixis) in the Triploid Flowering Plant Erigeron annuus,” Genetics, Vol. 155, No. 1, 2000, pp. 379-390.
[18]	P. J. van Dijk and J. M. Bakx-Schotman, “Formation of Unreduced Megaspores (Diplospory) in Apomictic Dandelions (Taraxacum officinale, s.l.) Is Controlled by a Sex-Specific Dominant Locus,” Genetics, Vol. 166, No. 1, 2004, pp. 483-492. doi:10.1534/genetics.166.1.483
[19]	K. Vijverberg, R. G. van der Hulst, P. Lindhout and P. J. van Dijk, “A Genetic Linkage Map of the Diplosporous Chromosomal Region in Taraxacum officinale (Common Dandelion; Asteraceae),” Theoretical and Applied Genetics, Vol. 108, No. 4, 2004, pp. 725-732. doi:10.1007/s00122-003-1474-y
[20]	D. Grimanelli, O. Leblanc, E. Espinosa, E. Perotti, D. Gonzáles de León and Y. Savidán, “Mapping Diplosporous Apomixis in Tetraploid Tripsacum: One Gene or Several Genes?” Heredity, Vol. 80, No. 1, 1998, pp. 33-39. doi:10.1046/j.1365-2540.1998.00263.x
[21]	O. Leblanc, D. Grimanelli, D. Gonzalez de Leon and Y. Savidán, “Detection of the Apomictic Mode of Reproduction in Maize-Tripsacum Hybrids Using Maize RFLP Markers,” Theoretical and Applied Genetics, Vol. 90, No. 7-8, 1995, pp. 1198-1203. doi:10.1007/BF00222943
[22]	Y. Savidan, D. Grimanelli, E. Perotti and O. Leblanc, “Means for Identifying Nucleotide Sequences Involved in Apomixis,” US Patent No. 2008/0155712 A1, 2008.
[23]	O. Calderini, S. B. Chang, H. de Jong, A. Busti, F. Paolocci, S. Arcioni, S. C. de Vries, M. H. Abma-Henkens, R. M. Lankhorst, I. S. Donnison and F. Pupilli, “Molecular Cytogenetics and DNA Sequence Analysis of an Apomixis-Linked BAC in Paspalum simplex Reveal a Non Pericentromere Location and Partial Microcolinearity with Rice,” Theoretical and Applied Genetics, Vol. 112, No. 6, 2006, pp. 1179-1191. doi:10.1007/s00122-006-0220-7
[24]	O. Calderini, I. Donnison, L. Polegri, F. Panara, A. Thomas, S. Arcioni and F. Pupilli, “Partial Isolation of the Genomic Region Linked with Apomixis in Paspalum simplex,” Molecular Breeding, Vol. 28, No. 2, 2011, pp. 265- 276. doi:10.1007/s11032-010-9480-7
[25]	J. A. Conner, S. Goel, G. Gunawan, M. M. Cordonnier-Pratt, V. Ed Johnson, C. Liang, H. Wang, L. H. Pratt, J. E. Mullet, J. DeBarry, L. Yang, J. L. Bennetzen, P. E. Klein and P. Ozias-Akins, “Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus,” Plant Physiology, Vol. 147, No. 3, 2008, pp. 1396-1411. doi:10.1104/pp.108.119081
[26]	C. B. Yadav, Anuj, S. Kumar, M. G. Gupta and V. Bhat, “Genetic Linkage Maps of the Chromosomal Regions Associated with Apomictic and Sexual Modes of Reproduction in Cenchrus ciliaris,” Molecular Breeding, 2011.
[27]	O. Leblanc, D. Grimanelli, M. Hernandez-Rodriguez, P. A. Galindo, A. M. Soriano-Martinez and E. Perotti, “Seed Development and Inheritance Studies in Apomictic Maize-Tripsacum Hybrids Reveal Barriers for the Transfer of Apomixis into Sexual Crops,” The International Journal of Developmental Biology, Vol. 53, No. 4, 2009, pp. 585-596. doi:10.1387/ijdb.082813ol
[28]	V. Olmedo-Monfil, N. Durán-Figueroa, M. Arteaga-Vázquez, E. Demesa-Arévalo, D. Autran, D. Grimanelli, R. K. Slotkin, R. A. Martienssen and J. P. Vielle-Calzada, “Control of female Gamete Formation by a Small RNA Pathway in Arabidopsis,” Nature, Vol. 464, No. 7288, 2010, pp. 628-632. doi:10.1038/nature08828
[29]	M. Singh, S. Goel, R. B. Meeley, C. Dantec, H. Parrinello, C. Michaud, O. Leblanc and D. Grimanelli, “Production of Viable Gametes without Meiosis in Maize Deficient for an ARGONAUTE Protein,” The Plant Cell, Vol. 23, No. 2, 2011, pp. 443-458. doi:10.1105/tpc.110.079020
[30]	M. Garcia-Aguilar, C. Michaud, O. Leblanc, D. Grimanelli, “Inactivation of a DNA Methylation Pathway in Maize Reproductive Organs Results in Apomixis-Like Phenotypes,” The Plant Cell, Vol. 22, No. 10, 2010, pp. 3249-3267. doi:10.1105/tpc.109.072181
[31]	S. Cardone, P. Polci, J. P. Selva, M. Mecchia, S. Pessino, P. Hermann, V. Cambi, P. Voigt, G. Spangenberg and V. Echenique, “Novel Genotypes of the Subtropical Grass Eragrostis curvula for the Study of Apomixis (Diplospory),” Euphytica, Vol. 151, No. 2, 2006, pp. 263-272. doi:10.1007/s10681-006-9156-x
[32]	M. A. Mecchia, A. Ochogavía, J. P. Selva, N. Laspina, S. Felitti, L. G. Martelotto, G. Spangenberg, V. Echenique and S. C. Pessino, “Genome Polymorphisms and Gene Differential Expression in a ‘Back-and-Forth’ Ploidy-Altered Series of Weeping Lovegrass (Eragrostis curvula),” Journal of Plant Physiology, Vol. 164, No. 8, 2007, pp. 1051-1061. doi:10.1016/j.jplph.2006.07.002
[33]	A. C. Ochogavía, G. Cervigni, J. P. Selva, V. C. Echenique and S. C. Pessino, “Variation in Cytosine Methylation Patterns during Ploidy Level Conversions in Eragrostis curvula,” Plant Molecular Biology, Vol. 70, No. 1-2, 2009, pp. 17-29. doi:10.1007/s11103-009-9454-5
[34]	G. D. L. Cervigni, N. Paniego, M. Díaz, J. P. Selva, D. Zappacosta, D. Zanazzi, I. Landerreche, L. Martelotto, S. Felitti, S. Pessino, G. Spangenberg and V. Echenique, “Expressed Sequence Tag Analysis and Development of Gene Associated Markers in a Near-Isogenic Plant System of Eragrostis curvula,” Plant Molecular Biology, Vol. 67, No. 1-2, 2008, pp. 1-10. doi:10.1007/s11103-007-9282-4
[35]	G. D. L. Cervigni, N. Paniego, S. Pessino, J. P. Selva, M. Díaz, G. Spangenberg and V. Echenique, “Gene Expression in Diplosporous and Sexual Eragrostis curvula Genotypes with Differing Ploidy Levels,” Plant Molecular Biology, Vol. 67, No. 1-2, 2008, pp. 11-23. doi:10.1007/s11103-008-9305-9
[36]	P. Liang and A. B. Pardee, “Differential Display of Eukaryotic Messenger RNA by Means of the Polymerase Chain Reaction,” Science, Vol. 257, No. 5072, 1992, pp. 967-971. doi:10.1126/science.1354393
[37]	M. V. Matz and S. A. Lukyanov, “Different Strategies of Differential Display: Areas of Application,” Nucleic Acids Research, Vol. 26, No. 24, 1998, pp. 5537-5543. doi:10.1093/nar/26.24.5537
[38]	T. Murashige and F. Skoog, “A Revised Medium for Rapid Growth and Bioassay with Tobacco Tissue Cultures,” Physiologia Plantarum, Vol. 15, No. 3, 1962, pp. 473-497. doi:10.1111/j.1399-3054.1962.tb08052.x
[39]	D. A. Johansen, “Plant Microtechnique,” McGraw-Hill Book Co., New York and London, 1940.
[40]	P. Jaccard, “Nouvelles Recherches sur la Distribution Florale,” Société Vaudoise des Sciences Naturelles Bulletin, Vol. 44, 1908, pp. 223-270.
[41]	S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D. Lipman, “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research, Vol. 25, No. 27, 1997, pp. 3389-3402. doi:10.1093/nar/25.17.3389
[42]	Z. Zhang, S. Schwartz, L. Wagner and W. Miller, “A - Greedy Algorithm for Aligning DNA Sequences,” Journal of Computational Biology, Vol. 7, No. 1-2, 2000, pp. 203-214. doi:10.1089/10665270050081478
[43]	K. J. Livak and T. D. Schmittgen, “Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-ΔΔCt Method,” Methods, Vol. 25, No. 4, 2001, pp. 402-408. doi:10.1006/meth.2001.1262
[44]	N. Laspina, T. Vega, G. Seijo, A. Gonzalez, L. Martelotto, J. Stein, M. Podio, J. P. Ortiz, V. Echenique, C. Quarin and S. Pessino, “Gene Expression Analysis at the Onset of Aposporous Apomixis in Paspalum notatum,” Plant Molecular Biology, Vol. 67, No. 6, 2008, pp. 615-628. doi:10.1007/s11103-008-9341-5
[45]	L. Martelotto, J. P. Ortiz, F. Espinoza, C. Quarin and S. Pessino, “A Comprehensive Analysis of Gene Expression Alterations in a Newly Synthesized Paspalum notatum Autotetraploid,” Plant Science, Vol. 169, No. 1, 2005, pp. 211-220. doi:10.1016/j.plantsci.2005.03.015
[46]	Y. Haoa, X. Wen and X. Deng, “Genetic and Epigenetic Evaluations of Citrus Calluses Recovered from Slow-Growth Culture,” Journal of Plant Physiology, Vol. 161, No. 4, 2004, pp. 479-484. doi:10.1078/0176-1617-01102
[47]	L. Xiong, C. Xu, M. Shagai Maroof and Q. Zhang, “Patterns of Cytosine Methylation in an Elite Rice Hybrid and Its Parental Genotypes, Detected by a Methylation-Sensitive Amplification Polymorphism Technique,” Molecular and General Genetics, Vol. 261, No. 3, 1999, pp. 439-446. doi:10.1007/s004380050986
[48]	E. L. Peredo, M. A. Revilla and R. Arroyo-Garcia, “Assessment of Genetic and Epigenetic Variation in Hop Plants Regenerated from Sequential Sub-Cultures of Organogenic Calli,” Journal of Plant Physiolgy, Vol. 163, No. 10, 2006, pp. 1071-1079. doi:10.1016/j.jplph.2005.09.010
[49]	H. Ozkan, A. A. Levy and M. Feldman, “Rapid Differentiation of Homoeologous Chromosomes in Newly-Formed Allopolyploid Wheat,” Israel Journal of Plant Sciences, Vol. 50, Suppl. 1, 2002, pp. S65-S76. doi:10.1560/E282-PV55-G4XT-DRWJ
[50]	Y. Savidan, “Apomixis: Genetics and Breeding,” In: J. Janick, Ed., Plant Breeding Reviews, Vol. 18, Kluwer Academic Publ., Dordrecht, 2000, pp. 13-86.
[51]	Y. Akiyama, W. W. Hanna and P. Ozias-Akins, “High-Resolution Physical Mapping Reveals that the Apospory-Specific Genomic Region (ASGR) in Cenchrus ciliaris Is Located on a Heterochromatic and Hemizygous Region of a Single Chromosome,” Theoretical and Applied Genetics, Vol. 111, No. 6, 2005, pp. 1042-1051. doi:10.1007/s00122-005-0020-5
[52]	J. Stein, S. Pessino, E. Martínez, M. Rodriguez, L. Siena, C. Quarin and J .Ortiz, “A Genetic Map of Tetraploid Paspalum notatum Flügge (Bahiagrass) Based on Single-Dose Molecular Markers,” Molecular Breeding, Vol. 20, No. 2, 2007, pp. 153-166. doi:10.1007/s11032-007-9083-0
[53]	E. Albertini, G. Marconi, G. Barcaccia, L. Raggi and M. Falcinelli, “Isolation of Candidate Genes for Apomixis in Poa pratensis,” Plant Molecular Biology, Vol. 56, No. 6, 2004, pp. 879-894. doi:10.1007/s11103-004-5211-y
[54]	R. M. Stupar, P. B. Bhaskar, B. S. Yandell, W. A. Rensink, A. L. Hart, S. Ouyang, R. E. Veilleux, J. S. Busse, R. J. Erhardt, C. R. Buell and J. Jiang, “Phenotypic and Transcriptomic Changes Associated with Potato Autopolyploidization,” Genetics, Vol. 176, No. 4, 2007, pp. 2055- 2067. doi:10.1534/genetics.107.074286
[55]	H. Yamada-Akiyama, Y. Akiyama, M. Ebina, Q. Xu, S. Tsuruta, J. Yazaki, N. Kishimoto, S. Kikuchi, M. Takahara, T. Takamizo, S. Sugita and H. Nakagawa, “Analysis of Expressed Sequence Tags in Apomictic Guineagrass (Panicum maximum),” Journal of Plant Physiology, Vol. 166, No. 7, 2009, pp. 750-761. doi:10.1016/j.jplph.2008.10.001
[56]	L. Polegri, O. Calderini, S. Arcioni and F Pupilli, “Specific Expression of Apomixis-Linked Alleles Revealed by comparative Transcriptomic Analysis of Sexual and Apomictic Paspalum simplex Morong Flowers,” Journal of Experimental Botany, Vol. 61, No. 6, 2010, pp. 1869-1883. doi:10.1093/jxb/erq054