Cytogenetics of legumes in the Phaseoloid clade

Plant Genome

Volumn 6, Issue 3, 2013, Pages 3-

  Iwata, Aiko ^a   Greenland, Christopher M ^a   Jackson, Scott A ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890691906     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2013.03.0004     Document Type: Article

References (103)

1. Abirached-Darmency, M., E. Prado-Vivant, L. Chelysheva, and T. Pouthier. 2005. Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH. Genome 48:556-561. doi:10.1139/g05-015.
2. Altrock, S., A. Fonsêca, and A. Pedrosa-Harand. 2011. Chromosome identification in the Andean common bean accession G19833 (Phaseolus vulgaris L., Fabaceae). Genet. Mol. Biol. 34:459-463. doi:10.1590/S1415-47572011005000029.
3. Appels, R., W.L. Gerlach, E.S. Dennis, H. Swift, and W.J. Peacock. 1980. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma 78:293-311. doi:10.1007/BF00327389.
4. Bennett, M.D., and J.B. Smith. 1976. Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. Lond. B Biol. Sci. 274:227-274. doi:10.1098/rstb.1976.0044.
5. Bertioli, D.J., M.C. Moretzsohn, L.H. Madsen, N. Sandal, S.C. Leal-Bertioli, P.M. Guimaraes, B.K. Hougaard, J. Fredslund, L. Schauser, A.M. Nielsen, S. Sato, S. Tabata, S.B. Cannon, and J. Stougaard. 2009. An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 10:45. doi:10.1186/1471-2164-10-45.
6. Birchler, J.A., and F. Han. 2009. Maize centromeres: Structure, function, epigenetics. Annu. Rev. Genet. 43:287-303. doi:10.1146/annurevgenet-102108-134834.
7. Bonifacio, E.M., A. Fonsêca, C. Almeida, K.G.B. dos Santos, and A. Pedrosa-Harand. 2012. Comparative cytogenetic mapping between the lima bean (Phaseolus lunatus L.) and the common bean (P. vulgaris L.). Theor. Appl. Genet. 124:1513-1520. doi:10.1007/s00122-012-1806-x.
8. Cannon, S.B., G.D. May, and S.A. Jackson. 2009. Three sequenced legume genomes and many crop species: Rich opportunities for translational genomics. Plant Physiol. 151:970-977. doi:10.1104/pp.109.144659.
9. Carvalheira, G.M.G. 2000. Plant polytene chromosomes. Genet. Mol. Biol. 23:1043-1050. doi:10.1590/S1415-47572000000400050.
10. Carvalheira, G., and M. Guerra. 1994. The polytene chromosomes of anther tapetum of some Phaseolus species. Cytologia (Tokyo) 59:211-217. doi:10.1508/cytologia.59.211.
11. Castel, S.E., and R.A. Martienssen. 2013. RNA interference in the nucleus: Roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet. 14:100-112. doi:10.1038/nrg3355.
12. Cerbah, M., T. Souza-Chies, M.F. Jubier, B. Lejeune, and S. Siljak-Yakovlev. 1998. Molecular phylogeny of the genus Hypochaeris using internal transcribed spacers of nuclear rDNA: Inference for chromosomal evolution. Mol. Biol. Evol. 15:345-354. doi:10.1093/oxfordjournals.molbev.a025931.
13. Chaowen, S., J.Y. Liu, Z.Y. Xiong, and Y.C. Song. 2004. Karyotype analysis of Psophocarpus tetragonolobus (L.) DC by chromosome banding and fluorescence in situ hybridization. Caryologia 57:387-394.
14. Choi, H.K., J.H. Mun, D.J. Kim, H. Zhu, J.M. Baek, J. Mudge, B. Roe, N. Ellis, J. Doyle, G.B. Kiss, N.D. Young, and D.R. Cook. 2004. Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA 101:15289-15294. doi:10.1073/pnas.0402251101.
15. Chung, M.C., Y.I. Lee, Y.Y. Cheng, Y.J. Chou, and C.F. Lu. 2008. Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor. Appl. Genet. 116:745-753. doi:10.1007/s00122-007-0705-z.
16. Cuadrado, A., and N. Jouve. 2002. Evolutionary trends of different repetitive DNA sequences during speciation in the genus Secale. J. Hered. 93:339-345. doi:10.1093/jhered/93.5.339.
17. Danna, K.J., R. Workman, V. Coryell, and P. Keim. 1996. 5S rRNA genes in tribe Phaseoleae: Array size, number, and dynamics. Genome 39:445-455. doi:10.1139/g96-056.
18. David, P., N.W. Chen, A. Pedrosa-Harand, V. Thareau, M. Sevignac, S.B. Cannon, D. Debouck, T. Langin, and V. Geffroy. 2009. A nomadic subtelomeric disease resistance gene cluster in common bean. Plant Physiol. 151:1048-1065. doi:10.1104/pp.109.142109.
19. de Jong, H., P. Fransz, and P. Zabel. 1999. High resolution FISH in plants: Techniques and applications. Trends Plant Sci. 4:258-263. doi:10.1016/S1360-1385(99)01436-3.
20. de Moraes, A.P., W.D. Soares, and M. Guerra. 2007. Karyotype diversity and the origin of grapefruit. Chromosome Res. 15:115-121. doi:10.1007/s10577-006-1101-2.
21. Doyle, J.J., and M.A. Luckow. 2003. The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol. 131:900-910. doi:10.1104/pp.102.018150.
22. Du, J., Z. Tian, C.S. Hans, H.M. Laten, S.B. Cannon, S.A. Jackson, R.C. Shoemaker, and J. Ma. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: Insights from genome-wide analysis and multi-specific comparison. Plant J. 63:584-598. doi:10.1111/j.1365-313X.2010.04263.x.
23. Dvorak, J., H.B. Zhang, R.S. Kota, and M. Lassner. 1989. Organization and evolution of the 5s-ribosomal RNA gene family in wheat and related species. Genome 32:1003-1016. doi:10.1139/g89-545.
24. Findley, S.D., S. Cannon, K. Varala, J. Du, J. Ma, M.E. Hudson, J. Birchler, and G. Stacey. 2010. A fluorescence in situ hybridization system for karyotyping soybean. Genetics 185:727-744. doi:10.1534/genetics.109.113753.
25. Flavell, R.B. 1986. The structure and control of expression of ribosomal RNA genes. Oxf. Surv. Plant Mol. Cell Biol. 3:251-274.
26. Fonsêca, A., J. Ferreira, T.R. dos Santos, M. Mosiolek, E. Bellucci, J. Kami, P. Gepts, V. Geffroy, D. Schweizer, K.G. dos Santos, and A. Pedrosa-Harand. 2010. Cytogenetic map of common bean (Phaseolus vulgaris L.). Chromosome Res. 18:487-502. doi:10.1007/s10577-010-9129-8.
27. Fransz, P., R. ten Hoopen, and F. Tessadori. 2006. Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Res. 14:71-82. doi:10.1007/s10577-005-1022-5.
28. Fuchs, J., D. Demidov, A. Houben, and I. Schubert. 2006. Chromosomal histone modification patterns-From conservation to diversity. Trends Plant Sci. 11:199-208. doi:10.1016/j.tplants.2006.02.008.
29. Fukui, K., and K. Iijima. 1991. Somatic chromosome map of rice by imaging methods. Theor. Appl. Genet. 81:589-596. doi:10.1007/BF00226723.
30. Galasso, I., G.E. Harrison, D. Pignone, A. Brandes, and J.S. Heslop-Harrison. 1997. The distribution and organization of Ty1-copia-like retrotransposable elements in the genome of Vigna unguiculata (L) Walp (cowpea) and its relatives. Ann. Bot. (London) 80:327-333. doi:10.1006/anbo.1997.0443.
31. Galasso, I., T. Schmidt, D. Pignone, and J.S. Heslop-Harrison. 1995. The molecular cytogenetics of Vigna unguiculata (L) Walp: The physical organization and characterization of 18s-5.8s-25s ribosomal RNA genes, 5s ribosomal RNA genes, telomere-like sequences, and a family of centromeric repetitive DNA sequences. Theor. Appl. Genet. 91:928-935.
32. Gent, J.I., Y.Z. Dong, J.M. Jiang, and R.K. Dawe. 2012. Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications. Nucleic Acids Res. 40:1550-1560. doi:10.1093/nar/gkr862.
33. Gent, J.I., N.A. Ellis, L. Guo, A.E. Harkess, Y. Yao, X. Zhang, and R.K. Dawe. 2013. CHH islands: De novo DNA methylation in neargene chromatin regulation in maize. Genome Res. 23:628-637. doi:10.1101/gr.146985.112.
34. Gill, N., S. Findley, J.G. Walling, C. Hans, J. Ma, J. Doyle, G. Stacey, and S.A. Jackson. 2009. Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol. 151:1167-1174. doi:10.1104/pp.109.137935.
35. Grewal, S.I., and S. Jia. 2007. Heterochromatin revisited. Nat. Rev. Genet. 8:35-46. doi:10.1038/nrg2008.
36. Grimanelli, D., and F. Roudier. 2013. Epigenetics and development in plants: Green light to convergent innovations. Curr. Top. Dev. Biol. 104:189-222. doi:10.1016/B978-0-12-416027-9.00006-1.
37. Guerra, M. 2001. Fluorescent in situ hybridization in plant polytene chromosomes. Methods Cell Sci. 23:133-138. doi:10.1023/A:1013134808249.
38. Guerra, M., A. Kenton, and M.D. Bennett. 1996. rDNA sites in mitotic and polytene chromosomes of Vigna unguiculata (L) Walp and Phaseolus coccineus L revealed by in situ hybridization. Ann. Bot. (London) 78:157-161. doi:10.1006/anbo.1996.0108.
39. Hall, K.J., and J.S. Parker. 1995. Stable chromosome fission associated with rDNA mobility. Chromosome Res. 3:417-422. doi:10.1007/BF00713891.
40. Hansen, C.N., G. Harper, and J.S. Heslop-Harrison. 2005. Characterization of pararetrovirus-like sequences in the genome of potato. Cytogenet. Genome Res. 110:559-565. doi:10.1159/000084989.
41. Hayasaki, M., T. Morikawa, and J.M. Leggett. 2001. Intraspecific variation of 18S-5.8S-26S rDNA sites revealed by FISH and RFLP in wild oat, Avena agadiriana. Genes Genet. Syst. 76:9-14. doi:10.1266/ggs.76.9.
42. Heslop-Harrison, J.S., and T. Schwarzacher. 2011. Organisation of the plant genome in chromosomes. Plant J. 66:18-33. doi:10.1111/j.1365-313X.2011.04544.x.
43. Iwata, A., A.L. Tek, M. Richard, B. Abernathy, A. Fonsêca, J. Schmutz, N. Chen, V. Thareau, G. Magdelenat, Y. Li, M. Murata, A. Pedrosa-Harand, V. Geffroy, K. Nagaki, and S.A. Jackson. 2013. Identification and characterization of functional centromeres of common bean (Phaseolus vulgaris). Plant J. doi:10.1111/tpj.12269.
44. Jasencakova, Z., W.J. Soppe, A. Meister, D. Gernand, B.M. Turner, and I. Schubert. 2003. Histone modifications in Arabidopsishigh methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33:471-480. doi:10.1046/j.1365-313X.2003.01638.x.
45. Jiang, J., J.A. Birchler, W.A. Parrott, and R.K. Dawe. 2003. A molecular view of plant centromeres. Trends Plant Sci. 8:570-575. doi:10.1016/j. tplants.2003.10.011.
46. Jiang, J.M., and B.S. Gill. 2006. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49:1057-1068. doi:10.1139/g06-076.
47. Kim, D.H., M.R. Doyle, S. Sung, and R.M. Amasino. 2009. Vernalization: Winter and the timing of flowering in plants. Annu. Rev. Cell Dev. Biol. 25:277-299. doi:10.1146/annurev.cellbio.042308.113411.
48. Kim, J.S., M.N. Islam-Faridi, P.E. Klein, D.M. Stelly, H.J. Price, R.R. Klein, and J.E. Mullet. 2005. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: Distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171:1963-1976. doi:10.1534/genetics.105.048215.
49. Krishnan, P., V.T. Sapra, K.M. Soliman, and A. Zipf. 2001. FISH mapping of the 5S and 18S-28S rDNA loci in different species of Glycine. J. Hered. 92:295-300. doi:10.1093/jhered/92.3.295.
50. Kulikova, O., G. Gualtieri, R. Geurts, D.J. Kim, D. Cook, T. Huguet, J.H. de Jong, P.F. Fransz, and T. Bisseling. 2001. Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J. 27:49-58. doi:10.1046/j.1365-313x.2001.01057.x.
51. Li, X., X. Wang, K. He, Y. Ma, N. Su, H. He, V. Stolc, W. Tongprasit, W. Jin, J. Jiang, W. Terzaghi, S. Li, and X.W. Deng. 2008. Highresolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20:259-276. doi:10.1105/tpc.107.056879.
52. Lima-de-Faria, A. 1976. The chromosome field. I. Prediction of the location of ribosomal cistrons. Hereditas 83:1-22. doi:10.1111/j.1601-5223.1976.tb01565.x.
53. Lin, J.Y., B.H. Jacobus, P. SanMiguel, J.G. Walling, Y. Yuan, R.C. Shoemaker, N.D. Young, and S.A. Jackson. 2005. Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile. Genetics 170:1221-1230. doi:10.1534/genetics.105.041616.
54. Lin, J.Y., R.M. Stupar, C. Hans, D.L. Hyten, and S.A. Jackson. 2010. Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris. Plant Cell 22:2545-2561. doi:10.1105/tpc.110.074229.
55. Lysak, M.A., A. Berr, A. Pecinka, R. Schmidt, K. McBreen, and I. Schubert. 2006. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc. Natl. Acad. Sci. USA 103:5224-5229. doi:10.1073/pnas.0510791103.
56. McClean, P.E., S. Mamidi, M. McConnell, S. Chikara, and R. Lee. 2010. Synteny mapping between common bean and soybean reveals extensive blocks of shared loci. BMC Genomics 11:184.
57. Mercado-Ruaro, P., and A Delgado-Salinas. 1998. Karyotypic studies on species of Phaseolus (Fabaceae: Phaseolinae). Am. J. Bot. 85:1-9. doi:10.2307/2446547.
58. Mercado-Ruaro, P, and A. Delgado-Salinas. 2000. Cytogenetic studies in Phaseolus L. (Fabaceae). Genet. Mol. Biol. 23:985-987. doi:10.1590/S1415-47572000000400043.
59. Moscone, E.A., F. Klein, M. Lambrou, J. Fuchs, and D. Schweizer. 1999. Quantitative karyotyping and dual-color FISH mapping of 5S and 18S-25S rDNA probes in the cultivated Phaseolus species (Leguminosae). Genome 42:1224-1233.
60. Murata, M., J.S. Heslop-Harrison, and F. Motoyoshi. 1997. Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones. Plant J. 12:31-37. doi:10.1046/j.1365-313X.1997.12010031.x.
61. Nagl, W. 1974. The Phaseolus suspensor and its polytene chromosomes. Z. Pflanzenphysiol. 73:1-44. doi:10.1016/S0044-328X(74)80142-X.
62. Nagl, W. 1991. Two human DNA sequences (aromatase, telomere) detected in Phaseolus (Fabaceae) by respectively blot and in situ hybridization. Polish Bot. Stud. 2:159-164.
63. Nenno, M., K. Schumann, and W. Nagl. 1993. Mapping phaseolin genes to polytene chromosomes by fluorescence in situ hybridization (FISH). Annu. Rep. Bean Improv. Coop. 36:3-4.
64. Nenno, M., K. Schumann, and W. Nagl. 1994. Detection of rRNA and phaseolin genes on polytene chromosomes of Phaseolus coccineus by fluorescence in situ hybridization after pepsin pretreatment. Genome 37:1018-1021. doi:10.1139/g94-144.
65. Nenno, M., D. Zink, and W. Nagl. 1996. Localization of different microsatellites and a minisatellite-like sequence on polytene chromosomes of Phaseolus coccineus. Annu. Rep. Bean Improv. Coop. 39:245-246.
66. Nenno, M., D. Zink, and W. Nagl. 1998. The Arabidopsis telomere sequence is highly abundant in the genome of Phaseolus acutifolius and preferentially located in the centromeres. Annu. Rep. Bean Improv. Coop. 41:103-104.
67. Ohmido, N., K. Fukui, and T. Kinoshita. 2010a. Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). Proc. Jpn. Acad., Ser. B, Phys. Biol. Sci. 86:103-116. doi:10.2183/pjab.86.103.
68. Ohmido, N., A. Ishimaru, S. Kato, S. Sato, S. Tabata, and K. Fukui. 2010b. Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res. 18:287-299. doi:10.1007/s10577-009-9103-5.
69. Pedrosa, A., N. Sandal, J. Stougaard, D. Schweizer, and A. Bachmair. 2002. Chromosomal map of the model legume Lotus japonicus. Genetics 161:1661-1672.
70. Pedrosa-Harand, A., C.C. de Almeida, M. Mosiolek, M.W. Blair, D. Schweizer, and M. Guerra. 2006. Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution. Theor. Appl. Genet. 112:924-933. doi:10.1007/s00122-005-0196-8.
71. Peters, S.A., J.W. Bargsten, D. Szinay, J. van de Belt, R.G. Visser, Y. Bai, and H. de Jong. 2012. Structural homology in the Solanaceae: Analysis of genomic regions in support of synteny studies in tomato, potato and pepper. Plant J. 71:602-614. doi:10.1111/j.1365-313X.2012.05012.x.
72. Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura, D.S. Brar, S. Jackson, R.A. Wing, and O. Panaud. 2006. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 16:1262-1269. doi:10.1101/gr.5290206.
73. Raina, S., and Y. Mukai. 1999. Detection of a variable number of 18S-5.8S-26S and 5S ribosomal DNA loci by fluorescent in situ hybridization in diploid and tetraploid Arachis species. Genome 42:52-59.
74. Raskina, O., J.C. Barber, E. Nevo, and A. Belyayev. 2008. Repetitive DNA and chromosomal rearrangements: Speciation-related events in plant genomes. Cytogenet. Genome Res. 120:351-357. doi:10.1159/000121084.
75. Raskina, O., A. Belyayev, and E. Nevo. 2004. Quantum speciation in Aegilops: Molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc. Natl. Acad. Sci. USA 101:14818-14823. doi:10.1073/pnas.0405817101.
76. SanMiguel, P., A. Tikhonov, Y.K. Jin, N. Motchoulskaia, D. Zakharov, A. MelakeBerhan, P.S. Springer, K.J. Edwards, M. Lee, Z. Avramova, and J.L. Bennetzen. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768. doi:10.1126/science.274.5288.765.
77. Saxena, K.B. 2005. Pigeonpea. In: R.J. Singh and P.P. Jauhar, editors, Genetic resources, chromosome engineering, and crop improvement series: Grain legumes. Vol. 1. CRC Press, Boca Raton, FL. p. 85-115.
78. Schmutz, J., S.B. Cannon, J. Schlueter, J.X. Ma, T. Mitros, W. Nelson, D.L. Hyten, Q.J. Song, J.J. Thelen, J.L. Cheng, D. Xu, U. Hellsten, G.D. May, Y. Yu, T. Sakurai, T. Umezawa, M.K. Bhattacharyya, D. Sandhu, B. Valliyodan, E. Lindquist, M. Peto, D. Grant, S.Q. Shu, D. Goodstein, K. Barry, M. Futrell-Griggs, B. Abernathy, J.C. Du, Z.X. Tian, L.C. Zhu, N. Gill, T. Joshi, M. Libault, A. Sethuraman, X.C. Zhang, K. Shinozaki, H.T. Nguyen, R.A. Wing, P. Cregan, J. Specht, J. Grimwood, D. Rokhsar, G. Stacey, R.C. Shoemaker, and S.A. Jackson. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463:178-183. doi:10.1038/nature08670.
79. Schubert, I. 2007. Chromosome evolution. Curr. Opin. Plant Biol. 10:109-115. doi:10.1016/j.pbi.2007.01.001.
80. Schubert, I., P.F. Fransz, J. Fuchs, and J.H. de Jong. 2001. Chromosome painting in plants. Methods Cell Sci. 23:57-69. doi:10.1023/A:1013137415093.
81. Schubert, I., and U. Wobus. 1985. In situ hybridization confirms jumping nucleolus organizing regions in Allium. Chromosoma 92:143-148. doi:10.1007/BF00328466.
82. Schumann, K., A. Baumann, and W. Nagl. 1990. Localization of phaseolin genes in the polytene chromosomes of Phaseolus coccineus (Leguminosae). Genetica (The Hague) 83:73-76.
83. Schweizer, D., and P. Ambros. 1979. Analysis of nucleolus organizer regions (NORs) in mitotic and polytene chromosomes of Phaseolus coccineus by silver staining and giemsa C-banding. Plant Syst. Evol. 132:27-51. doi:10.1007/BF00983083.
84. Singh, R.J., R.L. Nelson, and G.H. Chung. 2007. Soybean. In: R.J. Singh, editor, Genetic resources, chromosome engineering, and crop improvement series: Oilseed crops. Vol. 4. CRC Press, Boca Raton, FL. p. 13-50.
85. Sousa, A., A.E. Barros e Silva, A. Cuadrado, Y. Loarce, M.V. Alves, and M. Guerra. 2011. Distribution of 5S and 45S rDNA sites in plants with holokinetic chromosomes and the "chromosome field" hypothesis. Micron 42:625-631. doi:10.1016/j.micron.2011.03.002.
86. Staginnus, C., W. Gregor, M.F. Mette, C.H. Teo, E.G. Borroto-Fernandez, M.L. Machado, M. Matzke, and T. Schwarzacher. 2007. Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol. 7:24. doi:10.1186/1471-2229-7-24.
87. Szinay, D., E. Wijnker, R. van den Berg, R.G. Visser, H. de Jong, and Y. Bai. 2012. Chromosome evolution in Solanum traced by crossspecies BAC-FISH. New Phytol. 195:688-698. doi:10.1111/j.1469-8137.2012.04195.x.
88. Tang, X., D. Szinay, C. Lang, M.S. Ramanna, E.A. van der Vossen, E. Datema, R.K. Lankhorst, J. de Boer, S.A. Peters, C. Bachem, W. Stiekema, R.G. Visser, H. de Jong, and Y. Bai. 2008. Cross-species bacterial artificial chromosome-fluorescence in situ hybridization painting of the tomato and potato chromosome 6 reveals undescribed chromosomal rearrangements. Genetics 180:1319-1328. doi:10.1534/genetics.108.093211.
89. Tek, A.L., K. Kashihara, M. Murata, and K. Nagaki. 2010. Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Res. 18:337-347. doi:10.1007/s10577-010-9119-x.
90. Thomas, H.M., J.A. Harper, M.R. Meredith, W.G. Morgan, I.D. Thomas, E. Timms, and I.P. King. 1996. Comparison of ribosomal DNA sites in Lolium species by fluorescence in situ hybridization. Chromosome Res. 4:486-490. doi:10.1007/BF02261775.
91. Varshney, R.K., W. Chen, Y. Li, A.K. Bharti, R.K. Saxena, J.A. Schlueter, M.T. Donoghue, S. Azam, G. Fan, A.M. Whaley, A.D. Farmer, J. Sheridan, A. Iwata, R. Tuteja, R.V. Penmetsa, W. Wu, H.D. Upadhyaya, S.P. Yang, T. Shah, K.B. Saxena, T. Michael, W.R. McCombie, B. Yang, G. Zhang, H. Yang, J. Wang, C. Spillane, D.R. Cook, G.D. May, X. Xu, and S.A. Jackson. 2011. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30:83-89. doi:10.1038/nbt.2022.
92. Varshney, R.K., S.M. Mohan, P.M. Gaur, N.V. Gangarao, M.K. Pandey, A. Bohra, S.L. Sawargaonkar, A. Gorantla, P.K. Kimurto, P. Janila, K.B. Saxena, A. Fikre, M. Sharma, A. Rathore, A. Pratap, S. Tripathi, S. Datta, S.K. Chaturvedi, N. Mallikarjuna, G. Anuradha, A. Babbar, A.K. Choudhary, M.B. Mhase, C. Bharadwaj, D.M. Mannur, P.N. Harer, B. Guo, X. Liang, N. Nadarajan, and C.L. Gowda. 2013. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol. Adv. doi:10.1016/j. biotechadv.2013.01.001.
93. Vicient, C.M., A. Suoniemi, K. Anamthawat-Jonsson, J. Tanskanen, A. Beharav, E. Nevo, and A.H. Schulman. 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11:1769-1784.
94. Vitte, C., and O. Panaud. 2005. LTR retrotransposons and flowering plant genome size: Emergence of the increase/decrease model. Cytogenet. Genome Res. 110:91-107. doi:10.1159/000084941.
95. Walling, J.G., J.C. Pires, and S.A. Jackson. 2005. Preparation of samples for comparative studies of plant chromosomes using in situ hybridization methods. Methods Enzymol. 395:443-460.
96. Wu, Y., S. Kikuchi, H. Yan, W. Zhang, H. Rosenbaum, A.L. Iniguez, and J. Jiang. 2011. Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell 23:4054-4064. doi:10.1105/tpc.111.090043.
97. Yan, H.H., and J.M. Jiang. 2007. Rice as a model for centromere and heterochromatin research. Chromosome Res. 15:77-84. doi:10.1007/s10577-006-1104-z.
98. Young, H.A., G. Sarath, and C.M. Tobias. 2012. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. BMC Plant Biol. 12. doi:10.1186/1471-2229-12-117.
99. Young, N.D., and A.K. Bharti. 2012. Genome-enabled insights into legume biology. Annu. Rev. Plant Biol. 63:283-305. doi:10.1146/annurev-arplant-042110-103754.
100. Zhang, W., B. Friebe, B.S. Gill, and J. Jiang. 2010. Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres. Chromosoma 119:553-563. doi:10.1007/s00412-010-0278-5.
101. Zhang, W., H.R. Lee, D.H. Koo, and J. Jiang. 2008a. Epigenetic modification of centromeric chromatin: Hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell 20:25-34. doi:10.1105/tpc.107.057083.
102. Zhang, W., X. Wang, Q. Yu, R. Ming, and J. Jiang. 2008b. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Res. 18:1938-1943. doi:10.1101/gr.078808.108.
103. Zheng, J.Y., M. Nakata, K. Irifune, R. Tanaka, and H. Morikawa. 1993. Fluorescent banding pattern analysis of eight taxa of Phaseolus and Vigna in relation to their phylogenetic relationships. Theor. Appl. Genet. 87:38-43. doi:10.1007/BF00223741.