A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

Functional and Integrative Genomics

Volumn 13, Issue 1, 2013, Pages 19-32

  Michalak De Jimenez, Monika K ^a   Bassi, Filippo M ^a   Ghavami, Farhad ^a   Simons, Kristin ^a   Dizon, Rissa ^a   Seetan, Raed I ^b   Alnemer, Loai M ^c   Denton, Anne M ^b   Doǧramaci, Münevver ^d   Šimková, Hana ^e   Doležel, Jaroslav ^e   Seth, Kiran ^a   Luo, Ming Cheng ^f   Dvorak, Jan ^f   Gu, Yong Qiang ^g   Kianian, Shahryar F ^a  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

^b North Dakota State University   (United States)

^c UNIVERSITY OF JORDAN   (Jordan)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e INSTITUTE OF EXPERIMENTAL BOTANY   (Czech Republic)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g WESTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

Alloplasmic; Cytoplasm substitution; Paleofusion; Species cytoplasm specific; Synteny; Wheat Zapper

Indexed keywords

ARTICLE; BRACHYPODIUM; CENTROMERE; CHROMOSOME 1; CHROMOSOME 1D; GENE LOCATION; GENE LOCUS; GENETIC CONSERVATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RADIATION HYBRID MAPPING; RICE; SORGHUM; SPECIES CYTOPLASM SPECIFIC GENE; SPECIES DIFFERENTIATION; SYNTENY; TELOMERE; TRITICUM AESTIVUM;

CENTROMERE; CHROMOSOMES, PLANT; GENES, PLANT; GENETIC LOCI; GENETIC MARKERS; RADIATION HYBRID MAPPING; SYNTENY; TELOMERE; TRITICUM;

BRACHYPODIUM DISTACHYON; ORYZA SATIVA; SORGHUM BICOLOR; TRITICUM AESTIVUM;

EID: 84875739056     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-013-0318-3     Document Type: Article

References (81)

1. Akagi H, Nakamura A, Yokozeki-Misono Y et al (2004) Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein. Theor Appl Genet 108:1449-1457
2. Al-Kaff N, Knight E, Bertin I et al (2008) Detailed dissection of the chromosomal region containing the Ph1 locus in wheat Triticum aestivum: with deletion mutants and expression profiling. Ann Bot 101:863-872
3. Alnemer LM, Seetan RI, Bassi FM, et al. (2013) Wheat Zapper: a flexible online tool for colinearity studies in plants. Functional Integrative Genomics (in press)
4. Amarnath D, Choi I, Moawad AR, Wakayama T, Campbell KH (2011) Nuclear-cytoplasmic incompatibility and inefficient development of pig-mouse cytoplasmic hybrid embryos. Reproduction 142:295-307
5. Asakura N, Nakamura C, Ohtsuka I (2000) Homoeoallelic gene Ncc-tmp of Triticum timopheevii conferring compatibility with the cytoplasm of Aegilops tauschii in the tetraploid wheat nuclear background. Genome 43:503-511
6. Bogdanova VS (2007) Inheritance of organelle DNA markers in a pea cross associated with nuclear-cytoplasmic incompatibility. Theor Appl Genet 114:333-339
7. Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: anything goes. Trends Genet 19(12):709-716
8. Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial-nuclear interactions. Trends Genet 23:81-90
9. Cisar G, Cooper DB (2002) Hybrid wheat. In: Curtis BC, Rajaram S, Macpherson GH (eds) Bread wheat: improvement and production, plant production and protection series no. 30. FAO, Rome, pp 317-330
10. de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T (2005) Carthagene: multipopulation intergrated genetic and radiated hybrid mapping. Bioinformatics 21:1703-1704
11. Devos KM (2010) Grass genomes organization and evolution. Curr Opin Plant Biol 13:139-145
12. Dolezel J, Simkova H, Kubalakova M et al (2009) Chromosome genomics in the Triticeae. In: Feuillet C, Muehlbauer GJ (eds) Genetics and Genomics of the Triticeae. Springer, New York, pp 285-316
13. Erayman M, Sandhu D, Sidhu D et al (2004) Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res 32:3546-3565
14. Ferreri GC, Liscinsky DM, Mack JA, Eldridge MD, O'Neill RJ (2005) Retention of latent centromeres in the Mammalian genome. J Hered 96(3):217-224
15. Garcion C, Guilleminot J, Kroj T et al (2006) AKRP and EMB506 are two ankyrin repeat proteins essential for plastid differentiation and plant development in Arabidopsis. Plant J 48:895-906
16. d) derived from durum wheat. J Hered 96(4):404-409
17. Haider N (2012) Evidence for the origin of the B genome of bread wheat based on chloroplast DNA. Turk J Agric For 36:13-25
18. Hanson MR (1991) Plant mitochondrial mutations and male sterility. Annu Rev Genet 25:461-486
19. Heazlewood JL, Whelan J, Millar AH (2003) The products of the mitochondrial orf25 and orfB genes are FO components in the plant F1FO ATP synthase. FEBS Lett 540:201-205
20. ae ) gene in wheat. Genetics 168:415-423
21. ae gene. Genome 47:206-214
22. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
23. Jia L, Dienhart M, Schramp M et al (2003) Yeast Oxa1 interacts with mitochondrial ribosomes: the importance of the C-terminal region of Oxa1. EMBO J 22:6438-6447
24. Jia L, Dienhart MK, Stuart RA (2007) Oxa1 directly interacts with Atp9 and mediates its assembly into the mitochondrial F1Fo-ATP synthase complex. Mol Biol Cell 18:1897-1908
25. Joppa LR (1993) Chromosome engineering in tetraploid wheat. Crop Sci 33:908-913
26. Kalavacharla V, Hossain K, Gu YQ et al (2006) High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 173:1089-1099
27. Kilian B, Özkan H, Deusch O et al (2007) Independent wheat B and G genome origins in outcrossing Ae. progenitor haplotypes. Mol Biol Evol 24:217-227
28. Klein RR, Klein PE, Mullet JE et al (2005) Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12. Theor Appl Genet 111:994-1012
29. Knopf RR, Adam Z (2012) Rhomboid proteases in plants - still in square one? Physiol Plant 145:41-51
30. Kumar A, Bassi FM, Paux E et al (2012) DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. BMC Genomics 13:339
31. Kynast R, Okagaki R, Rines H, Phillips R (2002) Maize individualized chromosome and derived radiation hybrid lines and their use in functional genomics. Funct Integr Genom 2:60-69
32. Leister D (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21:655-663
33. Li W, Zhang P, Fellers JP, Friebe B, Gill BS (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500-511
34. Liu F, Cui S, Horner HT, Weiner H, Schnable PS (2001) Mitochondrial aldehyde dehydrogenase activity is required for male fertility in maize. Plant Cell 13:1063-1078
35. Liu S, Chao S, Anderson JA (2008) New DNA markers for high molecular weight glutenin subunits in wheat. Theor Appl Genet 118:177-183
36. Luo MC, Deal KR, Akhunov ED et al (2009) Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc Natl Acad Sci USA 106:15780-15785
37. Maan SS (1973) Cytoplasmic variability in Triticinae. In: E.R. Sears and. L.M.S. Sears (ed.) Proc IV Int Wheat Genet Symp (pp. 367-373). Columbia, MO
38. Maan SS (1978) Cytoplasmic relationships among the D- and M-genome Ae. species. In: Ramanujam (ed.) Proc V Int Wheat Genet Symp (pp. 232-250). New Delhi, India
39. Maan SS (1991) Nucleo-cytoplasmic genetics of wheat. In: Sasakuma T, Kinoshita T (eds) Proceedings of the international symposium on nuclear and organeller genetics of wheat. Hokkaido University, Sapporo, Japan, pp 75-l94
40. Maan SS (1992a) Genetic analyses of male fertility restoration in wheat: V anomalous results of a monosomic analysis. Crop Sci 32:28-35
41. Maan SS (1992b) A gene for embryo-endosperm compatibility and seed viability in alloplasmic Triticum turgidum. Genome 35:772-779
42. Maan SS (1992c) Transfer of the species specific cytoplasm (scs) from Triticum timopheevii to Triticum turgidum. Genome 35:238-243
43. Maan SS (1992d) The scs and Vi genes correct a syndrome of cytoplasmic effects in alloplasmic durum wheat. Genome 35:780-787
44. Maan SS, Joppa LR, Kianian SF (1999) Linkage between the centromere and a gene producing nucleocytoplasmic compatibility in durum wheat. Crop Sci 39:1044-1048
45. Martin A, Simpfendorfer S, Hare RA, Eberhard FS, Sutherland MW (2011) Retention of D genome chromosomes in pentaploid wheat crosses. Heredity 107:315-319
46. McIntosh RA, Yamazaki Y, Dubcovsky J, et al. (2008) Catalogue of gene symbols for wheat. In: 11th International Wheat Genetics Symposium 24-29 August 2008 Brisbane, Qld Australia
47. Michalak MK, Ghavami F, Lazo GR, Gu YQ, Kianian SF (2009) Evolutionary relationship of nuclear genes encoding mitochondrial proteins across four grass species and Arabidopsis thaliana. Maydica 54:471-483
48. Murat F, Xu J-H, Tannier E et al (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res 20:1545-1557
49. Neumann P, Navrátilová A, Koblížková A et al (2011) Plant centromeric retrotransposons: a structural and cytogenetic perspective. Mob DNA 2:4
50. Nott A, Jung H-S, Koussevitzky S, Chory J (2006) Plastid-to-nucleus retrograde signaling. Annu Rev Plant Biol 57:739-759
51. Panneerselvam P, Singh LP, Ho B, Chen J, Ding JL (2012) Targeting of pro-apoptotic TLR adaptor SARM to mitochondria: definition of the critical region and residues in the signal sequence. Biochem J 442:263-271
52. Paterson AH, Bowers JE, Bruggmann R et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556
53. Paux E, Roger D, Badaeva E et al (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463-474
54. Peng JH, Zadeh H, Lazo GR et al (2004) Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 168:609-623
55. Qi LL, Echalier B, Chao S et al (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genome of polyploidy wheat. Genetics 168:701-712
56. Qi L, Friebe B, Wu J, et al. (2010) The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice. Funct and Integr Genomics
57. Rasko JEJ, Battini J-L, Kruglyak L, Cox DR, Miller AD (2000) Precise gene localization by phenotypic assay of radiation hybrid cells. PNAS 97:7388-7392
58. Riera-Lizarazu O, Vales MI, Kianian SF (2008) Radiation hybrid (RH) and HAPPY mapping in plants. Cytogenet Genome Res 120:3-4
59. Romisch K (2006) Cdc48p is UBX-linked to ER ubiquitin ligases. Trends Biochem Sci 31:24-25
60. Saha D, Prasad AM, Srinivasan R (2007) Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Phys Biochem 45:521-534
61. Sasakuma T, Maan SS (1978) EMS-induced male-sterile mutants in euplasmic and alloplasmic common wheat. Crop Sci 18:850-853
62. Schnurbusch T, Collins NC, Eastwood RF et al (2007) Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat. Theor Appl Genet 115:451-461
63. ti gene in durum wheat and conserved colinearity across three grass genomes: wheat, rice and Brachypodium. PhD Thesis Dissertation, North Dakota State University, Fargo
64. Simons KJ, Gelhar SB, Maan SS, Kianian SF (2003) Detailed mapping of the species cytoplasm-specific (scs) gene in durum wheat. Genetics 165:2129-2136
65. Somers DJ, Kirkpatrick R, Moniwa M, Walsh W (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49:431-437
66. Song SQ, Tian MH, Kan J, Cheng HY (2009) The response difference of mitochondria in recalcitrant Antiaris toxicaria axes and orthodox Zea mays embryos to dehydration injury. J Integr Plant Biol 51:646-653
67. Spielmeyer W, Singh RP, McFadden H et al (2008) Fine scale genetic and physical mapping using interstitial deletion mutants of Lr34/Yr18: a disease resistance locus effective against multiple pathogens in wheat. Theor Appl Genet 116:481-490
68. Sykora P, Croteau DL, Bohr VA, Wilson DM III (2011) Aprataxin localizes to mitochondria and preserves mitochondrial function. PNAS 108:7437-7442
69. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763-768
70. Tsunewaki K (1980) Genetic diversity of the cytoplasm in Triticum and Ae. pp 49-100, Japan Society for the promotion of science 5-3-1 Kojimachi, Chiyodaku, Tokyo, Japan
71. Tsunewaki K (2009) Plasmon analysis in the Triticum-Ae. complex. Breed Sci 59:455-470
72. Vrána J, Kubaláková M, Simková H et al (2000) Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156:2033-2041
73. Wang CW, Lee SC (2012) The ubiquitin-like (UBX)-domain-containing protein Ubx2/Ubxd8 regulates lipid droplet homeostasis. J Cell Sci 125:2930-2939
74. Wanjugi H, Coleman-Derr D, Huo N et al (2009) Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 52:576-587
75. Wardrop J, Snape J, Powell W, Machray GC (2002) Constructing plant radiation hybrid panels. Plant J 31:223-228
76. Whitworth AJ, Lee JR, Ho VM et al (2008) Rhomboid-7 and HtrA2/Omi act in a common pathway with the Parkinson's disease factor Pink1 and Parkin. Dis Model Mech 1:168-174
77. Wicker T, Mayer KFX, Gundlach H et al (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23:1706-1718
78. Wu Y, Zhang C, Liu C, Shuxin R, Yan Z (1998) Breeding technology of alloplasmic wheat. Sci China C Life Sci 41:449-458
79. Ye J, Coulouris G, Zaretskaya I et al (2012) Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinforma 13:134
80. Yu F, Shi J, Zhou J et al (2010) ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana. Proc Natl Acad Sci USA 107:22332-22337
81. Zubko MK, Zubko EI, Ruban AV et al (2001) Extensive developmental and metabolic alterations in cybrids Nicotiana tabacum (Hyoscyamus niger) are caused by complex nucleo-cytoplasmic incompatibility. Plant J 25:627-639