Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus

Plant Science

Volumn 183, Issue , 2012, Pages 131-142

  Nakano, Michiharu ^a,b   Shimada, Takehiko ^a   Endo, Tomoko ^a   Fujii, Hiroshi ^a   Nesumi, Hirohisa ^a   Kita, Masayuki ^a   Ebina, Masumi ^c   Shimizu, Tokurou ^a   Omura, Mitsuo ^b,d  

^a NATIONAL INSTITUTE OF FRUIT TREE SCIENCE   (Japan)

^b GIFU UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF LIVESTOCK AND GRASSLAND SCIENCE   (Japan)

^d SHIZUOKA UNIVERSITY   (Japan)

Author keywords

Apomixis; Citrus; Haplotype; Polyembryony; Synteny

Indexed keywords

PLANT DNA;

APOMIXIS; ARTICLE; ASPEN; BACTERIAL ARTIFICIAL CHROMOSOME; CITRUS; DNA SEQUENCE; GENETICS; GENOMICS; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLANT GENOME; PLANT SEED; PRENATAL DEVELOPMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SYNTENY; VITIS;

APOMIXIS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CITRUS; DNA, PLANT; GENOME, PLANT; GENOMICS; HAPLOTYPES; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULUS; SEEDS; SEQUENCE ANALYSIS, DNA; SYNTENY; VITIS;

CITRUS; POPULUS; POPULUS TRICHOCARPA; VITACEAE; VITIS; VITIS VINIFERA;

EID: 84155189115     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2011.08.002     Document Type: Article

References (57)

1. Carman J.G. Asynchronous expression of duplicate genes in angiosperms may cause apomixis, bispory, tetraspory, and polyembryony. Biol. J. Linn. Soc. 1997, 61:51-94.
2. Koltunow A.M. Apomixis: embryo sacs and embryos formed without meiosis or fertilization in ovules. Plant Cell 1993, 5:1425-1437.
3. Ueno I., Iwamasa M., Nishiura M. Embryo number of various varieties of Citrus and its relatives. Bull. Hort. Res. Stn. Jpn. Ser. B 1967, 7:11-22. (In Japanese with English summary).
4. Parlevliet J.E., Cameron J.W. Evidence on the inheritance of nucellar embryony in Citrus. Proc. Am. Soc. Hortic. Sci. 1959, 74:252-260.
5. Iwamasa M., Ueno I., Nishiura M. Inheritance of nucellar embryony in Citrus. Bull. Hort. Res. Stn. Jpn. Ser. B 1967, 7:1-10.
6. Hong Q.B., Xiang S.Q., Chen K.L., Chen L.G. Two complementary dominant genes controlling apomixis in genus Citrus and Poncirus. Yi Chuan Xue Bao 2001, 28:1062-1067.
7. Nishiura M., Shichijo T., Ueno I., Iwamasa M., Kihara T., Yamada Y., Yoshida T., Iwasaki T. New citrus cultivar 'Kiyomi' tangor. Bull. Fruit Tree Res. Stn. B 1983, 10:1-9. (In Japanese with English summary).
8. McMeniman S., Lubulwa G. Project Development Assessment: An Economic Evaluation of the Potential Benefits of Integrating Apomixis into Hybrid Rice 1997, Australian Centre for International Agricultural Research, Canberra.
9. Ozias-Akins P., Van Dijk P.J. Mendelian genetics of apomixis in plants. Annu. Rev. Genet. 2007, 41:509-537.
10. Nakano M., Shimizu T., Kuniga T., Nesumi H., Omura M. Mapping and haplotyping of the flanking region of the polyembryony locus in Citrus unshiu Marcow. J. Jpn. Soc. Hort. Sci. 2008, 77:109-114.
11. Kepiro J.L., Roose M.L. AFLP markers closely linked to a major gene essential for nucellar embryony (apomixis) in Citrus maxima×Poncirus trifoliate. Tree Genet. Genomes 2010, 6:1-11.
12. Nakano M., Shimizu T., Fujii H., Shimada T., Endo T., Nesumi H., Kuniga T., Omura M. Marker enrichment and construction of haplotype-specific BAC contigs for the polyembryony genomic region in Citrus. Breed. Sci. 2008, 58:375-383.
13. Luo M., Thomas C., You F.M., Hsiao J., Ouyang S., Buell C.R., Malandro M., McGuire P.E., Anderson O.D., Dvorak J. High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 2003, 82:378-389.
14. Soderlund C., Longden I., Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 1997, 13:523-535.
15. Chou H.H., Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104.
16. Chevreux B., Wetter T., Suhai S. Genome sequence assembly using trace signals and additional sequence information computer science and biology. Proc. German Conf. Bioinform. (GCB) 1999, 99:45-56.
17. Salamov A., Solovyev V. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000, 10:516-522.
18. Mayor C., Brudno M., Schwartz J.R., Poliakov A., Rubin E.M., Frazer K.A., Pachter L.S., Dubchak I. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 2000, 16:1046-1047.
19. Bray N., Dubchak I., Pachter L. AVID: a global alignment program. Genome Res. 2003, 13:97-102.
20. Barrett J.C., Fry B., Maller J., Daly M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21:263-265.
21. Stephens M., Smith N.J., Donnelly P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 2001, 68:978-989.
22. Ozias-Akins P., Roche D., Hanna W.W. Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes. Proc. Natl. Acad. Sci. U.S.A. 1998, 95:5127-5132.
23. Goel S., Chen Z., Conner J.A., Akiyama Y., Hanna W.W., Ozias-Akins P. Delineation by fluorescence in situ hybridization of a single hemizygous chromosomal region associated with aposporous embryo sac formation in Pennisetum squamulatum and Cenchrus ciliaris. Genetics 2003, 163:1069-1082.
24. Akiyama Y., Conner J.A., Goel S., Morishige D.T., Mullet J.E., Hanna W.W., Ozias-Akins P. High-resolution physical mapping in Pennisetum squamulatum reveals extensive chromosomal heteromorphism of the genomic region associated with apomixis. Plant Physiol. 2004, 134:1733-1741.
25. Vyskot B., Hobza R. Gender in plants: sex chromosomes are emerging from the fog. Trends Genet. 2004, 20:432-438.
26. Angiosperm Phylogeny Group An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot. J. Linn. Soc. 2009, 161:105-121.
27. Terol J., Naranjo M.A., Ollitrault P., Talon M. Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genomics 2008, 9:423.
28. Jung S., Jiwan D., Cho I., Lee T., Abbott A., Sosinski B., Main D. Synteny of Prunus and other model plant species. BMC Genomics 2009, 10:76-92.
29. Vrinten P.L., Nakamura T., Kasha K.J. Characterization of cDNAs expressed in the early stages of microspore embryogenesis in barley (Hordeum vulgare) L. Plant Mol. Biol. 1999, 41:455-463.
30. Pulido A., Bakos F., Devic M., Barnabas B., Olmedilla A. HvPG1 and ECA1: two genes activated transcriptionally in the transition of barley microspores from the gametophytic to the embryogenic pathway. Plant Cell Rep. 2009, 28:551-559.
31. Becerra C., Jahrmann T., Puigdome'nech P., Vicient C.M. Ankyrin repeat-containing proteins in Arabidopsis: characterization of a novel and abundant group of genes coding ankyrin-transmembrane proteins. Gene 2004, 340:111-121.
32. Albert S., Despre's B., Guilleminot J., Bechtold N., Pelletier G., Delseny M., Devic M. The EMB 506 gene encodes a novel ankyrin repeat containing protein that is essential for the normal development of Arabidopsis embryos. Plant J. 1999, 17:169-179.
33. Kobayashi S., Ikeda I., Nakatani M. Studies on nucellar embryogenesis in Citrus. II. Formation of the primordium cell of the nucellar embryo in the ovule of the flower bud, and its meristematic activity. J. Jpn. Soc. Hort. Sci. 1979, 48:179-185.
34. Stone S.L., Braybrook S.A., Paula S.L., Kwong L.W., Meuser J., Pelletier J., Hsieh T., Fischer R.L., Goldberg R.B., Harada J.J. Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:3151-3156.
35. Braybrook S.A., Harada J.J. LECs go crazy in embryo development. Trends Plant Sci. 2008, 13:624-630.
36. Endo T., Shimada T., Fujii H., Omura M. Cloning and characterization of 5 MADS-box cDNAs isolated from citrus fruit tissue. Sci. Hort. 2006, 109:315-321.
37. Guerin J., Rossel J.B., Robert S., Tsuchiya T., Koltunow A. A DEFICIENS homologue is down-regulated during apomictic initiation in ovules of Hieracium. Planta 2000, 210:914-920.
38. Ravi M., Marimuthu M.P.A., Siddiqi I. Gamete formation without meiosis in Arabidopsis. Nature 2008, 451:1121-1124.
39. Grossniklaus U., Spillane C., Page D.R., Kohler C. Genomic imprinting and seed development: endosperm formation without sex. Curr. Opin. Plant Biol. 2001, 4:21-27.
40. Schallau A., Arzenton F., Johnston A.J., Hahnel U., Koszegi A., Blattner F.R., Altschmied L., Haberer G., Barcaccia G., Baumlein H. Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L. Plant J. 2010, 62:773-784.
41. Conner J.A., Goel S., Gunawan G., Cordonnier-Pratt M., Johnson V.E., Liang C., Wang H., Pratt L.H., Mullet J.E., Debarry J., Yang L., Bennetzen J.L., Klein P.E., Ozias-Akins P. Sequence analysis of bacterial artificial chromosome clones from the apospory-specific genomic region of Pennisetum and Cenchrus. Plant Physiol. 2008, 147:1396-1411.
42. Nakatani M., Ikeda I., Kobayashi S. Studies on an effective method for getting hybrid seedlings in polyembryonic citrus, 4: Artificial control of the number of embryos per seed in King mandarin (Citrus nobilis) and Funadoko (C. funadoko) using high temperature conditions. Bull. Fruit Tree Res. Stn. E 1984, 5:29-34.
43. Nakatani M., Ikeda I., Kobayashi S. Studies on an effective method for getting hybrid seedlings in polyembryonic citrus, 2: difference of the number of embryos per seed in strains of Satsuma mandarin (Citrus unshiu Marc.). Bull. Fruit Tree Res. Stn. E 1980, 3:15-23.
44. Yoshida T., Yamada Y., Ueno I., Shichijo T., Nesumi H., Hidaka T., Ito Y., Yoshioka T., Kihara T., Ieki H., Hirai M., Tominaga S. New citrus cultivar 'Akemi'. Bull Natl. Inst. Fruit Tree Sci. 2000, 34:53-62.
45. Matsumoto R., Okudai N., Yamamoto M., Yamada Y., Asada K., Oiyama I., Ikemiya H., Murata H., Yoshinaga K., Koizumi M., Iwanami T. A new citrus cultivar 'Amakusa'. Bull. Fruit Tree Res. Stn. 1999, 33:37-46.
46. Matsumoto R., Okudai N., Yamamoto M., Yamada Y., Takahara T., Oiyama I., Ishiuchi D., Asada K., Ikemiya H., Murata H., Yoshinaga K., Uchihara S., Ieki H., Shichijo T. A new citrus cultivar 'Hareyaka'. Bull. Natl. Inst. Fruit Tree Sci. 1999, 33:47-56.
47. Yoshida T., Yamada Y., Nesumi H., Ueno I., Ito Y., Yoshioka T., Hidaka T., Ieki H., Shichijo T., Kihara T., Tominaga S. New citrus cultivar 'Harumi'. Bull. Natl. Inst. Fruit Tree Sci. 2000, 34:43-52.
48. Okudai N., Matsumoto R., Oiyama I., Takahara T., Yamamoto M., Asada K., Ishiuchi D., Murata H. New citrus cultivar 'Hayaka'. Bull. Fruit Tree Res. Stn. 1991, 21:51-57.
49. Matsumoto R., Okudai N., Yamamoto M., Yamada Y., Takahara T., Oiyama I., Ishiuchi D., Asada K., Ikemiya H., Murata H., Yoshinaga K., Uchihara S., Ieki H. A new citrus cultivar 'Miho-core'. Bull. Natl. Inst. Fruit Tree Sci. 1999, 33:57-66.
50. Okudai N., Matsumoto R., Oiyama I., Takahara T., Asada K., Yamamoto M., Ishiuchi D., Murata H. New citrus cultivar 'Seihou'. Bull. Fruit Tree Res. Stn. 1991, 21:43-49.
51. Matsumoto R., Yamamoto M., Kuniga T., Yoshioka T., Mitani N., Okudai N., Yamada Y., Asada K., Ikemiya H., Yoshinaga K., Uchihara S., Oiyama I., Murata H. New citrus cultivar 'Setoka'. Bull. Natl. Inst. Fruit Tree Sci. 2003, 2:25-31.
52. Matsumoto R., Okudai N., Oiyama I., Takahara T., Yamamoto M., Asada K., Ishiuchi D., Murata H. New citrus cultivar 'Tsunokaori'. Bull. Fruit Tree Res. Stn. 1991, 21:59-65.
53. Matsumoto R., Yamamoto M., Okudai N., Takahara T., Yamada Y., Kuniga T., Oiyama I., Asada K., Ishiuchi D., Ikemiya H., Murata H., Uchihara S., Yoshinaga K., Ieki H., Iwanami T. A new citrus cultivar 'Amaka'. Bull. Natl. Inst. Fruit Tree Sci. 2001, 35:47-56.
54. Yamada Y., Okudai N., Matsumoto R., Yamamoto M., Takahara T., Oiyama I., Ishiuchi D., Asada K., Ikemiya H., Murata H. A new citrus cultivar 'Ariake'. Bull. Fruit Tree Res. Stn. 1995, 28:1-13.
55. Yoshida T., Nesumi H., Yoshioka T., Nakano M., Ito Y., Murase S., Takishita F. New citrus cultivar 'Harehime'. Bull. Natl. Inst. Fruit Tree Sci. 2005, 4:37-45.
56. Okudai N., Matsumoto R., Oiyama I., Takahara T., Ishiuchi D., Asada K., Murata H. New citrus cultivar 'Nankou'. Bull. Fruit Tree Res. Stn. 1991, 20:71-77.
57. Matsumoto R., Yamamoto M., Kuniga T., Okudai N., Yamada Y., Takahara T., Oiyama I., Ishiuchi D., Murata H., Asada K., Ikemiya H., Shichijo T., Yoshinaga K., Uchihara S., Ieki H. New citrus cultivar 'Nishinokaori'. Bull. Natl. Inst. Fruit Tree Sci. 2003, 2:17-23.