Abstract
To determine the chromosomal location of bunching onion (Allium fistulosum L.) simple sequence repeats (SSRs) and bulb onion (A. cepa L.) expressed sequence tags (ESTs), we used a complete set of bunching onion–shallot monosomic addition lines and allotriploid bunching onion single alien deletion lines as testers. Of a total of 2,159 markers (1,198 bunching onion SSRs, 324 bulb onion EST–SSRs and 637 bulb onion EST-derived non-SSRs), chromosomal locations were identified for 406 markers in A. fistulosum and/or A. cepa. Most of the bunching onion SSRs with identified chromosomal locations showed polymorphism in bunching onion (89.5%) as well as bulb onion lines (66.1%). Using these markers, we constructed a bunching onion linkage map (1,261 cM), which consisted of 16 linkage groups with 228 markers, 106 of which were newly located. All linkage groups of this map were assigned to the eight basal Allium chromosomes. In this study, we assigned 513 markers to the eight chromosomes of A. fistulosum and A. cepa. Together with 254 markers previously located on a separate bunching onion map, we have identified chromosomal locations for 766 markers in total. These chromosome-specific markers will be useful for the intensive mapping of desirable genes or QTLs for agricultural traits, and to obtain DNA markers linked to these.
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Abbreviations
- EST:
-
Expressed sequence tag
- InDel:
-
Insertion–deletion
- SNP:
-
Single nucleotide polymorphism
- SSR:
-
Simple sequence repeat
References
Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186
Budahn H, Schrader O, Peterka H (2008) Development of a complete set of disomic rape-radish chromosome-addition lines. Euphytica 162:117–128
Chatelat RT, Rick CM, Cisneros P, Alpert KB, De Verna JW (1998) Identification, transmission, and cytological behavior of Solanum lycopersicoides Dun. monosomic alien addition lines in tomato (Lycopersicon esculentum Mill.). Genome 41:40–50
Emsweller SL, Jones HA (1935a) An interspecific hybrid in Allium. Hilgardia 9:265–273
Emsweller SL, Jones HA (1935b) Meiosis in Allium fistulosum, Allium cepa and their hybrid. Hilgardia 9:277–288
Fischer D, Bachmann K (2000) Onion microsatellites for germplasm analysis and their use in assessing intra- and interspecific relatedness within the subgenus Rhizirideum. Theor Appl Genet 101:153–164
Fox SL, Jellen EN, Kianian SF, Rines HW, Phillips RL (2001) Assignment of RFLP linkage groups to chromosomes using monosomic F1 analysis in hexaploid oat. Theor Appl Genet 102:320–326
Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy. Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI Publishing, Oxfordshire, pp 5–30
Hang TTM, Shigyo M, Yamauchi N, Tashiro Y (2004a) Production and characterization of alien chromosome additions in shallot (Allium cepa L. Aggregatum group) carrying extra chromosome(s) of Japanese bunching onion (A. fistulosum L.). Genes Genet Syst 79:263–269
Hang TTM, Shigyo M, Yamauchi N, Tashiro Y (2004b) Effect of single alien chromosome from shallot (Allium cepa L. Aggregatum group) on carbohydrate production in leaf blade of bunching onion (A. fistulosum L.). Genes Genet Syst 79:345–350
Jakše J, Martin W, McCallum J, Havey MJ (2005) Single nucleotide polymorphisms, indels, and simple sequence repeats for onion cultivar identification. J Am Soc Hortic Sci 130:912–917
Kam-Morgan LNW, Gill BS, Muthukrishnan S (1989) DNA restriction fragment length polymorphisms: a strategy for genetic mapping of D genome of wheat. Genome 32:724–732
King JJ, Bradeen JM, Bark O, McCallum JA, Havey MJ (1998) A low-density map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome. Theor Appl Genet 96:52–62
Kosambi D (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175
Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, MaCallum J, Catanach A, Rutherford P, Sink KC, Jenderk M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11, 008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114–125
Kukita Y, Hayashi K (2002) Multicolor post-PCR labeling of DNA fragments with fluorescent ddNTPs. Biotechniques 33:502–506
Lander E, Green P, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Levan A (1941) The cytology of the species hybrid Allium cepa × A. fistulosum and its polyploidy derivatives. Hereditas 27:253–272
Lohithaswa HC, Feltus FA, Singh HP, Bacon CD, Bailey CD, Paterson AH (2007) Leveraging the rice genome sequence for monocot comparative and translational genomics. Theor Appl Genet 115:237–243
Maeda T (1937) Chiasma studies in Allium fistulosum, Allium cepa and F1, F2 and backcross hybrids. Jpn J Genet 13:146–159
MAFF (2008) Nousanbutsu-Sanshutsugaku no Jun-I (The ranking of vegetables for annual output in Japan). Pocket nourinsuisan toukei, 2005 (in Japanese). http://www.tdb.maff.go.jp/toukei/toukei
Martin WJ, McCallum J, Shigyo M, Jakše J, Kuhl JC, Yamane N, Pither-Joyce M, Gökçe AF, Sink KC, Town CD, Havey MJ (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genomics 274:197–204
Masuzaki S, Shigyo M, Yamauchi N (2006a) Complete assignment of structural genes involved flavonoid biosynthesis influencing bulb color to individual chromosomes of the shallot (Allium cepa L.). Genes Genet Syst 81:255–263
Masuzaki S, Araki N, Yamauchi N, Yamane T, Wako T, Kojima A, Shigyo M (2006b) Chromosomal locations of microsatellites in onion. Hort Sci 41:315–318
McCallum J, Leite D, Pither-Joyce M, Havey MJ (2001) Expressed sequence markers for genetic analysis of bulb onion (Allium cepa L.). Theor Appl Genet 103:979–991
McCallum J, Pither-Joyce M, Shaw M, Kanel F, Davis S, Butler R, Schffer J, Jakše J, Havey MJ (2007) Genetic mapping of sulfur assimilation genes a QTL for bulb onion pungency. Theor Appl Genet 114:815–822
McCallum J, Thomson S, Pither-Joyce M, Kenel F, Clarke A, Havey MJ (2008) Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. J Am Soc Hortic Sci 133:810–818
Mesbah M, de Bock TSM, Sandbrink JM (1997) Molecular and morphological characterization of monosomic additions in Beta vulgaris, carrying extra chromosomes of B. procumbens or B. patellaris. Mol Breed 3:147–157
Narayan RKJ (1988) Constraints upon the organization and evolution of chromosomes in Allium. Theor Appl Genet 75:319–329
Ohara T, Song YS, Tsukazaki H, Wako T, Nunome T, Kojima A (2005) Construction of a genetic linkage map of Japanese bunching onion (Allium fistulosum) based on AFLP and SSR markers. Euphytica 144:255–263
Peffley EB, Corgan JN, Horak HG, Tanksley SD (1985) Electrophoretic analysis of Allium alien addition lines. Theor Appl Genet 71:176–184
Ricroch A, Yockteng R, Brown SC, Nadot S (2005) Evolution of genome size across some cultivated Allium species. Genome 48:511–520
Shigyo M, Tashiro Y, Issiki S, Miyazaki S (1996) Establishments of a series of alien monosomic addition lines of Japanese bunching onion (Allium fistulosum L.) with extra chromosomes from shallot (A. cepa L. Aggregatum group). Genes Genet Syst 71:363–371
Shigyo M, Iino M, Isshiki S, Tashiro Y (1997) Morphological characteristics of a series of alien monosomic addition lines of Japanese bunching onion (Allium fistulosum L.) with extra chromosomes from shallot (A. cepa L. Aggregatum group). Genes Genet Syst 72:181–186
Song YS, Suwabe K, Wako T, Ohara T, Nunome T, Kojima A (2004) Development of microsatellite markers in Japanese bunching onion (Allium fistulosum L.). Breed Sci 54:361–365
Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560
Tashiro Y (1984) Cytogenetic studies on the origin of Allium wakegi Araki. Bull Fac Agric Saga Univ 56:1–63
Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, Yamashita K, Wako T, Kojima A (2007) Isolation of 1, 796 SSR clones from SSR-enriched DNA libraries of bunching onion (Allium fistulosum). Euphytica 157:83–94
Tsukazaki H, Yamashita K, Yaguchi S, Masuzaki S, Fukuoka H, Yonemaru J, Kanamori H, Kono I, Hang TTH, Shigho M, Kojima A, Wako T (2008) Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theor Appl Genet 117:1213–1223
van Heusden AW, van Ooijen JW, Vrielink-van Ginkel R, Verbeek WHJ, Wietsma WA, Kik C (2000a) A genetic map of an interspecific cross in Allium based on amplified fragment length polymorphisms (AFLP™) markers. Theor Appl Genet 100:118–126
van Heusden AW, Shigyo M, Tashiro Y, Vrielink-van Ginkel R, Kik C (2000b) AFLP linkage group assignment to the chromosomes of Allium cepa L. via monosomic addition lines. Theor Appl Genet 100:480–486
Yaguchi S, McCallum J, Shaw M, Pither-Joyce M, Onodera S, Shimoi N, Yamauchi N, Shigyo M (2008) Biochemical and genetic analysis of carbohydrate accumulation in Allium cepa L. Plant Cell Physiol 49:730–739
Yaguchi S, Hang TTM, Tsukazaki H, Hoa VQ, Masuzaki S, Wako T, Masamura N, Onodera S, Shimoi N, Yamauchi N, Shigyo M (2009) Molecular and biochemical identification of alien chromosome additions in shallot (Allium cepa L. Aggregatum group) carrying extra chromosome(s) of bunching onion (A. fistulosum L.). Genes Genet Syst 84:43–55
Acknowledgments
We are grateful to Misses K. Tanaka and S. Negoro for the technical assistance. This work was supported by the project NARO Research Project No. 211 “Establishment of Integrated Basis for Development and Application of Advanced Tools for DNA Marker-Assisted Selection in Horticultural Crops”, National Institute of Vegetable and Tea Science Priority Research Program, and Grant-in-Aid for Young Scientists (B) (19780010), Japan Society for the Promotion of Science.
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Communicated by M. Havey.
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Suppl. Table
1 Primer sequences of 353 bunching onion SSR markers identified chromosome locations (XLS 234 kb)
Suppl. Table
2 Primer sequences of 57 bulb onion EST-derived SSR markers identified chromosome locations (XLS 47 kb)
Suppl. Table 3
Primer sequences of 160 bulb onion EST-derived non-SSR markers identified chromosome locations (XLS 100 kb)
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Tsukazaki, H., Yamashita, Ki., Yaguchi, S. et al. Direct determination of the chromosomal location of bunching onion and bulb onion markers using bunching onion–shallot monosomic additions and allotriploid-bunching onion single alien deletions. Theor Appl Genet 122, 501–510 (2011). https://doi.org/10.1007/s00122-010-1464-9
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DOI: https://doi.org/10.1007/s00122-010-1464-9