Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.

Genetic Resources and Crop Evolution

Volumn 58, Issue 5, 2011, Pages 741-752

  Khar, Anil ^a   Lawande, K E ^a   Negi, K S ^b  

^a National Research Centre for Onion and Garlic   (India)

^b NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

Author keywords

A. roylei; Alliumcepa L.; Genetic diversity; Molecular markers; Onion; SSR; Wild species

Indexed keywords

GENETIC MARKER; GENETIC RESOURCE; GENETIC VARIATION; HYBRID; MOLECULAR ANALYSIS; MONOCOTYLEDON; NATIVE SPECIES; PLANT BREEDING; WILD POPULATION;

ALLIUM; ALLIUM CAROLINIANUM; ALLIUM CEPA; ALLIUM CHINENSE; ALLIUM FISTULOSUM; ALLIUM HOOKERI; ALLIUM ROYLEI; ALLIUM SATIVUM;

EID: 79959799953     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-010-9616-y     Document Type: Article

References (53)

1. Araki N, Masuzaki SI, Tsukazaki H, Yaguchi S, Wako T, Yashiro Y, Yamauchi N, Shigyo M (2010) Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodon in Allium. Euphytica 173: 321-328.
2. Basak R (1987) The Hindu concept of the natural world. In: Morgan K (ed) The religion of the Hindus. Motilal Banarsidass, Delhi, pp 111-112.
3. Bhargava R, Koul A, Sharma M (1984) Origin of Alliumcepa var. viviparum as revealed from isozyme analysis. Allium Newsl 1: 59-69.
4. Bradeen JM, Havey MJ (1995) Restriction fragment length polymorphisms reveal considerable nuclear divergence within a well-supported maternal clade in Allium section cepa (Alliaceae). Amer J Bot 82: 1455-1462.
5. Cho YG, Ishii T, Temmykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and genebank sequences in rice (Oryzasativa L.). Theor Appl Genet 100: 713-722.
6. Currah L (2002) Onions in the tropics: cultivars and country reports. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent Advances. CAB International, Wallingford, pp 379-407.
7. Currah L, Ockendon DJ (1988) A hybrid index for Alliumcepa × A. fistulosum crosses. In: Proceedings of 4th Allium symposium, Wellesbourne, pp 190-196.
8. de Vries JN (1992) What's in a name? In quest of the origin, proper name of C502, known as Alliumroylei Stearn. In: Hanelt P, Hammer K, Knüpffer H (eds) The genus Allium-taxonomic problems and genetic resources IGCPR. Gatersleben, Germany, pp 327-330.
9. DeWoody JA, Honeycutt RL, Skow LC (1995) Microsatellite markers in white tailed deer. J Hered 86: 317-319.
10. Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12: 13-15.
11. 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.
12. Friesen N, Klaas M (1998) Origin of some minor vegetatively propagated Allium crops studied with RAPD and GISH. Genet Resour Crop Evol 45: 511-523.
13. Fritsch RM, Friesen N (2002) Evolution, domestication, and taxonomy. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI, Wallingford, pp 5-30.
14. Havey MJ (1991a) Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome. Theor Appl Genet 81: 752-757.
15. Havey MJ (1991b) Molecular characterization of the interspecific origin of viviparous onion. J Hered 82: 501-508.
16. Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9: 63-71.
17. Jakse J, Martin W, McCallum J, Havey MJ (2005) Single nucleotide polymorphisms, indels, and simple sequence repeats for onion cultivar identification. J Amer Soc Hort Sci 130: 912-917.
18. Joshi SP, Ranjekar PK, Vidya SG (1999) Molecular markers in plant genome analysis. Curr Sci 77: 230-240.
19. Karthikeyan S, Jain SK, Nayar MP, Sanjappa M (1989) Floraeindicae enumeration monocotyledonae. Botanical Survey of India, India, p 435.
20. Khar A, Asha Devi A, Lawande KE (2000) Interspecific hybridization in short day tropical onion (Allium cepa L.) with Allium fistulosum L. Allium Improv Newsl 10: 1-2.
21. Khrustaleva LI, Kik C (2000) Introgression of Allium fistulosum into A. cepa mediated by A. roylei. Theor Appl Genet 100: 17-26.
22. Kim DW, Jung TS, Nam SH, Kwon HR, Kim A, Chae SH, Choi SH, Kim DW, Kim RN, Park HS (2009) GarlicESTdb: an online database and mining tool for garlic EST sequences. BMC Plant Biol 9: 61.
23. Koul A, Gohil R (1971) Further studies on natural triploidy in viviparous onion. Cytologia 36: 253-261.
24. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek 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.
25. Langer A, Koul AK (1983) Studies on nucleolus and nucleolar chromosomes in Angiosperms VIII. nature of nucleolar chromosome polymorphism in Allium cepa var. viviparum (Metzg.) Alef. Cytologia 48: 323-332.
26. Maaß HI (1997) Studies on triploid viviparous onions and their origin. Genet Resour Crop Evol 44: 95-99.
27. Martin W, McCallum J, Shigyo M, Jakse J, Kuhl J, Yamane N, Pither-Joyce M, Gokce A, Sink C, Town C, Havey M (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genomics 274: 197-204.
28. McCallum J, Clarke A, Pither-Joyce M, Shaw M, Butler R, Brash D, Scheffer J, Sims I, van Heusden S, Shigyo M, Havey M (2006) Genetic mapping of a major gene affecting onion bulb fructan content. Theor Appl Genet 112: 958-967.
29. 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 Amer Soc Hort Sci 133: 810-818.
30. Negi KS (2006) Allium species in Himalayas and their uses with special reference to Uttaranchal. Ethnobot 18: 53-66.
31. NHB (2009) In: Kumar B, Mistry NC, Singh B, and Gandhi CP (eds) Indian Horticulture Database - 2009. National Horticulture Board, Gurgaon, New Delhi. http://nhb. gov. in/database-2009. pdf. Accessed 10 June 2010.
32. Pandey A, Pandey R, Negi KS, Radhamani J (2008) Realizing value of genetic resources of Allium in India. Genet Resour Crop Evol 55: 985-994.
33. Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin. cirad. fr/darwin.
34. Polunin O, Stainton A (1984) Flowers of the Himalaya. Oxford University Press, New Delhi, pp 413-416.
35. Puizina J, Papeš D (1996) Cytogenetical evidences for hybrid structure and origin structure and origin of diploid and triploid shallots (Alliumcepa var. viviparum, Liliaceae) from Dalmatia (Croatia). Pl Syst Evol 208: 11-23.
36. Puizina J, Papeš D, Klein F, Schweizer D, Bohanec B, Javornik B, Maluszynska J (1997) Genomic in situ hybridisation in viviparous onions (Alliumcepa var. viviparum). Abstract in Spring symposium on Plant Cytogenetics, Cieszyn, 19-22 May 1997, pp61.
37. Rochow VBM (2009) Food taboos: their origins and purposes. J Ethnobiol Ethnomed. doi: 10. 1186/1746-4269-5-18.
38. Santos CAF, Oliveira VR, Rodrigues MA, Ribeiro HLC (2010) Caracterização molecular de cultivares de cebola com marcadores microssatélites. Pesq Agropec Bras Brasília 45: 49-55.
39. Scholten OE, van Heusden AW, Khrustaleva LI, Burger-Meijer K, Mank RA, Antonise RGC, Harrewijn JL, van Haecke W, Oost EH, Peters RJ, Kik C (2007) The long and winding road leading to the successful introgression of downy mildew resistance into onion. Euphytica 156: 345-353.
40. Sharma G, Gohil RN (2008) Intrapopulation karyotypic variability in Allium roylei Stearn - a threatened species. Bot J Linn Soc 158: 242-248.
41. Sharma RK, Gupta V, Sharma V, Sood A, Mohapatra T, Ahuja PS (2008) Evaluation of rice and sugarcane SSR markers for phlogenetic and genetic diversity analyses in bamboo. Genome 51: 91-103.
42. Shastri JL (1995) Garuda Purana. In: Shastri JL, Bhatt GP, Tagare GV (eds) Ancient Indian tradition and mythology, vol 12. Motilal Banarsidass Publishers, Delhi, p 30.
43. Singh BP, Rana RS (1994) Collection and conservation of Allium genetic resources: an Indian perspective. Acta Hort (ISHS) 358: 181-190. http://www. actahort. org.
44. Song YS, Suwabe K, Wako T, Ohara T, Nunome T, Kojima A (2004) Development of microsatellite markers in bunching onion (Alliumfistulosum L.). Breed Sci 54: 361-365.
45. Tanikawa T, Takagi M, Ichii M (2002) Cultivar identification and genetic diversity in onion (Alliumcepa L.) as evaluated by random amplified polymorphic DNA (RAPD) analysis. J Jpn Soc Hort Sci 71: 249-251.
46. Tsukazaki H, Nunome T, Fukuoka H, Kanamori H, Kono I, Yamashita KI, Wako T, Kojima A (2007) Isolation of 1. 796 SSR clones from SSR-enriched DNA libraries of bunching onion (Alliumfistulosum). Euphytica 157: 83-94.
47. van Loon V (2003) CharakaSamhita. Handbook on Ayurveda. Volume I. www. ayurveda-berkeley. com/Charaka's/Charaka-Samhita-2003-rev2_Vol_I. pdf261. Accessed 10 June 2010.
48. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers: features and applications. Trends Biotechnol 23: 48-55.
49. Varshney RK, Mahender T, Aggrawal RK, Borner A (2007) Genic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomics assisted crop improvement, vol I: genomics approaches and platforms. Springer, Dordrecht, pp 13-30.
50. Verma VD, Pradheep K, Khar A, Negi KS, Rana JC (2008) Collection and characterization of Allium species from Himachal Pradesh. Indian J Plant Genet Resour 21: 225-228.
51. Walter KS, Gillet HJ (1997) 1997 IUCN red list of threatened plants. Compiled by the World conservation monitoring center.
52. Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland.
53. Woodward PW (1996) Garlic and friends: The history, growth and use of edible Alliums. Hyland House, Melbourne, pp 2-22.