Skip to main content
SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

This paper deals with the diversity assessment of tropical Indian onion and cross amplification of genomic and EST-SSR markers in distantly related native wild species. Out of 60 SSRs, 10% genomic SSRs were able to amplify as compared to EST-SSR where 53.3% primers were able to reveal amplicons. Clustering revealed five groups and indigenous short day onion formed separate cluster from the exotic short day and long day onions. A. roylei accessions exhibited a dissimilarity index of 35.5% between themselves whereas ‘Pran’ and A. × proliferum grouped together at a genetic distance of 0.4. A. fistulosum accessions formed a tight cluster and distantly related wild species A. carolinianum, A. chinense and A. hookeri formed neutral nodes. Present results are important to aid in analyzing the diversity present in short day onion and its utilization in breeding programs. Further, this is the first time that three accessions of A. roylei Stearn were used and rare alleles amplified in wild species will aid in detecting population structure and molecular marker aided selection for interspecific hybrid development.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • 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

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Bhargava R, Koul A, Sharma M (1984) Origin of Allium cepa var. viviparum as revealed from isozyme analysis. Allium Newsl 1:59–69

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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 (Oryza sativa L.). Theor Appl Genet 100:713–722

    Article  CAS  Google Scholar 

  • 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

    Chapter  Google Scholar 

  • Currah L, Ockendon DJ (1988) A hybrid index for Allium cepa × A. fistulosum crosses. In: Proceedings of 4th Allium symposium, Wellesbourne, pp 190–196

  • de Vries JN (1992) What’s in a name? In quest of the origin, proper name of C502, known as Allium roylei Stearn. In: Hanelt P, Hammer K, Knüpffer H (eds) The genus Allium-taxonomic problems and genetic resources IGCPR. Gatersleben, Germany, pp 327–330

    Google Scholar 

  • DeWoody JA, Honeycutt RL, Skow LC (1995) Microsatellite markers in white tailed deer. J Hered 86:317–319

    PubMed  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Chapter  Google Scholar 

  • Havey MJ (1991a) Phylogenetic relationships among cultivated Allium species from restriction enzyme analysis of the chloroplast genome. Theor Appl Genet 81:752–757

    Article  PubMed  CAS  Google Scholar 

  • Havey MJ (1991b) Molecular characterization of the interspecific origin of viviparous onion. J Hered 82:501–508

    CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Joshi SP, Ranjekar PK, Vidya SG (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240

    CAS  Google Scholar 

  • Karthikeyan S, Jain SK, Nayar MP, Sanjappa M (1989) Florae indicae enumeration monocotyledonae. Botanical Survey of India, India, p 435

    Google Scholar 

  • 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

    Google Scholar 

  • Khrustaleva LI, Kik C (2000) Introgression of Allium fistulosum into A. cepa mediated by A. roylei. Theor Appl Genet 100:17–26

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Koul A, Gohil R (1971) Further studies on natural triploidy in viviparous onion. Cytologia 36:253–261

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • Maaß HI (1997) Studies on triploid viviparous onions and their origin. Genet Resour Crop Evol 44:95–99

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Negi KS (2006) Allium species in Himalayas and their uses with special reference to Uttaranchal. Ethnobot 18:53–66

    Google Scholar 

  • 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

  • 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

    Article  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin

  • Polunin O, Stainton A (1984) Flowers of the Himalaya. Oxford University Press, New Delhi, pp 413–416

    Google Scholar 

  • Puizina J, Papeš D (1996) Cytogenetical evidences for hybrid structure and origin structure and origin of diploid and triploid shallots (Allium cepa var. viviparum, Liliaceae) from Dalmatia (Croatia). Pl Syst Evol 208:11–23

    Article  Google Scholar 

  • Puizina J, Papeš D, Klein F, Schweizer D, Bohanec B, Javornik B, Maluszynska J (1997) Genomic in situ hybridisation in viviparous onions (Allium cepa var. viviparum). Abstract in Spring symposium on Plant Cytogenetics, Cieszyn, 19–22 May 1997, pp61

  • Rochow VBM (2009) Food taboos: their origins and purposes. J Ethnobiol Ethnomed. doi:10.1186/1746-4269-5-18

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Sharma G, Gohil RN (2008) Intrapopulation karyotypic variability in Allium roylei Stearn – a threatened species. Bot J Linn Soc 158:242–248

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

  • 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

  • Song YS, Suwabe K, Wako T, Ohara T, Nunome T, Kojima A (2004) Development of microsatellite markers in bunching onion (Allium fistulosum L.). Breed Sci 54:361–365

    Article  CAS  Google Scholar 

  • Tanikawa T, Takagi M, Ichii M (2002) Cultivar identification and genetic diversity in onion (Allium cepa L.) as evaluated by random amplified polymorphic DNA (RAPD) analysis. J Jpn Soc Hort Sci 71:249–251

    Article  Google Scholar 

  • 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 (Allium fistulosum). Euphytica 157:83–94

    Article  CAS  Google Scholar 

  • Van Loon V (2003) Charaka Samhita. Handbook on Ayurveda. Volume I. www.ayurveda-berkeley.com/…/Charaka’s…/Charaka-Samhita-2003-rev2_Vol_I. pdf261. Accessed 10 June 2010

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers: features and applications. Trends Biotechnol 23:48–55

    Article  PubMed  CAS  Google Scholar 

  • 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

    Chapter  Google Scholar 

  • 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

    Google Scholar 

  • Walter KS, Gillet HJ (1997) 1997 IUCN red list of threatened plants. Compiled by the World conservation monitoring center

  • Weir BS (1996) Genetic data analysis II. Sinauer Associates, Sunderland

    Google Scholar 

  • Woodward PW (1996) Garlic and friends: The history, growth and use of edible Alliums. Hyland House, Melbourne, pp 2–22

    Google Scholar 

Download references

Acknowledgments

We are thankful to Dr. MJ Havey, USDA and Univ. of Wisconsin, USA for supplying DNA of long day varieties and A. roylei; Dr. Sanjeet Kumar, AVRDC, Niger for seed supply of exotic lines and Dr. J. McCallum, New Zealand for providing some microsatellite primer sequences.

Author information

Authors and Affiliations

  1. Directorate of Onion and Garlic Research (ICAR), Rajgurunagar, Pune, Maharashtra, 410505, India

    Anil Khar & K. E. Lawande

  2. National Bureau of Plant Genetic Resources, Regional Station Bhowali, Nainital, Uttarakhand, 263132, India

    K. S. Negi

Authors
  1. Anil Khar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K. E. Lawande
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. S. Negi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anil Khar.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Khar, A., Lawande, K.E. & Negi, K.S. Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp.. Genet Resour Crop Evol 58, 741–752 (2011). https://doi.org/10.1007/s10722-010-9616-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-010-9616-y

Keywords

Search

Navigation