Czech J. Genet. Plant Breed., 2013, 49(4):131-139 | DOI: 10.17221/111/2013-CJGPB

Molecular markers in the improvement of Allium cropsReview

Lakshmana Reddy Dhoranalapalli CHINNAPPAREDDY, Kiran KHANDAGALE, Aswath CHENNAREDDY, Veere Gowda RAMAPPA
Indian Institute of Horticultural Research, Bangalore, India

The genus Allium (Family: Alliaceae) is the most important among the bulbous vegetable crops. characterization of Alliums based on phenotypic traits is influenced by the environment and leads to biased diversity estimates. Recognizing the potential of DNA markers in plant breeding, researchers have adopted the molecular markers for marker-assisted selection (MAS), quantitative trait loci (QTL) mapping and characterization of different quality traits in Alliums. This review presents details about the use of DNA markers in Alliums for cultivar identification, diversity studies, SSR development, colour improvement, total soluble solids (TSS), cytoplasmic male sterility (CMS) and efforts of DNA sequencing. As there are no such reports to describe the above work under a single heading, we decided to mine literature for those who are working in onion, garlic, chives and leek improvement to generate new insights in the subject.

Keywords: cytoplasmic male sterility; diversity; garlic; onion; quantitative trait loci; simple sequence repeat

Published: December 31, 2013  Show citation

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CHINNAPPAREDDY LRD, KHANDAGALE K, CHENNAREDDY A, RAMAPPA VG. Molecular markers in the improvement of Allium crops. Czech J. Genet. Plant Breed. 2013;49(4):131-139. doi: 10.17221/111/2013-CJGPB.
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References

  1. Abdoli M., Habibi-Khaniani B., Baghalian K., Shahnazi S., Rassouli H. (2009): Classification of Iranian garlic (A. sativum L.) ecotypes using RAPD marker. Journal of Medicinal Plants, 8: 45-51.
  2. Al-Zahim M.A., Ford-Lloyd B.V., Newbury H.J. (2005): Detection of somaclonal variation in garlic (A. sativum L.) using RAPD and cytological analysis. Plant Cell Reports, 18: 473-477. Go to original source...
  3. Arumuganathan K., Earle E. (1991): Nuclear DNA content of some important plant species. Plant Molecular Biology Reports, 9: 208-218. Go to original source...
  4. Baldwin S.J., Meeghan P.J., Roopashree R., Mark F., Ross C., Richard M., Mccallum J. (2010): Application of 454™ sequencing for marker development in onion. In: 18th Conf. Plant and Animal Genomes. San Diego.
  5. Basak R. (1987): The Hindu concept of the natural world. In: Morgan K. (ed.): The Religion of the Hindus. Motilal Banarsidass, Delhi, 111-112.
  6. Bhasi A., Doug S., Philipp W.S., Brajendra K., Vinu M., Philge P., Periannan S. (2010): RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. BMC Plant Biology, 10: 161-166. Go to original source... Go to PubMed...
  7. Bradeen J.M., Havey M.J. (1995): Randomly amplified polymorphic DNA in bulb onion and its use to assess inbred integrity. Journal of American Society of Horticultural Science, 120: 752-758. Go to original source...
  8. Cardle L., Ramsay L., Milbourne D., Macaulay M., Marshall D., Waugh R. (2000): Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 156: 847-854. Go to original source... Go to PubMed...
  9. Chaurasia A.K., Adsul G.G., Nair D., Subramaniam V.R., Krishna B., Sane P.V. (2010): Diversity in Indian and some exotic onion cultivars as revealed by genomic and mitochondrial DNA. Acta Horticulturae (ISHS) 859: 207-220. Go to original source...
  10. Cho K.S., Yang T.J., Hong S.Y., Kwon Y.S., Woo J.G., Park H.G. (2006): Determination of cytoplasmic male sterile factors in onion plants (A. cepa L.) using PCR-RFLP and SNP markers. Molecular Cells, 21: 411-417. Go to original source...
  11. El-Shafie M.W., Davis G.N. (1967): Inheritance of bulb color in the onion (A. cepa L.). Hilgardia, 38: 607-622. Go to original source...
  12. Gai S., Meng X. (2010): Application of molecular markers linking to cytoplasmic male sterile loci to assist maintainer line selection and their selection efficiency in Welsh onion (A. fistulosum L.). Agricultural Sciences in China, 9: 1571-1576. Go to original source...
  13. Galmarini C.R., Goldman I.L., Havey M.J. (2001): Genetic analyses of correlated solids, flavor, and healthenhancing traits in onion (A. cepa L.). Molecular Genetics and Genomics, 265: 543-551. Go to original source... Go to PubMed...
  14. Gantait S., Mandal N., Bhattacharyya S., Das P.K. (2010): Determination of genetic integrity in long-term micro-propagated plantlets of A. ampeloprasum L. using ISSR markers. Biotechnology, 9: 218-223. Go to original source...
  15. Havey M.J. (2013): Single nucleotide polymorphisms in linkage disequilibrium with the male-fertility restoration (Ms) locus in open-pollinated and inbred populations of onion. Journal of the American Society for Horticultural Science, 138: 306-309. Go to original source...
  16. Havey M., King J.J., Bradeen J.M., Bark O., Sato Y., Gökçe A.F. (2001): A low-density genetic map of onion (A. cepa L.) and its use for marker-facilitated selection of maintainer lines. Acta Horticulturae (ISHS) 555: 87-89 Go to original source...
  17. Hye-Ran L., Eun-Mi E., Yong-Pyo L., Jae-Wook B., DongHee L. (2003): Construction of a garlic BAC library and chromosomal assignment of BAC clones using the FISH technique. Genome, 46: 514-520. Go to original source... Go to PubMed...
  18. Ipek M., Ipek A., Philipp W.S. (2008): Rapid characterization of garlic clones with locus-specific DNA markers. Turkish Journal of Agriculture and Forestry, 32: 357-362.
  19. Ipek M., Ipek A., Almquist S.G., Simon P.W. (2005): Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers. Theoretical and Applied Genetics, 110: 228-236. Go to original source... Go to PubMed...
  20. Jabbes N., Clerc V., Dridi B., Hannechi C. (2011): Inter simple sequence repeat fingerprints for assess genetic diversity of Tunisian garlic populations. Journal of Agricultural Science, 3: 77-85. Go to original source...
  21. Jakse J., Martin W., Mccallum J., Havey J.M. (2005): Single nucleotide polymorphism, Indels, simple sequence repeats for onion cultivar identification. Journal of American Society for Horticultural Science, 130: 912-917. Go to original source...
  22. Jakse J., Jenelle D.F., Suzuki G., Mccallum J., Foo C., Christopher D., Havey J.M. (2008): Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration. Molecular Genetics Genomics, 280: 287-292. Go to original source... Go to PubMed...
  23. Joseph C., Foo C., Qiaoping Y., William M., Yayeh Z., McCallum J., Andrew C., Paul R., Kenneth C., Maria J., James P.P., Christopher D.T., Havey J.M. (2004): A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. The Plant Cell, 16: 114-125. Go to original source... Go to PubMed...
  24. Joshi S.P., Ranjekar P.K., Vidya S.G. (1999): Molecular markers in plant genome analysis. Current Science, 77: 230-240.
  25. Joshi S.P., Gupta V.S., Aggarwal R.K., Ranjekar P.K., Brar D.S. (2000): Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theoretical and Applied Genetics, 100: 1311-1320. Go to original source...
  26. Khar A., Lawande K.E., Negi K.S. (2010): 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, 58: 741-752. Go to original source...
  27. Kim S., Jones R., Yoo K., Pike L.M. (2004): Gold colour in onions (A. cepa): a natural mutation of the chalcone isomerase gene resulting in a pre-mature termination codon. Molecular Genetics and Genomics, 272: 411-419. Go to original source... Go to PubMed...
  28. Kim S., Rick J., Kil-Sun Y., Leonard M.P. (2005a): The L locus, one of complementary genes required for anthocyanin production in onions (A. cepa L.), encodes anthocyanidin synthase. Theoretical and Applied Genetics, 111: 120-127. Go to original source... Go to PubMed...
  29. Kim S., Kil-Sun Y., Leonard M.P. (2005b): Development of a co-dominant, PCR-based marker for allelic selection of the pink trait in onions (A. Cepa L.), based on the insertion mutation in the promoter of the anthocyanidin synthase gene. Theoretical and Applied Genetics, 110: 628-633. Go to original source... Go to PubMed...
  30. Kim S., Haejeen B., Kil-Sun Y., Leonard M.P. (2006): Identification of the fourth allele of the ANS (anthocyanidin synthase) gene and its effect on red colour intensity in onions (A. cepa L.). Euphytica, 149: 45-51. Go to original source...
  31. Kim S., Haejeen B., Kil-Sun Y., Leonard M.P. (2007): Marker-assisted genotype analysis of bulb colours in segregating populations of onions (A. cepa L.). Molecular Cell, 23: 192-197. Go to original source...
  32. Kim S., Doohyun B., Dong Y.C., Eul-Tai L., Moo-Kyoung Y. (2009a): Identification of two novel inactive DFR-A alleles responsible for failure to produce anthocyanin and development of a simple PCR-based molecular marker for bulb color selection in onion (A. cepa L.). Theoretical and Applied Genetics, 118: 1391-1399. Go to original source... Go to PubMed...
  33. Kim S., Lee E.T., Kim C.W., Yoon M.K. (2009b): Distribution of three cytoplasm types in onion (A. cepa L.) cultivars bred in Korea and Japan. Korean Journal of Horticultural Science & Technology, 27: 275-279.
  34. Kim S., Bang H., Patil B.S. (2013): Origin of three characteristic onion (Allium cepa L.) mitochondrial genome rearrangements in Allium species. Scientia Horticulturae, 157: 24-31. Go to original source...
  35. Koops A.J., Hall R.D., Kik C. (1991): Bolkleurvorming bij de ui:een biochemisch genetisch model. Prophyta, 6: 20-22.
  36. Kuhl J.C., Cheung F., Yuan Q., Martin W., Zewdie Y., Mccallum J., Catanach A., Rutherford P., Sink K.C., Jenderek M., Prince J.P., Town C.D., Havey M.J. (2004): A unique set of 11 008 onion (A. cepa L.) ESTs reveals expressed sequence and genomic differences between monocot orders Asparagales and Poales. Plant Cell, 16: 114-125. Go to original source... Go to PubMed...
  37. Kyung-Ho M., Jae-Gyun K., Weiguo Z., Anupam D., GiAn L., Haeng-Hoon K., Ill-Min C., Nam-Soo K. (2009): Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (A. sativum L.). Scientia Horticulturae, 122: 355-361. Go to original source...
  38. Lampasona S.G., Asprelli P., Burba J.L. (2012): Genetic analysis of a garlic (Allium sativum L.) germplasm collection from Argentina. Scientia Horticulturae, 138: 183-189. Go to original source...
  39. Lotito S.B., Frei B. (2006) Consumption of flavonoidsrich foods and increased plasma antioxidant capacity in humans: cause, consequence, or epiphenomenon? Free Radical Biology Medicin, 41: 1727-17. Go to original source... Go to PubMed...
  40. Mahajan V., Jakse J., Havey M.J., Lawande K.E. (2009): Genetic fingerprinting of onion cultivars using SSR markers. Indian Journal of Horticulture, 66: 62-68.
  41. Maniruzzaman M.E., Haque M.M., Haque M.A. (2010): Molecular characterization of onion (A. cepa L.) using RAPD markers. Bangladesh Journal of Agricultural Research, 35: 313-322. Go to original source...
  42. Martin W.J., Mccallum J., Shigyo M., Jakse J., Kuhl J.C., Yamane N., Pither-Joyce M., Gokce A.F. Sink K.C., Town C.D., Havey M.J. (2005): Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Molecular Genetics Genomics, 3: 197-204. Go to original source... Go to PubMed...
  43. McCallum J., Leite D., Pither-Joyce M., Havey M.J. (2001): Expressed sequence markers for genetic analysis of bulb onion (A. cepa L.). Theoretical and Applied Genetics, 103: 979-991. Go to original source...
  44. McCallum J., Andrew C., Meeghan P.J., Martin S., Ruth B., John S., Ian S., Masayoshi S., Havey M.J. (2006): Genetic mapping of a major gene affecting onion bulb fructan content. Theoretical and Applied Genetics, 112: 958-96. Go to original source... Go to PubMed...
  45. McCallum J., Meeghan P.J., Martin S., Fernand K., Sheree D., Ruth B., John S., Jakse J., Havey M.J. (2007): Genetic mapping of sulfur assimilation genes reveals a QTL for onion bulb pungency. Theoretical and Applied Genetics, 114: 815-822. Go to original source... Go to PubMed...
  46. Mccallum J., Samantha B., Masayoshi S., Yanbo D., Sjaakvan H., Meeghan P., Fernand K. (2012): AlliumMap-A comparative genomics resource for cultivated Allium vegetables. BMC Genomics, 13: 168-173. Go to original source... Go to PubMed...
  47. Ovesna J., Kucera L., Hornickova J., Svobodova L., Stavelikova H., Velisek J., Milella L. (2011): Diversity of S-alk(en)yl cysteine sulphoxide content within a collection of garlic (Allium sativum L.) and its association with the morphological and genetic background assessed by AFLP. Scientia Horticulturae, 129: 541-547. Go to original source...
  48. Park J., Bang H., Cho D.Y., Yoon M., Patil B.S., Kim S. (2013a): Construction of high-resolution linkage map of the Ms locus, a restorer-of-fertility gene in onion (Allium cepa L.). Euphytica, 192: 267-278. Go to original source...
  49. Park J., Cho D.Y., Moon J.S., Yoon M.K., Kim S. (2013b): Development of functional markers for detection of inactive DFR-A alleles responsible for failure of anthocyanin production in onions (Allium cepa L.). Korean Journal of Horticultural Science & Technology, 31: 72-79. Go to original source...
  50. Qijiang C.C., Jia T. (2007): Genetic diversity analysis of onion (A. cepa L.) germplasm by ISSR markers. Chinese Agricultural Science Bulletin, 23: 126-130.
  51. Raines S., Havey M.J, Henson C.A. (2007): Candidate genes affecting fructan accumulation in onion. Plant and Animal Genome Conference. Available at http://www.intlpag.org/15/abstracts/PAG15_P05a_223.html
  52. Randle W.M., Lancaster J.E. (2002): Sulphur compounds in Alliums in relation to Flavour quality. In: Rabinowitch H., Currah L. (eds): Allium crop science - Recent advances. CABI Publishing, Oxford, 1-62. Go to original source...
  53. Sangeeta K.M., Gowda R.V., Lalitha A. (2006): Analysis of genetic diversity among Indian short-day onion (A. cepa L.) cultivars using RAPD markers. Journal of Horticultural Science and Biotechnology, 81: 774-777. Go to original source...
  54. Semagn K., Bjørnstad A., Ndjiondjop M.N. (2006): An overview of molecular marker methods for plants. African Journal of Biotechnology, 5: 2540-2568.
  55. Shirley B.W. (1996): Flavonoid biosynthesis: 'new' functions for an 'old' pathway. Trends Plant Sciences, 1: 377-382. Go to original source...
  56. Slimestad R., Fossen T., Vågen I.M. (2007): Onions: a source of unique dietary flavonoids. Journal of Agricultural Food Chemistry, 55: 10067-10080. Go to original source... Go to PubMed...
  57. Stack S.M., Commings D.E. (1979): Chromosome and DNA of Allium. Cromosoma, 70: 161-181. Go to original source...
  58. Susan E.W., Peter G.I., Robert J.S. (1993): Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theoretical and Applied Genetics, 86: 497-504. Go to original source... Go to PubMed...
  59. Szklarczyk M., Simlat M., Jagosz B., Ba G. (2002): The use of cytoplasmic markers in onion hybrid breeding. Cell Molecular Biology Letters, 7: 625-634.
  60. Takayoshi S., Yeon-Sang T., Hikaru W., Tadayuki N., Tsukasa K. (2005): Genetic mapping of AFLP markers in Japanese bunching onion (A. fistulosum). Euphytica, 144: 255-263. Go to original source...
  61. Tsukazaki H., Nunome T., Fukuoka H., Kanamori H., Kono I., Yamashita K., Wako T., Kojima A. (2007): Isolation of 1796 SSR clones from SSR-enriched DNA libraries of bunching onion (A. fistulosum). Euphytica, 157: 83-94. Go to original source...
  62. Tsukazaki H., Nunome T., Fukuoka H., Kanamori H., Kono I., Ohara T., Song Y.S., Yamashita K., Wako T., Kojima A. (2008a): Applications of DNA marker technology in Japanese bunching onion breeding. Acta Horticulturae (ISHS) 770: 153-158. Go to original source...
  63. Tsukazaki H., Ken-Ichiro Y., Shigenori Y., Shinichi M., Hiroyuki F., Junichi Y., Hiroyuki K., Izumi K., Masayoshi S. (2008b): Construction of SSR-based chromosome map in bunching onion (A. fistulosum). THeoretical and Applied Genetics, 117: 1213-1223. Go to original source... Go to PubMed...
  64. Tsukazaki H., Ken-Ichiro Y., Akio K., Tadayuki W. (2009): SSR-tagged breeding scheme for allogamous crops: a trial in bunching onion (A. fistulosum). Euphytica, 169: 327-334. Go to original source...
  65. Ved Brat S. (1965): Genetic system in Allium. I. Chromosomal variation. Chromosoma, 16: 486-499. Go to original source...
  66. Xu P., Liu H., Gao Z., Srinivas P., Yang C.Y. (2001): Genetic identification of garlic cultivars and lines by using RAPD assay. Acta Horticulturae (ISHS) 555: 213-220. Go to original source...

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