본문 바로가기
KERD
논문KCI 등재

Single Nucleotide Polymorphisms (SNPs) for Advanced Genomic Research in Sericulture

2

조회

0

다운로드

0

인용

0

참고문헌

키워드

초록

Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

Abstract

Single nucleotide polymorphisms (SNPs) are the most frequent form of variation in the genome of any organism. Owing to their greater abundance, they are considered useful for identifying cultivars, construction of higher density linkage maps, and detection of genes (QTLs) associated with complex agronomic traits and diseases. Although, SNPs have been used recently for constructing a high density genetic map in silkworm and a set of 118 SNPs have been identified in tasar silkworms, not much progress has been made in sericulture to utilize the vast potential of SNPs. Thus, this review mainly focuses on some of the important methods of SNP discovery, validation and genotyping. Emphasis has also been given to the possible uses of SNP genotyping in the improvement of silkworms and their host plants.

참고문헌 (82)

  1. Abravaya K., "Molecular beacons as diagnostic tools: technology and applications", Clin Chem Lab Med., 41, pp.468~474 (2003)
  2. Ahmadian A., "Genotyping by apyrase-mediated allele-specific extension", Nucl Acids Res., 29, pp.1~21 (2001)
  3. Aranzana MJ., "Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes", PLoS Genetics., 1, pp.531~539 (2005)
  4. Arunkumar KP., "WildSilkbase: An EST database of wild silkmoths", BMC Genomics, 9, pp.338~ (2008)
  5. Arunkumar KP., "Microsatellite markers for the Indian golden silkmoth, Antheraea assama (Saturniidae: Lepidoptera)", Mol Ecol Resour. (2008)
  6. Asakura N., "Single nucleotide polymorphism in an STS region linked to the Ncc-Tmp1A locusare informative for characterizing the differentiation of Chromosome 1A in wheat", Genes Genet Syst, 76, pp.295~304 (2001)
  7. Begun DJ., "Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster", Nature, 356, pp.519~520 (1992)
  8. Carlson CS., "Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans", Nature Genet., 33, pp.518~521 (2003)
  9. Chatterjee SN., "Identification of ISSR markers associated with productivity traits in silkworm, Bombyx mori L", Genome., 46, pp.438~447 (2003)
  10. Chatterjee SN., "Morphological and molecular variation of Morus laevigata in India", Genetica, 39, pp.1612~1624 (2004)
  11. Chatterjee SN., "ISSR profiling of genetic variability in the ecotypes of Antheraea mylitta Drury, the tropical tasar silkworm", Russ J Genetics, 40, pp.21~217 (2004)
  12. Cheng TC., "Mining single nucleotide polymorphism from EST data of silkworm, Bombyx mori, inbred strain Dazo", Insect Biochem Mol Biol., 34, pp.523~530 (2004)
  13. Ching A., "SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines", BMC Genet., 3, pp.19~ (2002)
  14. Collins FS., "Variations on a theme: Cataloging human DNA sequence variation", Science, 128, pp.1580~1581 (1997)
  15. Cardon LR., "Association study designs for complex diseases", Nat Rev Genet., 2, pp.91~99 (2001)
  16. Costabile M., "Molecular approaches in the diagnosis of primary immunodeficiency diseases", Hum Mutat., 27, pp.1163~1173 (2006)
  17. Ewing B., "Base-calling of automated sequencer traces using phred. II. Error probabilities", Genome Res., 8, pp.186~194 (1998)
  18. Ewing B., "Base-calling of automated sequencer traces using phred. I. Accuracy assessment", Genome Res., 8, pp.175~185 (1998)
  19. Flint-Garcia SA., "Structure of linkage disequilibrium in plants", Annu Rev Plant Biol., 54, pp.357~374 (2003)
  20. Gage LP., "The Bombyx mori genome: analysis by DNA reassociation kinentics", Chromosoma, 45, pp.27~42 (1974)
  21. Griffin TJ., "Single-nucleotide polymorphism analysis by MALDI-TOF mass spectrometry", TIBTECH, 18, pp.77~84 (2000)
  22. Gupta PK., "Single nucleotide polymorphism: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants", Curr Sci., 80, pp.524~535 (2001)
  23. Halushka MK., "Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis", Nat Genet., 22, pp.239~247 (1999)
  24. Howell W., "Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms", Nat Biotechnol., 17, pp.87~88 (1999)
  25. Hudson RR., "A test of neutral molecular evolution based on nucleotide data", Genetics., 116, pp.153~159 (1987)
  26. Hudson RR., "Two-locus sampling distributions and their application", Genetics, 15, pp.1805~1817 (2001)
  27. Jorde JB., "Linkage disequilibrium and the search for complex disease gene", Genome Res., 10, pp.1435~1444 (2000)
  28. Kar PK., "Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta) ecorace Daba as revealed through ISSR markers", Genetica., 125, pp.173~183 (2005)
  29. Kadono-Okuda K., "Linkage analysis of maternal EST cDNA clones covering all twenty-eight chromosomes in the silkworm, Bombyx mori", Insect Mol Biol., 11, pp.443~451 (2002)
  30. Karas M., "Laser desorption ionization of proteins with molecular masses exceeding 10000 daltons", Anal Chem., 60, pp.2299~2303 (1988)
  31. Kimiko Y., "Construction of a single nucleotide polymorphism linkage map for the silkworm , Bombyx mori, based on BAC endsequences", Genetics, 173, pp.151~161 (2006)
  32. Kirpekar F., "DNA sequence analysis by MALDI mass spectrometry", Nucl Acids Res., 26, pp.2554~2559 (1998)
  33. Kota R., "Snipping polymorphism from large EST collections in barley (Hordeum vulagre L.)", Mol Gen Genomics, 270, pp.24~33 (2003)
  34. Kruglyak L., "The use of genetic map of biallelic markers in linkage studies", Nat Genet., 17, pp.21~24 (1997)
  35. Lal S., "Repertoire of leaf expressed sequence tags (ESTs) and partial characterization of stress-related and membrane transporter genes from mulberry (Morus indica L.)" (2008), Tree Genet Genome
  36. Lipshutz RJ., "High density synthetic oligonucleotide arrays", Nat Genet., 21, pp.20~24 (1999)
  37. MacDonald B., "Pathogen population genetics, evolutionary potential and durable resistance", Ann Rev Phytopathol., 40, pp.349~379 (2002)
  38. Mahendran B., "Genetic variation in ecoraces of tropical tasar silkworm, Antherae mylitta D. using RFLF technique", Curr Sci., 90, pp.100~103 (2006)
  39. Mase K., "Genetic mapping of a food preference gene in the silkworm, Bombyx mori, using restriction fragment length polymorphism (RFLPs)", Genes Genet Syst., 82, pp.249~256 (2007)
  40. McGuigan FE., "Single nucleotide polymorphism detection: allelic discrimination using TaqMan", Psychiatr Genet., 12, pp.133~136 (2002)
  41. McVean G., "A genealogical interpretation of linkage disequilibrium", Genetics., 162, pp.987~991 (2002)
  42. Miao X., "Simple sequence repeat-based consensus linkage map of Bombyx mori", Proc Natl Acad Sci USA, 102, pp.16303~16308 (2006)
  43. Myers S., "A fine-scale map of recombination rates and hotspots across the human genome", Science, 310, pp.321~324 (2005)
  44. Nagaraja GM., "Genome fingerprinting in silkworm Bombyx mori using random arbitrary primers", Electrophoresis, 16, pp.1633~1638 (1995)
  45. Nagaraja GM., "Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori", Heredity, 95, pp.148~157 (2005)
  46. Newton CR., "Genetic analysis in cystic fibrosis using the amplification refractory mutation system (ARMS): the J3.11 MspI polymorphism", J Med Genet., 28, pp.248~251 (1991)
  47. Nguu EK., "Molecular linkage map for the silkworm, Bombyx mori, based on restriction fragment length polymorphism of cDNA clones", J Insect Biotechnol Sericol., 74, pp.5~13 (2005)
  48. Olivier M., "The Invader assay for SNP genotyping", Mutat Res., 573, pp.103~110 (2005)
  49. Picoult-Newberg L., "Mining SNPs from EST databases", Genome Res., 9, pp.167~174 (1999)
  50. Prasad MD., "Survey and analysis of microsatellites in the silkworm, Bombyx mori: frequency, distribution, mutations, marker potential and their conservation in heterologous species", Genetics, 169, pp.197~214 (2005)
  51. Promboon A., "Linkage map of random amplified polymorphic DNAs (RAPDs) in the silkworm, Bombyx mori", Genet Res Camb., 66, pp.1~7 (1995)
  52. Remington DL., "Structure of linkage disequilibrium and phenotypic associations in the maize genome", Proc Natl Acad Sci USA, 98, pp.11479~11484 (2001)
  53. Rao SN., "Phylogenetic relationships of three new microsporidian isolates from the silkworm, Bombyx mori", J Invertebr Pathol., 86, pp.87~95 (2004)
  54. Rao SN., "Characterization and phylogenetic relationships among microsporidia infecting silkworm, Bombyx mori, using inter simple sequence repeat (ISSR) and small subunit rRNA (SSU-rRNA) sequence analysis", Genome., 48, pp.355~366 (2005)
  55. Rapley R., "Molecular Analysis and Genome Discovery. Chichester" (2004), John Wiley & Sons
  56. Reddy KD., "Genetic characterization of silkworm Bombyx mori by simple sequence repeats (SSR)-anchored PCR", Heredity, 83, pp.681~687 (1999)
  57. Reddy KD., "Microsatellites of the silkworm, Bombyx mori: abundance, polymorphism and strain characterization", Genome, 42, pp.1057~1065 (1999)
  58. Reich DE., "Quality and completeness of SNP databases", Nat Genet., 33, pp.457~458 (2003)
  59. Rieder MJ., "Automating the identification of DNA variations using qualitybased fluorescence re-sequencing: analysis of the human mitochondrial genome", Nucl Acids Res., 26, pp.967~973 (1998)
  60. Ronaghi M., "A sequencing method based on real-time pyrophosphate", Science, 281, pp.363~365 (1998)
  61. Sachidanandam R., "A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms", Nature, 409, pp.928~933 (2001)
  62. Schneider K., "SNP frequency and allelic haplotype structure of Beta vulagris expressed genes", Mol Breed., 8, pp.63~74 (2001)
  63. Sethuraman BN., "DNA fingerprinting with homologous multilocus probes and search for DNA markers associated with yield attributes in silkworm, Bombyx mori", Eur J Entomol., 99, pp.267~276 (2002)
  64. Shi J., "A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms", Genet Res., 66, pp.109~126 (1995)
  65. Sharma A., "Assessment of genetic diversity in a Morus germplasm collection using fluorescence-based AFLP markers", Theor Appl Genet., 101, pp.1049~1055 (2000)
  66. Syvanen AC., "Accessing genetic variation: genotyping single nucleotide polymorphisms", Nat Rev Genet., 2, pp.930~942 (2001)
  67. Taillon-Miller P., "Overlapping genomic sequences: a treasure trove of single nucleotide polymorphisms", Genome Res., 8, pp.748~754 (1998)
  68. Tan YD., "An amplified fragment length polymorphism map of the silkworm", Genetics., 157, pp.1277~1284 (2001)
  69. Teotia RS., "Mulberry diseases in India and their control", Sericologia, 34, pp.1~18 (1994)
  70. Tyrka M., "Developement of single nucleotide polymorphism marker of the wheat Lr1 leaf rust resistance gene", Cell Mol Biol Lett., 9, pp.879~889 (2004)
  71. Tyagi S., "Multicolor molecular beacons for allele discrimination", Nat Biotechnol., 16, pp.49~53 (1998)
  72. Van K., "Discovery of SNPs in soybean phenotypes frequently used as the parents of mapping populations in the United States and Korea", J Heridity, 96, pp.529~535 (2005)
  73. Venkateswarlu M., "A first genetic linkage map of mulberry (Morus spp.) using RAPD, ISSR, and SSR markers and pseudotestcross mapping strategy", Tree Genet Genomes, 3, pp.15~24 (2006)
  74. Vijayan K., "Molecular evaluation of genetic variability in wild populations of mulberry (Morus serrata Roxb.)", Plant Breed., 123, pp.568~572 (2004)
  75. Vijayan K., "Molecular characterization of mulberry genetic resources indigenous to India", Genet Resour Crop Evol., 52, pp.77~86 (2005)
  76. Vijayan K., "Genetic diversity and differentiation among populations of the Indian eri silkworm, Samia cynthia ricini, revealed by ISSR markers", J Insect Sci., 6, pp.30~ (2006)
  77. Kunjupillai Vijayan, "Molecular Markers and Their Application in Mulberry Breeding", International Journal of Industrial Entomology, 15(2), pp.145~155 (2007), 한국잠사학회
  78. Wang DG., "Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome", Science, 280, pp.1077~1082 (1998)
  79. Watterson GA., "On the number of segregating sites in genetical models without recombination", Theor Popul Biol., 7, pp.256~276 (1975)
  80. Yamamoto K., "A BAC-based integrated linkage map of the silkworm, Bombyx mori", Genome Biol., 9, pp.21~ (2008)
  81. Yasukochi Y., "A second generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects", Genetics, 173, pp.1319~1328 (2006)
  82. Zhao W., "Genetic diversity of genus Morus revealed by RAPD markers in China", Int J Agric Biol., 6, pp.950~954 (2004)

관련 논문AI추천

Prospects of Application of Linkage Disequilibrium Mapping for Crop Improvement in Wild SilkwormBeera Saratchandra, Kunjupillai Vijayan, Ravindra Nath Singh한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2010 · 제20권 제2호Microsatellite Analysis of the Silkworm Strains (Bombyx mori) Originated from China김기환, 김익수, 류강선, Gyoo-Byung Sung, Kee Young Kim, Pil Don Kang, Sang Deok Ji한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2012 · 제25권 제1호Identification of domesticated silkworm varieties using single nucleotide polymorphisms detected from mitochondrial genomes김기영, 김익수, 박정선, 박종우, Chan Young Jeong, Nam-Suk Kim, Sang Kuk Kang, Seong-Wan Kim한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2022 · 제45권 제1호Microsatellite Analysis of Silkworm Strains (Bombyx mori) of Japan Origin Preserved in Korea강필돈, 김기영, 김익수, 류강선, 박정선한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2014 · 제28권 제2호Genetic diversity among Indian oak tasar silkworm, Antherea proylei J.revealed by ISSR markersKangayam M. Ponnuvel, Kanghujam Ibsorani Devi, Kangjam Chaoba Singh, Laishram Somen Singh한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2012 · 제24권 제2호Studies on the Hereditary Properties of SSR Marker in Silkworm (Bombyx mori L.)Cheng Lu, Minghui Li, Muwang Li, Xuexia Miao, Yongping Huang한국잠사학회 · International Journal of Industrial Entomology and Biomaterials2005 · 제11권 제1호

이 간행물의 다른 논문 (9건)