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2014 | 61 | 1 |

Tytuł artykułu

Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co - dominant cleaved amplified polymorphic site marker

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
 Cultivated carrot and its wild ancestor co-occur in most temperate regions of the world and can easily hybridize. The genetic basis of the process of domestication in carrot is not well understood. Recent results of an investigation on genetic diversity structure of cultivated and wild carrot and signatures for domestication using Diversity Arrays Technology (DArT) allowed identification of polymorphisms differentiating wild and cultivated accessions. We selected one of these polymorphisms, showing the strongest evidence for directional selection in the course of domestication, and converted it into a co-dominant cleaved amplified polymorphic site (CAPS) marker named cult. To achieve that, we designed site-specific primers anchored in sequences flanking the original DArT clone, amplified and sequenced the PCR products derived from cultivated and wild carrot. A PstI restriction site present in the 'cultivated' variant and absent in the 'wild' was subsequently used for routine differentiation the two variants. We validated the cult marker on 88 accessions of cultivated and wild carrot, each represented by five individuals. The allelic variant associated with the wild phenotype was only rarely observed in cultivated carrot, mostly in purple-rooted accessions originating Turkey and Iran, possibly indicating that the physical association between the diagnostic polymorphism and the putative 'domestication gene' has been broken in a group of Eastern carrots.

Słowa kluczowe

Wydawca

-

Rocznik

Tom

61

Numer

1

Opis fizyczny

p.19-22,fig.,ref.

Twórcy

  • Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Krakow, Poland
autor
  • Department of Horticulture, University of Wisconsin-Madison, Madison, USA
autor
  • Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Krakow, Poland
autor
  • Department of Horticulture, University of Wisconsin-Madison, Madison, USA
  • USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, Madison, USA
autor
  • Institute of Plant Biology and Biotechnology, University of Agriculture Krakow, Krakow, Poland

Bibliografia

  • Baranski R, Maksylewicz-Kaul A, Nothnagel T, Cavagnaro PF, Simon PW, Grzebelus D (2012) Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci. Genet Resour Crop Evol 59: 163-170.
  • Bradeen JM, Bach IC, Briard M, LeClerc V, Grzebelus D, Senalik DA, Simon PW (2002) Molecular diversity analysis of cultivated carrot (Daucus carota L.) and wild Daucus populations reveals a genetically nonstructured composition. J Amer Soc Hort Sci 127: 383-391.
  • Grebenstein C, Choi YH, Rong J, Jong TJ, Tamis WL (2011) Metabolic fingerprinting reveals differences between shoots of wild and cultivated carrot (Daucus carota L.) and suggests inheritance or wild trait dominance in hybrids. Phytochemistry 72: 1341-1347. 
  • Grebenstein C, Kos SP, Jong TJ, Tamis WL, Snoo GR (2013) Morphological markers for the detection of introgression from cultivated into wild carrot (Daucus carota L.) reveal dominant domestication traits. Plant Biol 15: 531-540. 
  • Grzebelus D, Baranski R, Spalik K, Allender C, Simon PW (2011) Daucus. In Wild Crop Relatives: Genomic and Breeding Resources. Kole C, eds, pp 91-113. Springer Berlin Heidelberg.
  • Grzebelus D, Iorizzo M, Senalik D, Ellison S, Cavagnaro P, Macko-Podgorni A, Heller-Uszynska K, Kilian A, Nothnagel T, Simon PW, Baranski R (2014) Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breed 33: 625-637. 
  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp 41: 95-98.
  • Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, Spooner D, Simon PW (2012) De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. BMC Plant Biol 12: 61. 
  • Iorizzo M, Senalik DA, Ellison SL, Grzebelus D, Cavagnaro PF, Allender C, Brunet J, Spooner DM, Van Deynze A, Simon PW (2013) Genetic structure and domestication of carrot (Daucus carota subsp. sativus)(Apiaceae). Am J Bot 100: 930-938. 
  • Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2010) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucl Acids Res 39: D225-D229. 
  • Rong J, Xu S, Meirmans PG, Vrieling K (2013) Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression. Ann Bot 112: 1361-1370. 
  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols: methods in molecular biology. Krawetz S, Misener S, eds, pp 365-386. Humana Press, Totowa, NJ, Source code available at  http://fokker.wi.mit.edu/primer3/ 
  • Shim SI, Jorgensen RB (2000) Genetic structure in cultivated and wild carrots (Daucus carota L.) revealed by AFLP analysis. Theor Appl Genet 101: 227-233.
  • Simon PW (1996) Inheritance and expression of purple and yellow storage root color in carrot. J Hered 87: 63-66.
  • Simon PW, Rubatzky VE, Bassett MJ, Strandberg OJ, White JM (1997) B7262, purple carrot inbred. Hort Science 32: 146-147.
  • Wijnheijmer EHM, Brandenburg WA, Ter Borg SJ (1989) Interaction between wild and cultivated carrots (Daucus carota L.) in the Netherlands. Euphytica 40: 147-154.

Typ dokumentu

Bibliografia

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