Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.)

Publication Overview
TitleMining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.)
AuthorsZhu H, Senalik D, McCown BH, Zeldin EL, Speers J, Hyman J, Bassil N, Hummer K, Simon PW, Zalapa JE
TypeJournal Article
Journal NameTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Volume124
Issue1
Year2012
Page(s)87-96
CitationZhu H, Senalik D, McCown BH, Zeldin EL, Speers J, Hyman J, Bassil N, Hummer K, Simon PW, Zalapa JE. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2012 Jan; 124(1):87-96.

Abstract

The American cranberry (Vaccinium macrocarpon Ait.) is a major commercial fruit crop in North America, but limited genetic resources have been developed for the species. Furthermore, the paucity of codominant DNA markers has hampered the advance of genetic research in cranberry and the Ericaceae family in general. Therefore, we used Roche 454 sequencing technology to perform low-coverage whole genome shotgun sequencing of the cranberry cultivar 'HyRed'. After de novo assembly, the obtained sequence covered 266.3 Mb of the estimated 540-590 Mb in cranberry genome. A total of 107,244 SSR loci were detected with an overall density across the genome of 403 SSR/Mb. The AG repeat was the most frequent motif in cranberry accounting for 35% of all SSRs and together with AAG and AAAT accounted for 46% of all loci discovered. To validate the SSR loci, we designed 96 primer-pairs using contig sequence data containing perfect SSR repeats, and studied the genetic diversity of 25 cranberry genotypes. We identified 48 polymorphic SSR loci with 2-15 alleles per locus for a total of 323 alleles in the 25 cranberry genotypes. Genetic clustering by principal coordinates and genetic structure analyzes confirmed the heterogeneous nature of cranberries. The parentage composition of several hybrid cultivars was evident from the structure analyzes. Whole genome shotgun 454 sequencing was a cost-effective and efficient way to identify numerous SSR repeats in the cranberry sequence for marker development.

Stocks
This publication contains information about 25 stocks:
Stock NameUniquenameType
BeckwithBeckwithcultivar
Ben LearBen Learcultivar
BergmanBergmancultivar
NJS98-23Crimson Queencultivar
WSU 72Crowleycultivar
Blue Hill 2Blue Hill 2wild_unimproved
Nova ScotiaNova Scotiawild_unimproved
Badger Pit CABadger Pit CAwild_unimproved
OregonOregonwild_unimproved
DemoranvilleDemoranvillecultivar
Early BlackEarly Blackcultivar
FranklinFranklincultivar
GH1GH1cultivar
HowesHowescultivar
HyRedHyRedcultivar
Norman Le MunyonLe Munyoncultivar
US93-3McFarlincultivar
CNJ97-105Mullica Queencultivar
Potter's FavoritePotter's Favoritecultivar
ProlificProlificcultivar
US88-33; US93-219Searlescultivar
StevensStevenscultivar
SundanceSundancecultivar
VMTL2VMTL2wild_unimproved
US88-34Wilcoxcultivar
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1432-2242
eISSN1432-2242
Publication Date2012 Jan
Journal AbbreviationTheor. Appl. Genet.
DOI10.1007/s00122-011-1689-2
Elocation10.1007/s00122-011-1689-2
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryGermany
Publication TypeResearch Support, U.S. Gov't, Non-P.H.S.
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:21904845
AGL: USDA National Agricultural LibraryAGL:4628225