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
BeckwithBeckwithaccession
Ben LearBen Learaccession
BergmanBergmanaccession
NJS98-23Crimson Queenaccession
WSU 72Crowleyaccession
Blue Hill 2Blue Hill 2accession
Nova ScotiaNova Scotiaaccession
Badger Pit CABadger Pit CAaccession
OregonOregonaccession
DemoranvilleDemoranvilleaccession
Early BlackEarly Blackaccession
FranklinFranklinaccession
GH1GH1accession
HowesHowesaccession
HyRedHyRedaccession
Norman Le MunyonLe Munyonaccession
US93-3McFarlinaccession
CNJ97-105Mullica Queenaccession
Potter's FavoritePotter's Favoriteaccession
ProlificProlificaccession
US88-33; US93-219Searlesaccession
StevensStevensaccession
SundanceSundanceaccession
VMTL2VMTL2accession
US88-34Wilcoxaccession
Features
This publication contains information about 48 features:
Feature NameUniquenameType
vm01649vm01649genetic_marker
vm04084vm04084genetic_marker
vm04249vm04249genetic_marker
vm05418vm05418genetic_marker
vm07778vm07778genetic_marker
vm09532vm09532genetic_marker
vm09703vm09703genetic_marker
vm10462vm10462genetic_marker
vm12486vm12486genetic_marker
vm13742vm13742genetic_marker
vm13780vm13780genetic_marker
vm13884vm13884genetic_marker
vm21169vm21169genetic_marker
vm23232vm23232genetic_marker
vm25796vm25796genetic_marker
vm26877vm26877genetic_marker
vm27120vm27120genetic_marker
vm28527vm28527genetic_marker
vm31502vm31502genetic_marker
vm31701vm31701genetic_marker
vm32279vm32279genetic_marker
vm33770vm33770genetic_marker
vm34671vm34671genetic_marker
vm38401vm38401genetic_marker
vm39030vm39030genetic_marker

Pages

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