TITLE

AlliumMap-A comparative genomics resource for cultivated Allium vegetables

AUTHOR(S)
McCallum, John; Baldwin, Samantha; Masayoshi Shigyo; Yanbo Deng; van Heusden, Sjaak; Pither-Joyce, Meeghan; Kenel, Fernand
PUB. DATE
January 2012
SOURCE
BMC Genomics;2012, Vol. 13 Issue 1, p168
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Vegetables of the genus Allium are widely consumed but remain poorly understood genetically. Genetic mapping has been conducted in intraspecific crosses of onion (Allium cepa L.), A. fistulosum and interspecific crosses between A. roylei and these two species, but it has not been possible to access genetic maps and underlying data from these studies easily. Description: An online comparative genomics database, AlliumMap, has been developed based on the GMOD CMap tool at http://alliumgenetics.org. It has been populated with curated data linking genetic maps with underlying markers and sequence data from multiple studies. It includes data from multiple onion mapping populations as well as the most closely related species A. roylei and A. fistulosum. Further onion EST-derived markers were evaluated in the A. cepa x A. roylei interspecific population, enabling merging of the AFLP-based maps. In addition, data concerning markers assigned in multiple studies to the Allium physical map using A. cepa-A. fistulosum alien monosomic addition lines have been compiled. The compiled data reveal extensive synteny between onion and A. fistulosum. Conclusions: The database provides the first online resource providing genetic map and marker data from multiple Allium species and populations. The additional markers placed on the interspecific Allium map confirm the value of A. roylei as a valuable bridge between the genetics of onion and A. fistulosum and as a means to conduct efficient mapping of expressed sequence markers in Allium. The data presented suggest that comparative approaches will be valuable for genetic and genomic studies of onion and A. fistulosum. This online resource will provide a valuable means to integrate genetic and sequence-based explorations of Allium genomes.
ACCESSION #
79970350

 

Related Articles

  • A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.).  // BMC Plant Biology;2011, Vol. 11 Issue 1, p111 

    The article presents information on a study conducted in botany, in which a consensus genetic map in melon was constructed by using highly transferable anchor markers that have broad potential use for mapping and comparative quantitative trait loci (QTL) analysis. Under the International...

  • Characterization of wheat DArT markers: genetic and functional features. Marone, Daniela; Panio, Giosuè; Ficco, Donatella; Russo, Maria; Vita, Pasquale; Papa, Roberto; Rubiales, Diego; Cattivelli, Luigi; Mastrangelo, Anna // Molecular Genetics & Genomics;Sep2012, Vol. 287 Issue 9, p741 

    Diversity array technology (DArT) markers are largely used for mapping, genetic diversity, and association mapping studies. For years, they have been used as anonymous genomic markers, as their sequences were not known. As the sequences of 2,000 wheat DArT clones are now available, this study...

  • A comparative genome approach to marker ordering. T. Faraut; S. de Givry // Bioinformatics;Jan2007, Vol. 23 Issue 2, pe50 

    Motivation: Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We...

  • A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa. Lambreghts, Randy; Mi Shi; Belden, William J.; deCaprio, David; Park, Danny; Henn, Matthew R.; Galagan, James E.; Baştürkmen, Meray; Birren, Bruce W.; Sachs, Matthew S.; Dunlap, Jay C.; Loros, Jennifer J. // Genetics;Feb2009, Vol. 181 Issue 2, p767 

    We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to...

  • Genetic Analysis and Molecular Mapping of a Novel Gene Conferring Resistance to Rice Stripe Virus. Feng Zhao; Zhijun Cai; Tiezhu Hu; Haigen Yao; Li Wang; Na Dong; Bin Wang; Zhengang Ru; Wenxue Zhai // Plant Molecular Biology Reporter;Sep2010, Vol. 28 Issue 3, p512 

    Rice stripe virus (RSV) is one of the most damaging diseases affecting rice in East Asia. Rice variety 502 is highly resistant to RSV, while variety 5112 is extremely susceptible. Field statistical data revealed that all “502 × 5112” F1 individuals were resistant to RSV and the...

  • Mapping of quantitative trait loci (QTLs) for rice protein and fat content using doubled haploid lines. Hu, Zhong-Li; Li, Ping; Zhou, Ming-Quan; Zhang, Zhi-Hong; Wang, Ling-Xia; Zhu, Li-Huang; Zhu, Ying-Guo // Euphytica;Jan2004, Vol. 135 Issue 1, p47 

    Rice protein content (RPC) and rice fat content (RFC) are two important components of rice nutritional quality. In order to examine the genetic basis of these traits, a doubled haploid (DH) population and an RFLP linkage map consisting of 232 marker loci were used to search QTLs for the traits...

  • The Y chromosome-specific STS marker MS2 and its peripheral regions on the Y chromosome of the dioecious plant Silene latifolia. Ishii, Kotaro; Sugiyama, Ryuji; Onuki, Megumi; Kazama, Yusuke; Matsunaga, Sachihiro; Kawano, Shigeyuki // Genome;Apr2008, Vol. 51 Issue 4, p251 

    Sex determination in Silene latifolia uses the XX/XY system. The recent evolution of dioecy in S. latifolia provides a unique opportunity to study the early stages of Y chromosome evolution. However, the current Y chromosome map still contains many large gaps with no available markers. In this...

  • Combined mapping of DALP and AFLP markers in cultivated sunflower using F9 recombinant inbred lines. Langar, K.; Lorieux, M.; Desmarais, E.; Griveau, Y.; Gentzbittel, L.; Bervillé, A. // Theoretical & Applied Genetics;Apr2003, Vol. 106 Issue 6, p1068 

    A genetic map was constructed with specific PCRs, DALPs and AFLPs using F8-generation sunflower recombinant inbred lines. RI lines generated from a F2 population of one cross between the two cultivated inbred lines HA89 (maintainer for Pet1 CMS) and LR4 (restorer for Pet1 CMS) were used. A total...

  • Genetic maps for Pinus elliottii var. elliottii and P. caribaea var. hondurensis using AFLP and microsatellite markers. Shepherd, M.; Cross, M.; Dieters, M. J.; Henry, R. // Theoretical & Applied Genetics;May2003, Vol. 106 Issue 8, p1409 

    Genetic maps for individual Pinus elliottii var. elliottii and P. caribaea var. hondurensis trees were generated using a pseudo-testcross mapping strategy. A total of 329 amplified fragment length polymorphic (AFLP) and 12 microsatellite markers were found to segregate in a sample of 93...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics