Document Detail

Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno.
MedLine Citation:
PMID:  23046423     Owner:  NLM     Status:  Publisher    
Agronomically important traits are frequently controlled by rare, genotype-specific alleles. Such genes can only be mapped in a population derived from the donor genotype. This requires the development of a specific genetic map, which is difficult in wheat because of the low level of polymorphism among elite cultivars. The absence of sufficient polymorphism, the complexity of the hexaploid wheat genome as well as the lack of complete sequence information make the construction of genetic maps with a high density of reproducible and polymorphic markers challenging. We developed a genotype-specific genetic map of chromosome 3B from winter wheat cultivars Arina and Forno. Chromosome 3B was isolated from the two cultivars and then sequenced to 10-fold coverage. This resulted in a single-nucleotide polymorphisms (SNP) database of the complete chromosome. Based on proposed synteny with the Brachypodium model genome and gene annotation, sequences close to coding regions were used for the development of 70 SNP-based markers. They were mapped on a Arina × Forno Recombinant Inbred Lines population and found to be spread over the complete chromosome 3B. While overall synteny was well maintained, numerous exceptions and inversions of syntenic gene order were identified. Additionally, we found that the majority of recombination events occurred in distal parts of chromosome 3B, particularly in hot-spot regions. Compared with the earlier map based on SSR and RFLP markers, the number of markers increased fourfold. The approach presented here allows fast development of genotype-specific polymorphic markers that can be used for mapping and marker-assisted selection.
Margarita Shatalina; Thomas Wicker; Jan P Buchmann; Simone Oberhaensli; Hana Simková; Jaroslav Doležel; Beat Keller
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-10-10
Journal Detail:
Title:  Plant biotechnology journal     Volume:  -     ISSN:  1467-7652     ISO Abbreviation:  Plant Biotechnol. J.     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-10     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101201889     Medline TA:  Plant Biotechnol J     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2012 The Authors Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.
Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
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