Journal article
Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)
BMC Plant Biology, Vol.12(1), Art. 10
2012
Abstract
Background
Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting.
Results
Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton.
Conclusions
The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.
Details
- Title
- Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)
- Authors/Creators
- H. Wang (Author/Creator) - Fujian Agriculture and Forestry UniversityR.V. Penmetsa (Author/Creator) - University of California, DavisM. Yuan (Author/Creator) - Shandong Peanut Research Institute, Qingdao, ChinaL. Gong (Author/Creator) - Tuskegee UniversityY. Zhao (Author/Creator) - Fujian Agriculture and Forestry UniversityB. Guo (Author/Creator) - Agricultural Research ServiceA.D. Farmer (Author/Creator) - National Center for Genome ResourcesB.D. Rosen (Author/Creator) - University of California, DavisJ. Gao (Author/Creator) - University of California, DavisS. Isobe (Author/Creator) - Kazusa DNA Research InstituteD.J. Bertioli (Author/Creator) - Universidade de BrasíliaR.K. Varshney (Author/Creator) - SEMID.R. Cook (Author/Creator) - University of California, DavisG. He (Author/Creator) - Tuskegee University
- Publication Details
- BMC Plant Biology, Vol.12(1), Art. 10
- Publisher
- BioMed Central Ltd as part of Springer Nature
- Identifiers
- 991005544386507891
- Copyright
- © 2012 Wang et al.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
7 File views/ downloads
26 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science