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Common bean genotyping panel

The common bean (Phaseolus vulgaris) is the most important grain legume in human diets and hundreds of millions of people depend on the crop as a primary source of protein. The LGC common bean genotyping panel features a set of nearly 1500 KASP SNP genotyping assays.

The assays are based on a panel of over 1500 SNPs identified by the Generation Challenge Program for the advancement of common bean varieties with the aim of helping the common bean breeding community accelerate marker assisted selection (MAS) and deliver improvements in yield, biotic and abiotic stresses in developing countries.
 
Unlike chip-based systems with fixed marker sets, our common bean genotyping panel allows flexible selection of informative markers, and easy adaptation to changing germplasm collections in individual breeding programmes. Furthermore, KASP genotyping assays are highly cost-effective, providing an economical option to use the same SNP assays throughout the course of a breeding programme.
 
LGC’s complete genomics solution also encompasses plant sample collection kits, DNA extraction and genotyping services, enabling breeders in even the most remote locations to apply MAS.
 
The Phaseolus vulgaris assay panel is derived from parental varieties Jalo EP558 and BAT 93 using a SNP discovery pipeline that combined the Roche 454-FLX System (454) and Illumina Genome Analyser (GA) methologies. SNPs were discovered using a multi-tier reduced representation library (mtRRL) in which 2,795 contained sufficient flanking genomic sequence to take forward for Goldengate assay development, of which 79% produced working Goldengate assays (D Hyten et al.). 1556 SNP sequences were chosen by the GCP to provide sufficient resolution for application to MAS breeding programs. The SNP sequences were submitted to LGC for the development of KASP SNP marker assays. Of this set 1496 (96%) were successfully converted to produce the common bean panel.
 
Common bean KASP assays were mapped against phytozome 11  Phaseolus vulgaris  genome  assembly developed by  Jeremy Schmutz et al.  2014 Nat. Gen. 46,707-712 | doi:10.1038/ng.3008. Genome assembly was from 473Mb of 587Mb of Phaseolus vulgaris using resequencing of 60 wild species and 100 landraces. Single KASP SNP marker hits were determined as correct where coverage was 99.9% . Linkage groups were chosen where more than a single hit to the genome assembly was obtained.

Advantages

  • Panel includes nearly 1,500 functionally validated markers, markers, which can be run as a complete panel or as individual KASP assays
  • Cost-effective and robust KASP genotyping technology
  • Flexible - pick and choose the assays that are relevant to your project based on genome and chromosome location
  • Convenient – use informative markers directly on breeding populations or novel cultivars
  • minimum order – order any number of assays from the library
  • KASP assays are easy to run in your own laboratory or can be used in a genotyping service project


Ordering

The common bean KASP assays can be provided as part of our genotyping service or as reagents to run KASP genotyping in your own laboratory.

With our Assay Search Tool, you can search for specific assays, export your selection, pick the required amount of KASP Master mix, and request a quote. To place an order straightaway for all assays in your cart, please use the “export assay cart” function and forward the exported Excel file together with your purchase order to orders.uk@lgcgroup.com. The assays are available in 2 pack sizes:

References:
High-throughput SNP discovery and assay development in common bean
Hyten, D. L., QijianS., fickus E,.W., ……& Cregan P. B.- BMC Genomics 2010, 11:475

Genetic mapping of microsatellite markers around the arcelin bruchid resistance locus in common bean
Blair et al., 2010 -Theor Appl Genet (2010) 121:393–402

Fine‑mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.)
KellerB., Manzanares  C., Carlos  J., Lobaton J. D., Studer B., Raatz  B., - Theor Appl Genet (2015) 128:813–826

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