Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L

Publication Overview
TitleDeveloping market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L
AuthorsMoghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE
TypeJournal Article
Journal NameFrontiers in plant science
Volume5
Year2014
Page(s)185
CitationMoghaddam SM, Song Q, Mamidi S, Schmutz J, Lee R, Cregan P, Osorno JM, McClean PE. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L. Frontiers in plant science. 2014; 5:185.

Abstract

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.

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Pages

Stocks
This publication contains information about 3 stocks:
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Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-eCollection
ISSN1664-462X
pISSN1664-462X
Publication Date2014
Journal AbbreviationFront Plant Sci
DOI10.3389/fpls.2014.00185
Elocation10.3389/fpls.2014.00185
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountrySwitzerland