NDLI: Development of versatile gene-based SNP assays in maize (Zea mays L.)

Content Provider	Springer Nature Link
Author	Mammadov, Jafar Chen, Wei Mingus, Jennifer Thompson, Steve Kumpatla, Siva
Copyright Year	2011
Abstract	A large number of maize single nucleotide polymorphism (SNP) candidate sequences have been generated and deposited in public databases. However, very little work has been done to date to comprehensively characterize those SNPs and identify a set of markers, which potentially would have high impact in molecular genetics research and breeding programs. Here we describe a multi-step process to identify highly polymorphic gene-based SNPs among ~130,000 public markers. A set of 695 highly polymorphic SNPs (minor allele frequency value >0.3), identified within exons, 5′ and 3′ untranslated regions of genes, were converted into four of the most popular high-throughput genotyping assays that include Illumina’s GoldenGate and Infinium chemistries, Life Technologies’ TaqMan assay and KBioSciences’ KASPar assay. The term “versatile” was applied to 162 gene-based SNPs that were successfully converted into all four chemistries and had perfect genotypic clustering patterns. This subset of discovered versatile SNP markers represents a universal tool for application in various molecular genetics and breeding projects in maize, where genotyping is based on one of the four above-mentioned chemistries. This study demonstrated that despite the availability of millions of discovered SNPs in maize, only a very small portion of those polymorphisms could be utilized for the development of robust, versatile assays, and has real practical value in marker-assisted selection.
Starting Page	779
Ending Page	790
Page Count	12
File Format	PDF
ISSN	13803743
Journal	Molecular Breeding
Volume Number	29
Issue Number	3
e-ISSN	15729788
Language	English
Publisher	Springer Netherlands
Publisher Date	2011-06-04
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Maize Single nucleotide polymorphism GoldenGate Infinium KASPar TaqMan Biotechnology Plant Physiology Plant Genetics & Genomics Plant Sciences Plant Pathology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Molecular Biology Biotechnology Agronomy and Crop Science

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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