NDLI: Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

Content Provider	Springer Nature Link
Author	Tian, Hong Li Wang, Feng Ge Zhao, Jiu Ran Yi, Hong Mei Wang, Lu Wang, Rui Yang, Yang Song, Wei
Copyright Year	2015
Abstract	Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea mays L.) genome. SNPs have several advantages over simple sequence repeats, such as ease of data comparison and integration, high-throughput processing of loci, and identification of associated phenotypes. SNPs are thus ideal for DNA fingerprinting, genetic diversity analysis, and marker-assisted breeding. Here, we developed a high-throughput and compatible SNP array, maizeSNP3072, containing 3072 SNPs developed from the maizeSNP50 array. To improve genotyping efficiency, a high-quality cluster file, maizeSNP3072_GT.egt, was constructed. All 3072 SNP loci were localized within different genes, where they were distributed in exons (43 %), promoters (21 %), 3′ untranslated regions (UTRs; 22 %), 5′ UTRs (9 %), and introns (5 %). The average genotyping failure rate using these SNPs was only 6 %, or 3 % using the cluster file to call genotypes. The genotype consistency of repeat sample analysis on Illumina GoldenGate versus Infinium platforms exceeded 96.4 %. The minor allele frequency (MAF) of the SNPs averaged 0.37 based on data from 309 inbred lines. The 3072 SNPs were highly effective for distinguishing among 276 examined hybrids. Comparative analysis using Chinese varieties revealed that the 3072SNP array showed a better marker success rate and higher average MAF values, evaluation scores, and variety-distinguishing efficiency than the maizeSNP50K array. The maizeSNP3072 array thus can be successfully used in DNA fingerprinting identification of Chinese maize varieties and shows potential as a useful tool for germplasm resource evaluation and molecular marker-assisted breeding.
Starting Page	1
Ending Page	11
Page Count	11
File Format	PDF
ISSN	13803743
Journal	Molecular Breeding
Volume Number	35
Issue Number	6
e-ISSN	15729788
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-05-31
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Maize variety Variety identification Single nucleotide polymorphism (SNP) DNA fingerprinting Molecular breeding Plant Sciences Plant Genetics & Genomics Plant Pathology Plant Physiology Biotechnology
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Molecular Biology Biotechnology Agronomy and Crop Science

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Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

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