title: Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties.
abstract: Single nucleotide polymorphisms (SNPs) are abundant and evenly distributed throughout the maize (Zea maysL.) 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.
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Hong-Li
authors.initials: HL
authors.lastname: Tian
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Feng-Ge
authors.initials: FG
authors.lastname: Wang
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Jiu-Ran
authors.initials: JR
authors.lastname: Zhao
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Hong-Mei
authors.initials: HM
authors.lastname: Yi
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Maize Research Center, Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Shuguang Garden Middle Road No. 9, Beijing, 100097 China.
authors.forename: Wei
authors.initials: W
authors.lastname: Song
keywords: DNA fingerprinting; Maize variety; Molecular breeding; Single nucleotide polymorphism (SNP); Variety identification