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 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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0335-0) contains supplementary material, which is available to authorized users.

Molecular mapping of quantitative trait loci for grain moisture at harvest in maize

“…, Tian et al. ). The average density of SNP markers on the maize genome is one every 48–104 bp (Tenaillon et al.…”

“…Therefore, we took advantage of the MaizeSNP3072 chip (Tian et al. ) to genotype the 240 DH lines and constructed a high‐density genetic linkage map covering 1546.4 cM using data of 964 polymorphic SNPs. This map was comparable to those previously established using SSR markers (Sala et al.…”

“…The MaizeSNP3072 (Tian et al. ) chip was used to genotype the DH population, and the genetic map was constructed as previously described (Xu et al. ).…”

Dek42 encodes an RNA‐binding protein that affects alternative pre‐mRNA splicing and maize kernel development

“…Another 1 μg of mutant genomic DNA was prepared as the mutant sample. The two DNA samples were hybridized and sequenced using the maize SNP3072 chip (Tian et al ). The genotype data from each sample were analyzed by the Illumina Genome Studio Genotyping Module according to the manufacturer's instructions (Chen et al ).…”

QTL mapping of three ear traits using a doubled haploid population of maize

“…The genetic linkage map established in our previous study (Song et al., ) was employed for QTL mapping. In particular, the genotyping of the DH population was conducted using MaizeSNP3072 chip (Tian et al., ), and a total of 964 SNPs that are polymorphic between two parents were used for map construction. The resulting linkage map was 1546.4 cM with the average marker interval of 1.6 cM.…”