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Temperate Maize Panel

We are now offering the Temperate Maize panel for full-service PlexSeq  genotyping, to be used as a tool to conduct molecular breeding.


The Temperate Maize panel consists of 2490 SNPs, and development was led by Professor Shawn Kaeppler and his laboratory at the University of Wisconsin- Madison.

 The Temperate Maize panel is offered to the public at a discounted price and expedited turnaround through the AgriPlex Connect program (accepting samples on an ongoing basis).

* The following is derived from the White Paper


Corn (maize, Zea mays) is an annual, monoecious grass in the family Poaceae. It is a diploid organism with a genome consisting of approximately 2.3 billion base pairs organized in ten chromosomes. The genome is characterized by a high proportion of repetitive DNA sequences, including transposable elements and regions with varying recombination rates.

Molecular markers have evolved over the past 80 years through sampling and comparing genomes. Over time, technology for interrogating genetic variation has progressed, and many DNA molecular marker systems were developed. Consequently, so did the resolution of the genomic picture the markers can depict. Single Nucleotide Polymorphisms (SNPs) have emerged as the ultimate molecular marker. SNPs are single nucleotide changes that are heritable, codominant, and distributed with relatively high frequency throughout eukaryotic genomes. SNPs can be the causative mutation that directly affects a phenotype or can be associated with such mutations. Marker-assisted selection (MAS) technologies offer an effective and accelerated approach for identifying and selecting desired traits in corn breeding programs by:

  • Allowing the identification of desired traits at early developmental stages, reducing the time and resources required for phenotypic evaluation.

  • Precision and Efficiency: MAS enables the selection of individuals with the desired alleles with higher accuracy and efficiency.

  • Increased Genetic Gain: MAS facilitates the stacking of multiple favorable alleles, leading to faster genetic gain in breeding programs.

  • Enhanced Selection Intensity: MAS provides the opportunity to select individuals with favorable traits that may not be apparent through phenotypic evaluation alone

We describe here in a mid-density SNP panel, designed to be used for marker assisted breeding applications of Temperate corn and its derivatives.

The Mid-Density, Temperate Maize Panel

The Temperate Corn mid density SNP panel is made of 2490 markers. The SNPs span the 10 maize chromosomes with an average of 249 SNPs per chromosome and a range of 178 SNPs on chromosome 10; the smallest chromosome, and 381 on the largest chromosome; chrome 1. The distance between adjacent SNPs ranges from 0.67 Mbp to 1.13 Mbp and averages 0.88 Mbp (Table 1). See Appendix A for a complete listing of the markers and their positions. SNP selection has been done by Prof. Shawn Kaeppler’s group at University of Wisconsin- Madison.


SNP selection was carried out with the objective of identifying a set SNPs that segregate in dent maize, are potentially associated with important agronomic traits, and are spaced evenly throughout the maize genome. Markers were selected based on both exome capture and genotype-by-sequencing markers previously generated for a six-parent synthetic MAGIC population (19, 20), and a set of 12 biparental populations formed from a factorial cross of seven parents. All populations are derived from inbreds adapted to temperate environments and therefore, all the SNPs in the panel were observed segregating in North American Dent germplasm.

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Table 1: Number of markers per chromosome and the average distance in Mbp between adjacent SNPs. The 2490 SNPs are evenly distributed among the 10 corn chromosomes with an average of 249 markers per chromosome

Marker-trait association analyses were performed across Stiff Stalk and non-Stiff Stalk mapping populations. However, none of the regions included in the final SNP selection were validated and further testing is required to confirm the effect of each SNP on agronomic trait of interest, therefore, trait associations are not listed on Appendix A until further validation. Markers in the panel are predicted to be associated with Agronomic traits such as plant growth and development, morphological features of maize kernels, cobs, and ears, flowering time, plant height and ear height, ear length and width, cob length and width, kernel mass, and disease resistance. A small number of SNPs were also associated with grain yield and grain moisture. Marker-trait association analyses for morphological traits of maize kernels, cobs, and ears were only performed among inbred lines while flowering time and plant and ear height association tests were conducted among both hybrids and inbred lines. Grain moisture and grain yield association tests were only conducted in hybrids when inbred lines were crossed to a tester in the opposite heterotic group.

The panel was validated experimentally using germplasm provided by Prof. Shawn Kaeppler’s laboratory at University of Wisconsin- Madison (188 lines), and a collection of lines put together by the Organic Research and Extension Initiative (OREI), coordinated by Prof. Paul Scott of Iowa State University and the USDA-ARS (94 lines). The University of Wisconsin samples were assembled to represent the three main corn heterotic groups, including 17 Iodent lines, 30 nonstiff stalk lines, and 41 Stiff stalk lines. In addition, a group of 56 Wisconsin Breeding Lines and 42 publicly released lines from the Genome Enhancement of Maize (22) project were included. Altogether, the participating lines can also be broken into 98 public lines and 90 ex-PVP lines.


Genomic Selection

The Temperate Corn SNP panel will enable genomic selection; the level of polymorphism observed indicates that there is a high likelihood of obtaining sufficient polymorphic markers for imputation to a higher marker density level. The average Genomic Selection predictive ability will vary for different combinations of parental lines and in different years.


The combination of rapid, cost-effective genotyping of a prediction population during the last generation of line fixation saves expenses on the cost of field space for seed increase and allows rapid recycling of progeny as parents

Marker-assisted backcrossing:

The Temperate Corn SNP panel can be used for background recovery estimates in marker-assisted backcrossing programs. The combination of informative background markers and a selection of trait markers allows for the accurate estimation of background recovery, ensures recovery of valuable genes from the recipient line, and can provide additional confirmation that a target gene is carried by the selected progeny. Background selection can reduce by 2 or more the number of backcross generations required to achieve >95% recipient parent recovery.

QTL Mapping

While not the primary target application, the Temperate Corn SNP panel can be used for biparental mapping purposes. The density of polymorphic markers may, in some cases, be lower than what is desirable (largely dependent on the parents involved), however, the panel does provide an option for genotyping much of the genome. Any remaining gaps could then be filled in with other marker systems or by further panel customization.

Seed Purity and Hybridity

The genome coverage of the Temperate Corn SNP panel includes the number of markers that will allow for the identification of diagnostic marker subsets for seed quality applications such as genetic purity testing (uniformity) and varietal identification in commercial production operations.


The Temperate Maize SNP panel is providing an excellent, cost-effective solution for applications requiring mid-density SNP numbers over any number of sample throughput. The panel fits with rapid line fixation protocols due to its low cost-per-sample and rapid turnaround time. This panel will allow for major-locus selection as part of genomic selection, or backcross introgressions amongst maize lines, or the transfer of genes and QTLs of interest from exotic germplasm into elite lines. The panel presents a valuable tool for saving critical time, expenses, and shortening the “time to market”. The panel primarily enables molecular breeding applications; however, the genome coverage expands its usefulness in a range of other research applications.


The flexibility of the PlexSeq platform permits continual revision and upgrading of the panel, ensuring the process keeps pace with the current breeding and seed production needs of the Maize breeding and research communities.

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