Data Sheet: Agrigenomics

MaizeLD BeadChip Kit
Cost-effective and scalable content for EDV assessment and other maize breeding applications.
Highlights• Comprehensive Solution for EDV Testing
High-discrimination coverage with 3047 evenly spaced
markers designed for EDV assessment• Add-On Content for Multiple Applications
Customizable to support varietal identification, genetic purity
testing, marker-assisted selection, and other applications• Affordable, Standard Platform
Single platform for various maize applications reduces costs
and eliminates manual processing errors• Unrivaled Call Rates and Accuracy> 99% average call rates and > 99.9% reproducibility

Introduction
Maize (Zea mays L. ssp. mays) was domesticated from the grass
teosinte in Central America1 over the last ~10,000 years, resulting indramatic expansion of the maize genome through proliferation of longterminal repeat retrotransposons.2 It is an important model organism
for fundamental research into gene inheritance and function,3 and astaple crop.
In 2009, researchers completed an improved draft sequence of the2.3-gigabase genome of the B73 maize line.4 This assembly wasused to compare sequence data of other key maize lines. From theseefforts, over 1 million SNPs have been identified.5
Maize exhibits high levels of both phenotypic and genetic diversity
and has been subject to high selective breeding pressure for yield
improvement, particularly among large companies supporting growers
with regionally appropriate seed. To create standards for recognizing
varietal development efforts, the International Union for the Protectionof New Varieties of Plants outlined definitions for essentially derived
varieties (EDV) in 1991.6 EDVs are obtained, either directly or indirectly,
from an initial variety (by selection of a natural or induced mutant), asomaclonal variant, a selection of variant plants from the initial variety,backcrossing, or transformation by genetic engineering. If they fulfill
these conditions, EDVs are eligible for plant breeders’ rights.
Under the guidance of the International Seed Federation, the American
Seed Trade Association and the French Breeders Association identified
SNPs that are equivalent to the simple sequence repeat (SSR)
markers traditionally used to determine EDV status.7 To provide theseed industry with a standard tool for EDV assessment, the MaizeLD
BeadChip (Figure 1) contains 3047 internationally recognized EDVmarkers based on genetic and physical maps. This array also offers
the capability to add custom markers, enabling other maize breeding
applications to be run on the same platform.

For Research Use Only. Not for use in diagnostic procedures.

®

4613390006

Figure 1: MaizeLD BeadChip—Designed for EDV assessment, theMaizeLD BeadChip features 3047 evenly spaced SNPs.

SNP Selection Strategy
SNP selection was based on a comparison of pairwise distancedata for inbred maize lines generated using SNP markers from theMaizeSNP50 BeadChip and SSR markers previously shown todiscern EDV status.7 In a collaboration between Illumina, Syngenta,and Pioneer, the markers were initially selected based on quality
assurance analysis criteria from genotyping of US and European publicand commercially relevant samples. SNP data were eliminated from
subsequent analyses if they exceeded the following thresholds:••••> 10% of missing SNPs per genotype> 10% of missing genotypes per SNP> 5% heterozygous SNPs per genotype> 10% heterozygous genotypes per SNP

After discarding 43 SNPs with insufficient data quality or vulnerability toascertainment bias, final comparisons were made using 26,874 SNPs.
Also, 3047 SNPs were selected to provide even genomic coverage tofacilitate SNP-based breeding applications.

Comprehensive Solution for EDV Testing
The MaizeLD BeadChip offers a comprehensive genotyping solution
for EDV testing in maize, providing the high discrimination necessary
to assess EDV status. Compared to traditional SSR markers, SNP
genotyping offers higher throughput, resolution, and reproducibility,resulting in high accuracy. Many agricultural researchers today aretransitioning from SSR analysis to SNP genotyping. With the MaizeLD
BeadChip, researchers can assess all EDV markers at the same time
across many samples rather than running separate assays for eachgene of interest.

Data Sheet: Agrigenomics

High-Quality Data
The proven Infinium® HD Assay powers the MaizeLD BeadChip,
providing the highest call rates in the industry. SNPs on the MaizeLD
BeadChip were subjected to rigorous functional testing across multiplelines to ensure strong performance (Table 1). Samples used for marker
validation include European and North American mapping populations,and the Plant Variety Protection Act panel used to establish the EDV
marker set.8 Validation of the MaizeLD BeadChip demonstrated a callrate of 99.4% across 280 samples. Reproducibility and Mendelianconsistencies were 99.9%.
Table 1: MaizeLD BeadChip Performance Data and Specifications

Parameter

Percent

Product Specification

Average Call Rate

99.4%

> 99%

Reproducibility

99.9%> 99.9%Mendelian Consistencies

99.9%< 0.1%

A standard cluster file is provided with the product to use as a starting point for calling
genotypes. Given the complexity and diversity of maize lines, it is important to evaluate cluster
positions for each data set. It is a best practice to include parental control inbred lines andtheir crosses for reference.

Flexibility for Multiple Applications
The MaizeLD BeadChip provides an ideal foundation for maize
breeding applications, with the ability to impute additional SNPs
for custom projects. Researchers can add up to 70,000 custom
markers onto the MaizeLD BeadChip to support marker-assisted
selection, varietal identification, genetic purity assessment, and otherapplications. By adding markers of interest to the base SNP content,
researchers can perform all maize genotyping applications on thesame platform, reducing costs.

Affordable, Standard Platform
With a focused set of SNP content containing all relevant markers,
the MaizeLD BeadChip minimizes per-sample costs for EDV testing.
Focused analysis produces a smaller data set compared to broader
approaches, enabling seed industry researchers to make accurate
EDV decisions with minimal amounts of data.

this 24-sample BeadChip has the capacity to add thousands ofcustom markers, presenting a standard platform for multiple maize
breeding applications.

Ordering Information
ProductCatalog No.

MaizeLD BeadChip Kit (48 samples)
Each package contains 2 BeadChips and reagents forprocessing 48 samples.

WG-455-1001

MaizeLD BeadChip Kit (288 samples)
Each package contains 12 BeadChips and reagents forprocessing 288 samples.

WG-455-1002

MaizeLD BeadChip Kit (1152 samples)
Each package contains 48 BeadChips and reagents forprocessing 1152 samples.

WG-455-1003

MaizeLD+ BeadChip Kit (48 samples)
Each package contains 2 BeadChips with custom add-on
content and reagents for processing 48 samples.

WG-455-1011

MaizeLD+ BeadChip Kit (288 samples)
Each package contains 12 BeadChips with custom add-on
content and reagents for processing 288 samples.

WG-455-1012

MaizeLD+ BeadChip Kit (1152 samples)
Each package contains 48 BeadChips with custom add-on
content and reagents for processing 1152 samples.

WG-455-1013

Each MaizeLD BeadChip can process 24 samples in parallel and assay 3047 markers
per sample.

References
1.
2.

3.
4.
5.
6.

Complete Genotyping Solution
The MaizeLD BeadChip is compatible with the iScan® System. This
array scanner features high-performance lasers and powerful optics
systems that enable rapid scan times and precise assay detection.
In addition, optional automation and the Laboratory Information
Management System (LIMS) lower costs by eliminating errors
associated with manual processing. Illumina genotyping products
can be accessed via Illumina FastTrackTM Genotyping Services or any
Illumina CSPro® Service.

7.

8.

Doebley JF, Gaut BS, Smith BD. The molecular genetics of crop
domestication. Cell. 2006;127:1309-1321.
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The
paleontology of intergene retrotransposons of maize. Nat Genet.
1998;20:43-54.
Bennetzen JL, Hake S. Handbook of Maize: Genetics and Genomics(Springer, New York, 2009).
Schnable PS, Ware D, Fulton RS, et al. The B73 maize genome: complexity,diversity, and dynamics. Science. 2009;326:1112-1115.
Gore MA, Chia JM, Elshire RJ, et al. A first-generation haplotype map ofmaize. Science. 2009;326:1115-1117.
International Union for the Protection of New Varieties of Plants (2009)
Explanatory Notes on Essentially Derived Varieties Under the 1991 Act ofthe UPOV Convention.
(www.upov.int/edocs/expndocs/en/upov_exn_edv_1.pdf) Accessed 05
May 2015.
Rousselle Y, Jones E, Charcosset A, et al. Study on essential derivationin maize: III. Selection and evaluation of a panel of single nucleotide
polymorphism loci for use in European and North American germplasm.
Crop Sci. 2015;55:1170-1180.
Kahler AL, Kahler JL, Thompson SA, et al. North American study on
essential derivation in maize: II. Selection and evaluation of a panel of simple
sequence repeat loci. Crop Sci. 2010;50:486-503.

Summary
Developed through a collaboration between Illumina scientists andthe seed industry, the MaizeLD BeadChip features 3047 evenlyspaced SNPs for comprehensive EDV assessment. In addition,Illumina • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
For Research Use Only. Not for use in diagnostic procedures.
© 2015 Illumina, Inc. All rights reserved. Illumina, CSPro, FastTrack, Infinium, iScan, and the pumpkin orange color are trademarks ofIllumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. Pub. No. 1370-2015-007 Current as of 25 June 2015