A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

Abstract

SNP genotyping arrays have been useful for many applications that require a large number of molecular markers such as high-density genetic mapping, genome-wide association studies (GWAS), and genomic selection. We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The markers, taken from more than 800,000 SNPs, were selected to be preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including North American and European inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes and 16,168 outside genes, were of good quality for genotyping, with an average failure rate of 4% and rates up to 8% in specific germplasm. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations – IBM (B73×Mo17) and LHRF (F2×F252) – were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five major regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the array's high quality, it will be a valuable resource for maize genetics and many aspects of maize breeding.

Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium

“…Both are composed of 300 lines. These panels were genotyped with the 50k SNPs array described in Ganal et al(2011), as presented in Bouchet et al (2013) and Rincent et al (2012). Individuals with marker missing rate higher than 0.1 and/or heterozygosity rate higher than 0.05 were eliminated.…”

“…Individuals removed were chosen at random. To avoid the ascertainment bias noted by Ganal et al (2011), we used only the markers that were developed by comparing the sequences of nested association mapping founder lines (PANZEA SNPs; Gore et al 2009) in the estimation of admixture and relationship coefficients (29996, 30119, and 29132 markers passed the filter criteria for the C-K, CF-Dent, and CF-Flint lines respectively).…”

A SNP-Based Genetic Linkage Map of Soybean Using the SoyS - NP6K Illumina Infinium BeadChip Genotyping Array

“…A universal linkage panel of soybean containing 1,536 SNPs was developed through Illumina GoldenGate platform. More than 50,000 SNPs were reported for both maize and soybean (Ganal et al, 2011;Song et al, 2013) that were developed using the Illumina Infinium platform. In this study, we analyzed the 'Maryland 96-5722' by 'Spencer' RIL population using the Infinium BeadChip genotyping array of soybean on Illumina platform.…”

Improved maize reference genome with single-molecule technologies

“…1), we assembled the genome of the maize inbred line B73 into 2,958 contigs, in which half of the total assembly is made up of contigs larger than 1.2 Mb (Table 1 Table 1) to create a hybrid assembly consisting of 625 scaffolds (Table 1). To build chromosome level super scaffolds, we combined the hybrid assembly with a minimum tiling path generated from the bacterial artificial chromosomes (BACs) 11 and a high density genetic map 12 (Extended Data Fig. 2b).…”