Abstract
With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events. To evaluate the performance of 55 K array, we genotyped 593 inbred lines with diverse genetic backgrounds. Compared with the widely-used Illumina® MaizeSNP50 BeadChip, our 55 K array has lower missing and heterozygous rates and more SNPs with lower minor allele frequency (MAF) in tropical maize, facilitating in-depth dissection of rare but possibly valuable variation in tropical germplasm resources. Population structure and genetic diversity analysis revealed that this 55 K array is also quite efficient in resolving heterotic groups and performing fine fingerprinting of germplasm. Therefore, this maize 55 K SNP array is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) for both tropical and temperate maize.
Highlights
Over the past 20 years, diverse genetic markers, such as restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP), have been adopted for assessing the genetic characteristics of populations or germplasm, mapping quantitative trait loci (QTL), and facilitating the selection of breeding materials that bear desired genes/alleles or haplotypes in both plant genetics and breeding programs
To demonstrate the utility of this array in genotyping both temperate and tropical lines, we tested 593 inbred lines with diverse genetic backgrounds. We found that this 55 K array is efficient in resolving heterotic groups and is potentially suitable for germplasm fingerprinting, QTL mapping, and genomewide association study (GWAS) in both tropical and temperate maize populations
The missing rate per sample based ranged from 0.33 to 5.17%, with an average of 1.83%, indicating that majority of our probes are located in the core genome (Hirsch et al 2014) (Supplementary Table S4)
Summary
Over the past 20 years, diverse genetic markers, such as restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP), have been adopted for assessing the genetic characteristics of populations or germplasm, mapping quantitative trait loci (QTL), and facilitating the selection of breeding materials that bear desired genes/alleles or haplotypes in both plant genetics and breeding programs. As the expense and labor costs for genotyping SNPs have decreased dramatically, a variety of SNP genotyping platforms has been widely applied to genetic research and breeding programs. These include multiplex chip-based SNP detection, uniplex SNP genotyping, and sequencing. High marker density is indispensable when conducting high-resolution fingerprinting, large-scale QTL mapping, genome-wide association studies (GWAS), and genome selection (GS). In this case, high-throughput chip-based and sequencing-based platforms are preferred to uniplex SNP genotyping platforms.
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