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Researchers Say New HD Maize SNP Chip Could Be Used for Genomic Selection, GWAS, Population Genetics

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NEW YORK (GenomeWeb) — A research team has developed a high-density SNP genotyping array for genotyping maize. With more than 600,000 markers, the chip is the first of its kind for crop researchers and could provide a new tool for diverse applications, including genomic selection, genome-wide association studies, population genetics, and fine mapping.

The Affymetrix-manufactured SNP chip, called the Axiom Maize Genotyping Array, is described in a new paper in the journal BMC Genomics.

Eva Bauer, one of the corresponding authors on the paper, told BioArray News that the chip was designed through Synbreed, a research consortium focused on plant and animal breeding funded by the German Federal Ministry of Education and Research. Synbreed is coordinated through by Chris-Carolin Schön at the Center of Life and Food Sciences at Technische Universität München where Bauer is a scientist.

According to Bauer, the Synbreed scientists set out to develop a high-density genotyping array in maize because they were both encouraged by the use of such chips in livestock species such as cattle and chicken and not satisfied with the alternative genotyping methods available.

"We worked for a long time using other approaches but we saw the success of animal high-density arrays and thought they might be better for studying maize, which is highly diverse and has a low level of linkage disequilibrium," Bauer said.

The tools currently available on the market did not always meet the Synbreed researchers' needs due to issues related to resolution, according to the researchers.

"Especially for maize with its large genome size and high level of diversity, high marker resolution is desirable," the authors noted in the paper. "In addition, LD decays rapidly in some germplasm ... emphazising the requirement of higher marker densities than so far available on genotyping arrays."

And though genotyping by sequencing remains an "attractive and cost attractive" option for maize research, "there are so many missing values" and a "not so trivial bioinformatics pipeline needed for SNP calling," Bauer noted. "There is so much diversity in maize that we would not feel comfortable working with low coverage GBS data for some applications, such as population genetics."

"We desired to develop an array that would be suited for both American and European material," said Bauer. "With a high-density chip, you don't have to bother with data imputation and missing values."

When asked why no high-density arrays had yet become available for crop studies, though several are available for genotyping livestock, Bauer noted that whole-genome sequencing projects for cattle and chicken, for example, began earlier than those for maize. Indeed, scientists published the draft genome sequence for B73 in Science just five years ago.

Array development

The 616,201 SNPs and indels included on the new maize array were culled from a master set of 57 million obtained by sequencing 30 representative temperate maize lines, according to the paper. These 30 maize inbreds included 17 European Flint lines as well as nine European and four US Dent lines. "The lines represent important founder lines for maize breeding in Europe and the US and have been used in previous studies," the authors wrote.

The researchers then filtered the 57 million variants for sequence quality scores, narrowing them down to an initial set of 1.2 million variants. To identify higher-confidence variants, the researchers genotyped 285 DNA samples using high-density screening arrays containing those 1.2 million variants provided by Affymetrix.

According to the paper, the 285 samples represented a "broad genetic diversity panel" of worldwide maize lines including lines important for European maize breeding and hybrids, such as Dent and Flint, which are widely used in cooler regions in Central Europe. The researchers also genotyped samples with European, US, semi-tropical, and tropical origins, which were used for experimental validation.

The authors wrote in the paper that they selected the final 616,201 variants according to performance during validation, support of genotype calls through sequencing data, and physical distribution. They noted that the chip includes 45,655 SNPs found on the Illumina MaizeSNP50 BeadChip.

Following validation, the authors determined that the chip is "well suited for dissecting the diversity and genetic composition of temperate maize lines," though the performance of the array with regard to the analysis of "tropical material or wild maize relatives" will need further investigation.

They added that the chip should have a "desired density for genome-wide association studies in maize, for which the currently available density of the Illumina MaizeSNP50 BeadChip was shown to "provide limited resolution."

According to Bauer, future applications for the new maize array include genomic selection, genome-wide association studies, population genetics," and, in some cases, fine mapping of genomic regions, and detection of marker-trait associations.

In the paper, the authors state that the chip could also be used to identify pedigree relationships, identity-by-descent regions, and ancestral lineages. Using the chips should enable "high accuracy in imputation of genotypes from genetic material analysed with lower density marker panels."

And, noted Bauer, custom sets of SNPs could be assembled from any genomic region and converted into other SNP assay formats, such as Fluidigm or KASP assays, for fine-mapping, map-based cloning studies, or marker-assisted selection.

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