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Arrays No Longer the Only Game in Town for Agrigenomics

Linda Seaton
| Apr 29, 2013

It used to be that microarrays, particularly Illumina Infinium BeadChips, were the technology to use in deciphering plant and animal genomes. Genotyping arrays forged the foundation of the genomics movement in agriculture, identifying single nucleotide polymorphisms (SNPs) associated with desired phenotypic traits that researchers have used to improve livestock breeding and crop yields. While they are no longer the only solution, arrays remain an excellent fit for screening of large populations where established trait-association and loss of function variants are known and where volume pricing offers a cost per sample that tips the scale toward an array approach. 

The rapid evolution of sequencing technologies is driving the development of lower cost sequencing-based genotyping methods that will enable agrigenomics researchers to study livestock, crops, and biological systems at a level never before possible. Providing a genome-wide view, next-generation genotyping (NGG) methods offer an efficient tool for genotype screening, genetic mapping, purity testing, screening backcross lines, constructing haplotype maps, and performing association mapping and genomic selection. 

The number of NGG methods continues to grow, with each offering the fundamental benefits sequencing provides, including reduced ascertainment bias, identification of variants other than SNPs (small insertions, deletions and microsatellites), and an ability to perform comparative analysis across samples in the absence of a reference genome. From amplicon sequencing to restriction site-associated sequencing (RAD-Seq), these methods are accelerating agricultural research, advancing the development of high-value trait screening methods, and enabling the swift deployment of these applications in the real world.

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