Understanding and utilizing crop genome diversity via high-resolution genotyping

High-resolution genome analysis technologies provide an unprecedented level of insight into structural diversity across crop genomes. Low-cost discovery of sequence variation has become accessible for all crops since the development of next-generation DNA sequencing technologies, using diverse methods ranging from genome-scale resequencing or skim sequencing, reduced-representation genotyping-by-sequencing, transcriptome sequencing or sequence capture approaches. High-density, high-throughput genotyping arrays generated using the resulting sequence data are today available for the assessment of genomewide single nucleotide polymorphisms in all major crop species. Besides their application in genetic mapping or genomewide association studies for dissection of complex agronomic traits, high-density genotyping arrays are highly suitable for genomic selection strategies. They also enable description of crop diversity at an unprecedented chromosome-scale resolution. Application of population genetics parameters to genomewide diversity data sets enables dissection of linkage disequilibrium to characterize loci underlying selective sweeps. High-throughput genotyping platforms simultaneously open the way for targeted diversity enrichment, allowing rejuvenation of low-diversity chromosome regions in strongly selected breeding pools to potentially reverse the influence of linkage drag. Numerous recent examples are presented which demonstrate the power of next-generation genomics for high-resolution analysis of crop diversity on a subgenomic and chromosomal scale. Such studies give deep insight into the history of crop evolution and selection, while simultaneously identifying novel diversity to improve yield and heterosis.