AN OPTIMIZED 25K WHEAT GENOTYPING ARRAY FOR GENETIC MAPPING, RELATIONSHIP ANALYSIS AND GENOMIC SELECTION Abstract uri icon

abstract

  • Genotyping arrays are ideal tools for molecular marker analyses within the framework of precision genetic mapping of genes underlying traits of interest and the analysis of genetic relationships. Furthermore, with the spread of Genomic Selection (GS) in the breeding process, costs per sample are an important factor. The earlier GS is used in the breeding process, the higher is the genetic gain per time unit - but this is associated with much larger sample numbers for analysis. We have established a new 25K Illumina wheat genotyping array that is optimally suited for wheat breeding and other genetics analyses. On this array are, firstly, the best and most informative markers from the legacy 90K wheat genotyping array based on selection criteria such as marker data quality, genetic mapping position, and linkage block data. Second, this array contains additional markers from the 35K Wheat Breeders Axiom array that have been selected based on the same criteria and overlap with the 90K array for cross-compatibility. Thirdly, gaps in the genetic and haplotype map have been filled with additional high quality markers from a 135K Axiom array that was designed based on markers identified through sequence capture analysis of a set of wheat lines. Finally, we have also included a large set (>250) of markers that have been reported to be linked to known traits including major phenology traits (Rht, Ppd, Vrn) as well as disease resistance genes, grain quality traits and other potentially interesting wheat breeding traits (e.g. anther extrusion, preharvest sprouting). The analysis of large wheat sample sets with this array indicates that it is highly suitable and costeffective for large scale genotyping within the framework of GS and the genome-wide characterization of worldwide hexaploid wheat and tetraploid Durum breeding material including the testing for important single gene traits. For large sample numbers, this array is comparable in costs to one yield plot in the field and thus can be easily integrated into wheat breeding programs.

publication date

  • July 2019