Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat

Genotyping-by-sequencing (GBS) provides a large number of markers, but its application for association mapping and genomics-assisted breeding is limited by a large proportion of missing data per marker. For species with a reference genomic sequence, markers can be ordered on the physical map. However, in the absence of reference marker order, the use and imputation of GBS markers is challenging. Population sequencing (POPSEQ) is a methodology that can be used to provide marker context for GBS in wheat. The utility of a POPSEQ-based genetic map as a reference map to create genetically ordered markers on a chromosome for hexaploid wheat was validated by constructing an independent de novo linkage map of GBS markers from a Synthetic W7984 x Opata M85 recombinant inbred line (SynOpRIL) population. The results indicated that there is strong agreement between the independent de novo linkage map and the POPSEQ mapping approach in mapping and ordering GBS markers for hexaploid wheat. Bread wheat (Triticum aestivum L.) is one of the world's most important cereal crops, providing approximately 20% of all calories consumed by humans and serving as a staple food crop for 30% of the human population. Increasing wheat production at the global scale is key to addressing the anticipated future food shortage gap due to global population increase and adverse effects of climate change on crop production. The application of advanced and precise molecular tools is needed to speed the development of new wheat varieties. Next-generation sequencing-based genotyping approaches, such as genotyping-by-sequencing (GBS), have been applied to understand the biological basis of agronomic traits in several plant species and for making selections via whole-genome prediction. Studies on major crop species, including wheat, have indicated that genomic selection has the advantage of reducing the time needed to release new cultivars for production in plant breeding programs. However, a drawback of genotypic data from the GBS platform is often a large proportion of missing data points across samples as genomic DNA fragments are sequenced at low depth. The POPSEQ methodology can be used to map, order, and impute marker data from GBS. This approach was demonstrated using a recombinant inbred line (RIL) population from a cross between Synthetic W7984 and Opata M85. The results showed that the POPSEQ-based genetic map can be used as a reference map to create genetically ordered markers on a chromosome for hexaploid wheat. This approach can be used to provide a high-quality reference map that can be used for QTL mapping for different traits.