HTPdb and HTPtools: Exploiting maize haplotype-tag polymorphisms for germplasm resource analyses and genomics-informed breeding

Along with rapid advances in high-throughput-sequencing technology, the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research. Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers. In this study, we developed a multiplex molecular marker, the haplotype-tag polymorphism (HTP), that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map. After applying strict filtering criteria, we obtained 6,163 highly polymorphic HTPs, which were evenly distributed in the genome. Furthermore, we developed a genome-wide HTP analysis toolkit, HTPtools, which we used to establish an HTP database (HTPdb) covering the whole genomes of 3,587 maize inbred lines commonly used in breeding. A total of 172,921 non-redundant HTP allelic variations were obtained. Three major HTPtools modules combine seven algorithms (e.g., chain Bayes probability and the heterotic-pattern prediction algorithm) and a new plotting engine named “BCplot” that enables rapid visualization of the background information of multiple backcross groups. HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction. The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping, germplasm resource analyses, and genomics-informed breeding in maize.