Development of a haplotype visualization method for modern rice cultivars

Abstract

In crop breeding, new cultivars are created by combining new chromosome blocks of parental cultivars. Visualization of these haplotype block combinations as haplotypes can provide important information for selecting breeding combinations. In this study, we defined haplotypes of chromosome blocks using genome sequence information of 147 modern rice cultivars and lines developed in Japan and created a haplotype visualization tool to confirm the transmission of chromosome blocks from ancestral cultivars as images based on genealogical information. Based on single nucleotide polymorphism (SNP) data, we defined the haplotype of the high-yielding cultivar ‘Akidawara’ and identified the differences between it and 147 other cultivars and lines. Furthermore, based on the haplotype variations among the cultivars and lines in the ‘Akidawara’ lineage, we were able to clarify the flow of chromosome block transmission from the ancestral cultivars and clearly distinguish the different chromosome blocks of Japonica-type cultivars in the lineage. The comparison of haplotype blocks also enabled us to estimate the position of chromosome recombination between the most recent parental cultivars. This visualization method is expected to provide important information for selecting breeding material and planning crosses and to contribute to the development of new cultivars and lines.