Strawberry (Fragaria × ananassa) is a heterozygous octoploid species comprising four sets of homologous chromosomes, which renders the identification of genomic regions associated with breeding traits challenging and obstructs the efficient selection of superior individuals using DNA markers. In this study, the polyploid QTL-seq method, developed for polyploid crops, was employed to investigate the feasibility of identifying quantitative trait loci (QTL) and developing DNA markers related to fruit flesh color and flowering day. In heterozygous polyploid crops, genetic analysis must distinguish between homologous chromosomes that exhibit extremely high sequence similarity. By extracting biallelic polymorphisms with a mapping depth exceeding 40 and an SNP index ranging from 0.40 to 0.64 after short-read mapping, polymorphisms uniquely retained by each homologous chromosome for QTL analysis were selectively utilized. In the F₁ generation resulting from the cross between the red-fleshed variety ‘Sachinoka’ and the white-fleshed variety ‘Koiminori’, individuals displaying a diverse spectrum of fruit flesh colors from white to red were observed. Using the reference genome sequence of ‘Koiminori’, three QTLs associated with red fruit flesh color (derived from “Sachinoka” on chr1-4 and chr2-3, and from ‘Koiminori’ on chr6-2) were identified. By selecting individuals that retained all three DNA markers, a high selection frequency of 92% for red-fleshed individuals was achieved. Conversely, in the F₁ generation from the cross between the early-maturing variety ‘Kaorino’ and the late-maturing variety ‘Koiminori’, individuals exhibiting varied flowering days emerged. Similarly, through the application of this method, an early-maturity QTL (from ‘Kaorino’ on chr2-3) and a de-maturity QTL that alleviates early-maturity effects (from ‘Koiminori’ on chr3-1) were identified. By selecting individuals that retained the DNA marker for the former QTL while lacking the marker for the latter QTL, a selection frequency of 90% for early-maturing individuals was attained. Thus, our findings demonstrate that rapid QTL identification and DNA marker development using the polyploid QTL-seq method are indeed feasible in heterozygous polyploid crops.

Genomic information is inherently large and complex, making it difficult to understand the big picture based on polymorphism data alone. We have developed “Genome Painting”, a Python and R-based visualization method, to address this issue. This tool compares the genomes of two rice varieties to the ‘Nipponbare’ reference genome, representing the twelve chromosomes as rectangles and polymorphisms as colored lines. The method uses VCF (Variant Call Format) files to visualize and compare polymorphisms between specific varieties. This tool enabled more accurate identification of substitution regions containing target genes and residual genetic background in near-isogenic lines. By comparing visualizations between pedigrees, it facilitated the understanding of gene and genetic region transfer. It also enabled the discovery of new correlations and relationships by analyzing genomic relationships between varieties. This comprehensive visualization approach improves the accessibility of whole genome data for rice breeders in the selection and variety evaluation processes. It also provides rice geneticists and molecular biologists with a tool to better understand and interpret complex genomic information. “Genome Painting” thus bridges the gap between complex genomic data and its practical application in rice breeding and research.

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.

The bread-making quality of wheat flour relies on a high grain protein content. High-protein bread wheat is used also in soy sauce brewing. Since the quality of soy sauce is greatly influenced by the content of proteins, which contributes to the umami taste, high-protein wheat is a crucial raw material. There is a demand for brewing cultivars in western Japan with the following critical traits: preharvest sprouting resistance, lodging resistance, disease resistance, and winter habit. The Western Region Agricultural Research Center, NARO, developed a new hard winter wheat cultivar, ‘Tatsukirari’, which has good adaptability and a high protein content, and is suitable for both bread-making and soy sauce brewing. ‘Tatsukirari’ is a standard amylose-type wheat. Its winter habit limits the risk of frost damage to young panicles in early spring. Its short culm provides strong resistance to lodging. And it has a higher grain protein content and stronger dough properties, resulting in better bread-making quality, than ‘Setokirara’, a cultivar widely grown in western Japan. Its suitability for soy sauce brewing is comparable to that of ‘Yumechikara’, a late-maturing cultivar grown for brewing in Hyogo Prefecture, and ‘Tatsukirari’ has been identified as suitable for brewing light soy sauce. The cultivation of ‘Tatsukirari’ in Hyogo Prefecture and surrounding areas as a bread and brewing cultivar will support regional industries such as the production of light soy sauce.