Ryo Ishikawa

Upland rice is cultivated in dry and rain-fed fields and is grown primarily in regions with limited water resources. Due to the development of irrigation systems and the comparatively lower yield and eating quality of upland rice relative to paddy rice, its cultivated area has decreased in Japan over the years. However, upland rice is known to carry genes controlling important agricultural traits such as drought tolerance and disease resistance. Therefore, they have a large potential serving as genetic resource to improve modern paddy cultivars. Although upland rice is cross-compatible with most paddy rice and shares a close genetic background, its evolutionary history and introduction pathways into Japan remain unclear. In this study, we employed a core collection of Japanese local upland rice to evaluate two domestication-related traits: seed shattering and awn length. Large variations were observed in the degree of seed shattering and awn length. Genetic analyses at known loci controlling these traits indicated that several upland cultivars may carry unidentified loci explaining their seed shattering and awn length. The Japanese local upland rice core collection represents a valuable genetic resource for elucidating genetic alterations in domestication-related traits and clarifying their introduction into Japan.

Understanding crop population history requires genetic material that predates modern breeding. Here, we analysed historical seeds of rice landraces assembled in Southeast Asia during 1957–1958. Target capture resequencing of coding regions yielded high-quality genomic data from 66 historical accessions (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the previously described major regional structure was recovered. Within the historical collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to the traditional growth seasons (fifth- and tenth-month rice). Notably, the fifth-month rice accessions were assigned to the recently reported Vietnam-I5 cluster. An admixture graph, f-statistics, and qpAdm analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage; however, this relationship was not fully explained by sampled indica, japonica, or aus proxies. Together, these results show that major components of the present-day indica regional structure were already present before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.

SUMMARY: Understanding crop population history requires genetic material that predates modern breeding. In rice ( Oryza sativa ), extant landraces have revealed a broad regional structure within indica , but the historical depth of these patterns remains uncertain. Here, we analyzed a historical collection of rice landraces assembled in Southeast Asia from 1957 to 1958 (henceforth the Hamada collection). Short-read resequencing yielded 66 high-quality historical samples (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica , and the major regional structure previously described for extant landraces was recovered. Within the Hamada collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous mainland Southeast Asian group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to two traditional growth seasons (fifth- and tenth-month rice). The fifth-month rice accessions were assigned to the previously reported distinct Vietnam-I5 cluster, showing that this lineage already existed before modern breeding. Admixture graph, f -statistics, and qpWave analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage with a distinct admixture event that cannot be adequately attributed to sampled indica, japonica , or aus groups. Together, these results show that the present-day regional structure of indica was established before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.

Rice is a staple food for almost half of the world’s population. During domestication from wild rice, the selection of plants with reduced seed shattering enabled efficient harvesting. Further selection for increased grain number improved yield potential. Breeding high-yielding cultivars remains necessary to support the growing world population. Despite success in increasing yield potential, improvements in micronutrient content in rice grains have lagged. Zinc (Zn) is an essential micronutrient for crop productivity and human health. Previously, we reported that reduced seed-setting rate was associated with increased grain Zn concentration, suggesting a trade-off between grain number and Zn concentration. Based on these findings, we investigated the grain Zn concentration in high-yielding rice conferred by Gn1a, a gene involved in the regulation of grain number per panicle. Lower grain Zn concentration was observed in high-yielding plants. However, reducing the seed-setting rate by artificially trimming spikelets at the flowering stage restored grain Zn concentrations in high-yielding plants. Other mineral element concentrations were less affected under high-yielding plants. Our results showed clear trade-off between grain number and Zn concentration, emphasizing the importance of enhancing grain Zn concentrations in breeding programs of high-yielding rice.

Reduced seed shattering is a key yield-improving trait selected during the domestication of the Asian rice, Oryza sativa, from its wild ancestor, O. rufipogon. Three quantitative trait loci, qSH1, sh4, and qSH3, are reported to be involved in the reduced seed-shattering behaviour of cultivated rice. Genotyping surveys of these loci have shown that the sh4 mutation is conserved in all cultivars, whereas the qSH1 mutation is only observed in some japonica cultivars. Furthermore, the qSH3 mutation is observed in indica and japonica cultivars; however, aus cultivars carry a functional allele of wild rice at qSH3, indicating there may be distinct genetic mechanisms in aus for its reduced seed-shattering behaviour independently of qSH1 and qSH3. Through genetic analysis of the segregating populations between an aus cultivar, Kasalath, and wild rice introgression lines carrying the domesticated allele at sh4, we detected three loci associated with the reduced seed-shattering behaviour of Kasalath. Subsequent progeny tests validated their effects on this trait. These findings indicate that there are common and distinct genetic loci governing seed-shattering reduction in rice cultivars, providing novel insights into the complex process of rice domestication. This knowledge may help improve breeding strategies to optimise yield through targeted genetic selection.

Asian rice (Oryza sativa L.) was domesticated from wild rice (O. rufipogon Griff.). During rice domestication, the wild characteristic of seed-shattering behaviour was suppressed, enabling an efficient harvest with increased yield. Rice, a stable food for humans, is one of the most important crops consumed by billions of people, especially in Asian countries. With advances in molecular genetic studies, genes or loci involved in reduced seed shattering via the inhibition of abscission layer formation have been identified. The mutations alone showed no inhibitory effect on abscission layer formation in the wild rice O. rufipogon, but their combination enabled a stepwise change in the degree of seed shattering, which may be associated with advances in harvesting tools. In the early stages of rice domestication, the closed panicle formation and slight inhibition of the abscission layer resulted in complementary effects that increased harvesting efficiency. Furthermore, common and distinct loci were found to contribute to reduced seed shattering in groups of rice cultivars, indicating that mutations at seed-shattering loci are important information for tracing the process of rice domestication.

Japanese apricot (Prunus mume) is an important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricots, usually suffers from scab, a disease caused by Venturia carpophila. However, there have been few reports on the phenotypic variation in scab resistance/susceptibility and the underlying genetic factors. In this study, we investigated the severity of naturally occurring scabs based on fruit lesions in 108 Japanese apricot accessions over four consecutive years. In each year, both resistant and susceptible accessions were observed, and significant annual correlations were detected among the ratios of diseased fruits (Rt; 0.52–0.76) and among the disease severity indices (Sv; 0.55–0.79). We also conducted a genome-wide association study (GWAS) based on exon-targeted resequencing, and significant peaks were detected in the data from 2017 and 2018. The candidate genes involved in disease resistance are located near nine single-nucleotide polymorphisms. These genes may be associated with the susceptibility of ‘Nanko’ lineages to scab. These findings shed light on the phenotypic and genetic profiles of scab resistance in P. mume and will assist future breeding programs with improving scab resistance.

Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of the Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scab results in the development of black spots on the fruit surface, which considerably reduces its commercial value. Despite being an economic concern for Japanese apricot, there have been few reports on the phenotypic variation in scab resistance/susceptibility, the underlying genetic factors, and the development of DNA markers. Therefore, in this study, we performed a comprehensive trait analysis for scab resistance and susceptibility for four years and conducted a genome-wide association study (GWAS) to identify the associated loci. The results showed that significant GWAS peaks were detected in 2017 and 2018. Promising candidate gene encoding domains associated with disease resistance were found at the nine single-nucleotide polymorphisms (SNPs) identified in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on the mechanisms of scab resistance in P. mume and will assist future breeding programs to improve scab resistance in ‘Nanko’ lineages.

Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC₁F₂ population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.