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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.

The Japanese apricot (Prunus mume) is a culturally and economically important fruit tree in East Asia. ‘Nanko’, the primary cultivar of Japanese apricot well known in Japan, usually suffers from scab, a disease caused by Venturia carpophila. Scabs result in the development of black spots on the fruit surface, which considerably reduce their commercial value. Despite being an economic concern, there have been few reports on 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 naturally occurring fruit scab resistance and susceptibility over four years. We also conducted a genome-wide association study (GWAS), and significant peaks were detected in 2017 and 2018. Candidate genes associated with disease resistance were located around the nine single-nucleotide polymorphisms (SNPs) detected in 2017 and 2018. These SNPs were thought to be associated with scab susceptibility of ‘Nanko’ lineages. These findings shed light on phenotypic and genetic profiles of scab resistance in P. mume and will assist future breeding programs to improve 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.

Raman spectroscopy is a powerful method for estimating the molecular structure of a target that can be adapted for biomedical analysis given its non-destructive nature. Inflammatory skin diseases impair the skin’s barrier function and interfere with the patient’s quality of life. There are limited methods for non-invasive and objective assessment of skin inflammation. We examined whether Raman spectroscopy can be used to predict skin inflammation with high sensitivity and specificity when combined with artificial intelligence (AI) analysis. Inflammation was chemically induced in mouse ears, and Raman spectra induced by a 785 nm laser were recorded. A principal component (PC) analysis of the Raman spectra was performed to extract PCs with the highest percentage of variance and to estimate the statistical score. The accuracy in predicting inflammation based on the Raman spectra with or without AI analysis was assessed using receiver operating characteristic (ROC) curves. We observed some typical changes in the Raman spectra upon skin inflammation, which may have resulted from vasodilation and interstitial oedema. The estimated statistical scores based on spectral changes correlated with the histopathological changes in the skin. The ROC curve based on PC2, which appeared to include some spectral features, revealed a maximum accuracy rate of 80.0% with an area under the curve (AUC) of 0.864. The AI analysis improved the accuracy rate to 93.1% with an AUC of 0.972. The current findings demonstrate that the combination of Raman spectroscopy with near-infrared excitation and AI analysis can provide highly accurate information on the pathology of skin inflammation.

Asian rice (Oryza sativa L.) is consumed by more than half of the world’s population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.