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 ( Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O . rufipogon . The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here 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 further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results 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 together led to the loss of shattering.

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.

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.