A stepwise route to domesticate rice by controlling seed shattering and panicle shape.

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.

Variations in Grain Traits among Local Rice Varieties Collected More Than Half-Century Ago in Indochinese Countries.

More than half-century ago, local rice varieties were collected from Indochinese countries (Cambodia, Thailand, Laos, and Vietnam). Of these, 162 local varieties were examined for 7 grain-size traits: seed length/width/thickness, brown rice length/width/thickness, and 100-seed weight. Since these traits varied considerably, a survey of functional mutations was performed in the genes related to these traits. In total, 19 markers (12 InDel and 7 dCAPS markers) were used to investigate the mutations at 14 grain-size loci of GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7, and GW8. Significant allele effects were observed with six markers detecting base substitution mutations at GW2 and GS3 and insertion/deletion mutations at GS5, GW5, and GW6a, suggesting that these mutations might have affected the grain trait and caused variation among local varieties in the Indochinese countries. In addition to grain size, the hull color, grain color, and glutinosity were also examined using a survey of loss-of-function mutations at major responsible loci. Most phenotypes were reflected based on functional mutations at these loci. Since the local varieties have wide genetic variation, they are important genetic resources for future rice breeding.

Genetic variation of rice (Oryza sativa L.) germplasm in Cambodia.

Genetic variations of 179 rice (Oryza sativa L.) accessions from Cambodia were clarified based on the analyses for heading date, chromosome components, and blast resistance. The dominant accessions were found in three regions; early heading in North East (NE), medium in Central (CT), and late in South East (SE) along the Mekong River in the investigation at Ishigaki, Japan. In contrast, wide variations were observed in two regions, South West (SW) and North West (NW) located around Tonle Sap Lake. Polymorphism data of SSR markers showed that accessions were classified into Japonica Group (cluster Ib), and Indica Groups (IIa and IIb). In the NW and SW, the accessions of all three clusters were found, but these accessions in NE, CT, and SE, were limited to one or two clusters. Accessions were classified again into two clusters, A1 as having high resistance and A2 as having moderate resistance. Remarkable differences of these frequencies of clusters, A1 and A2, were found in the SE, SW, and NW, and similar with these of the whole accessions were in NE and CT. Rice accessions varied among the five regions, and there was a dramatic difference between the regions along Mekong River and the regions around Tonle Sap Lake.

Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice.

Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa 'Nipponbare' and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9), which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa 'Nipponbare'. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains.

Evaluation of genetic variation among wild rice populations in Cambodia.

A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources.