Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1. We produced backcross recombinant inbred lines having chromosomal segments from IR36 in the genetic background of wild rice, O. rufipogon W630. Histological and quantitative trait loci analyses of abscission layer formation were conducted. In the analysis of quantitative trait loci, a strong peak was observed close to sh4. We, nevertheless, found that some lines showed complete abscission layer formation despite carrying the IR36 allele at sh4, implying that non-shattering of seeds of IR36 could be regulated by the combination of mutations at sh4 and other seed-shattering loci. We also genotyped qSH3, a recently identified seed-shattering locus. Lines that have the IR36 alleles at sh4 and qSH3 showed inhibition of abscission layer formation but the degree of seed shattering was different from that of IR36. On the basis of these results, we estimated that non-shattering of seeds in early rice domestication involved mutations in at least three loci, and these genetic materials produced in this study may help to identify novel seed-shattering loci.

Differences in floral morphologies affect pollination behaviour in many flowering plants. In the genus Oryza, several differences in the size of floral organs are known. In this study, we focused on the differences in the size of floral organs between common cultivated rice, Oryza sativa L. and its wild ancestor, O. rufipogon. We compared floral morphologies between cultivated rice O. sativa cv. Nipponbare and O. rufipogon W630. We first evaluated temporal changes in filament and anther lengths. W630 had longer filaments with rapid elongation within 15 min after spikelet opening. W630 also had longer anthers than Nipponbare, and size of anther was consistent throughout all time examined. We also analysed other six floral traits, and found that W630 had higher stigma and style length, as well as lemma and palea length, but lower lemma and palea width. Quantitative trait locus (QTL) analysis was performed to identify the loci controlling these floral traits, using backcross recombinant inbred lines derived from a cross between Nipponbare and W630. A total of 11 significant QTLs were identified. Of these, two pairs of QTLs for lemma and palea length and one pair for lemma and palea width overlapped, suggesting that common genetic factors may be the reason for the differences in these traits. In addition, we performed QTL analysis for grain size, and found that QTLs for grain size coincided with those for lemma and palea size, indicating that grain size is partly controlled by glume capacity. The QTLs identified in this study will be informative for understanding genetic changes associated with rice domestication.