Common cultivated rice (Oryza sativa) is known to be domesticated from Asian wild rice (O. rufipogon). A loss of seed shattering is one of the important traits selected during rice domestication. Previously, two major quantitative trait loci (QTLs), qSH1 and sh4, were reported to be involved in a loss of seed shattering of Japonica cultivated rice. In the present study, we produced introgression lines (ILs) carrying O. sativa Japonica Nipponbare alleles at both two loci of qSH1 and sh4 in the genetic background of wild rice O. rufipogon W630, (designated as IL(1+4)), and found that the cultivated alleles at two loci were not sufficient to inhibit abscission layer formation at basal part of seeds of the IL(1+4). An additional shattering QTL named qSH3 was detected by QTL analysis using an F2 population between Nipponbare and the IL(1+4). Although the Nipponbare allele at qSH3 alone had no strong effects on seed shattering, an IL carrying Nipponbare alleles at qSH1, qSH3 and sh4 (namely, IL(1+3+4)) showed significant reduction of seed-shattering degree. These results suggested that coordinated regulation among these three loci is important to explain loss of seed shattering in rice. However, IL(1+3+4) still showed partial abscission layer formation and lower seed-shattering degree than that of Nipponbare. We further produced F2 plants between Nipponbare and the IL(1+3+4) and examined their seed-shattering degree. As a result, normal distribution for seed-shattering degree was observed, indicating that additional loci are still involved in the loss of seed shattering in rice.
