Detection of three novel loci involved in reduced seed-shattering behaviour of an aus rice cultivar, Oryza sativa Kasalath.

Reduced seed shattering is a key yield-improving trait selected during the domestication of the Asian rice, Oryza sativa, from its wild ancestor, O. rufipogon. Three quantitative trait loci, qSH1, sh4, and qSH3, are reported to be involved in the reduced seed-shattering behaviour of cultivated rice. Genotyping surveys of these loci have shown that the sh4 mutation is conserved in all cultivars, whereas the qSH1 mutation is only observed in some japonica cultivars. Furthermore, the qSH3 mutation is observed in indica and japonica cultivars; however, aus cultivars carry a functional allele of wild rice at qSH3, indicating there may be distinct genetic mechanisms in aus for its reduced seed-shattering behaviour independently of qSH1 and qSH3. Through genetic analysis of the segregating populations between an aus cultivar, Kasalath, and wild rice introgression lines carrying the domesticated allele at sh4, we detected three loci associated with the reduced seed-shattering behaviour of Kasalath. Subsequent progeny tests validated their effects on this trait. These findings indicate that there are common and distinct genetic loci governing seed-shattering reduction in rice cultivars, providing novel insights into the complex process of rice domestication. This knowledge may help improve breeding strategies to optimise yield through targeted genetic selection.