Mapping quantitative trait loci (QTL) determining seed-shattering in weedy rice: evolution of seed shattering in weedy rice through de-domestication

Seed shattering is an important trait that distinguishes domesticated plants from their wild and weedy counterparts. This trait is essential for seed harvesting in the production of cereal crops, and therefore has attracted great attention of scientists to study the underlying genetic mechanisms of seed persistence/shattering during crop domestication. To study seed shattering in weedy rice, we analyzed the F-2 offspring derived from artificial crosses between a non-shattering rice variety Minghui86 and a weedy rice accession WD1292 with strong seed shattering. We identified three seed-shattering associated quantitative trait loci (QTL), wd-qsh1, wd-qsh3, and wd-qsh5 located on chromosome-1, -3 and -5, respectively, based on the microsatellite (SSR) variation pattern of the crop-weed F-2 offspring. The wd-qsh3 had the greatest contribution to seed shattering by explaining 31.41 % of the phenotypic variance, and the two remaining QTLs had relatively minor effects on phenotypic variation, ranging from 11.61 to 16.85 %. Comparative analysis indicated that the mapped QTLs (wd-qsh1, wd-qsh3 and wd-qsh5) from this study had no overlaps with any of the previously reported major shattering loci (e.g., SH4, qSH1, sh-h, and SHAT1) identified using a diverse set of rice germplasm, including cultivated, wild, and weedy rice lines. These results suggest that distinct genetic mechanisms should be evolved independently in different weedy rice groups, which allows weedy rice to adapt to the diverse agricultural environments. De-domestication plays a significant role in generating weedy rice without the involvement of wild rice in agro-ecosystems.