A Structure Variation in Detrimentally Affects Plant Architecture and Yield in Rice.

Plant height is an important agronomic trait associated with plant architecture and grain yield in rice ( L.). In this study, we report the identification of quantitative trait loci (QTL) for plant height using a chromosomal segment substitution line (CSSL) population with substituted segments from variety Nipponbare (NIP) in the background of the variety 9311. Eight stable QTLs for plant height were identified in three environments. Among them, six loci were co-localized with known genes such as () and () involved in gibberellin biosynthesis. A minor QTL on chromosome 8 was verified and fine-mapped to a 74 kb region. Sequence comparison of the genomic region revealed the presence/absence of a 42 kb insertion between NIP and 9311. This insertion occurred predominantly in temperate rice. Comparisons on the near-isogenic lines showed that the allele from NIP exhibits pleiotropic effects on plant growth, including reduced plant height, leaf length, photosynthetic capacity, delayed heading date, decreased yield, and increased tiller angle. These results indicate that from temperate triggers adverse effects on plant growth and yield when introduced into the rice, highlighting the importance of the inter-subspecies crossing breeding programs.