Abstract
Achieving increased grain productivity has long been the overriding focus of cereal breeding programs. The ideotype approach has been used to improve rice yield potential at the International Rice Research Institute and in China. However, the genetic basis of yield-related traits in rice remains unclear. Here, we show that a major quantitative trait locus, qNPT1, acts through the determination of a 'new plant type' (NPT) architecture characterized by fewer tillers, sturdier culms and larger panicles, and it encodes a deubiquitinating enzyme with homology to human OTUB1. Downregulation of OsOTUB1 enhances meristematic activity, resulting in reduced tiller number, increased grain number, enhanced grain weight and a consequent increase in grain yield in rice. Unlike human OTUB1, OsOTUB1 can cleave both K48- and K63-linked polyubiquitin. OsOTUB1 interacts with the E2 ubiquitin-conjugating protein OsUBC13 and the squamosa promoter-binding protein-like transcription factor OsSPL14. OsOTUB1 and OsSPL14 share common target genes, and their physical interaction limits K63-linked ubiquitination (K63Ub) of OsSPL14, which in turn promotes K48Ub-dependent proteasomal degradation of OsSPL14. Conversely, loss-of-function of OsOTUB1 is correlated with the accumulation of high levels of OsSPL14, resulting in the NPT architecture. We also demonstrated that pyramiding of high-yielding npt1 and dep1-1 alleles provides a new strategy for increasing rice yield potential above what is currently achievable.
Highlights
Rice feeds more than half the world’s population, and improving the productivity of this grain is necessary for food security
The candidate gene is predicted to encode a deubiquitinating enzyme with homology to human ovarian tumor domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) (Supplementary information, Figure S1), a protein associated with the regulation of p53 stability and DNA damage repair [20,21,22,23]
We found that the presence of either the npt1 or OsSPL14WFP allele was associated with the formation of the new plant type’ (NPT) architecture, whereas the phenotypes of ZH11-npt1 plants in which OsSPL14 had been silenced by RNAi were similar to those of ZH11 plants (Figure 7C-7H)
Summary
Rice feeds more than half the world’s population, and improving the productivity of this grain is necessary for food security. The molecular mechanisms underlying how other QTLs regulate grain yield remain largely unknown. The identification of alleles improving grain productivity would facilitate the breeding of new high-yield rice varieties and may be applicable to other crops. Previous studies have shown that K63-linked ubiquitination and deubiquitination are critical post-translational regulatory mechanisms for the recruitment of repair proteins to sites of DNA double-strand breaks [20, 21]. Recent structural and biochemical analyses have elucidated the mechanism underlying the inhibition of UBC13 and other E2 enzymes by OTUB1 [21], but the molecular mechanisms driving the interplay between K48- and K63-linked deubiquitination by OTUB1 have not been completely explained
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