QTL editing confers opposing yield performance in different rice varieties

Grain yield is one of the most important and complex trait for genetic improvement in crops; it is known to be controlled by a number of genes known as quantitative trait loci（QTLs）. In the past decade, many yield-contributing QTLs have been identified in crops.However, it remains unclear whether those QTLs confer the same yield performance in different genetic backgrounds. Here, we performed CRISPR/Cas_9-mediated QTL editing in five widely-cultivated rice varieties and revealed that the same QTL can have diverse, even opposing, effects on grain yield in different genetic backgrounds.

Chromatin-remodeling factor OsINO80 is involved in regulation of gibberellin biosynthesis and is crucial for rice plant growth and development

The phytohormone gibberellin（GA） plays essential roles in plant growth and development. Here,we report that OsINO80, a conserved ATP-dependent chromatin-remodeling factor in rice（Oryza sativa）, functions in both GA biosynthesis and diverse biological processes. OsINO80-knockdown mutants, derived from either T-DNA insertion or RNA interference, display typical GA-deficient phenotypes, including dwarfism, reduced cell length, late flowering, retarded seed germination and impaired reproductive development. Consistently, transcriptome analyses reveal that OsINO80 knockdown results in downregulation by more than two-fold of over 1,000 genes, including the GA biosynthesis genes CPS_1 and GA_3ox_2, and the dwarf phenotype of OsINO80-knockdown mutants can be rescued by the application of exogenous GA3. Chromatin immunoprecipitation（Ch IP） experiments show that OsINO80 directly binds to the chromatin of CPS1 and GA_3ox_2 loci. Biochemical assays establish that OsINO80 specially interacts with histone variant H_2A.Z and the H_2A.Z enrichments at CPS_1 and GA_3ox_2 are decreased in OsINO80-knockdown mutants. Thus, our study identified a rice chromatin-remodeling factor,OsINO80, and demonstrated that OsINO80 is involved in regulation of the GA biosynthesis pathway and plays critical functions for many aspects of rice plant growth and development.

TSC1 enables plastid development under dark conditions, contributing to rice adaptation to transplantation shock

Since its domestication from wild rice thousands of years ago, rice has been cultivated largely through transplantation. During transplantation from the nursery to the paddy field, rice seedlings experience transplantation shock which affects their physiology and production.However, the mechanisms underlying transplantation shock and rice adaptation to this shock are largely unknown. Here,we isolated a transplant-sensitive chloroplast-deficient（tsc_1）rice mutant that produces albino leaves after transplantation.Blocking light from reaching the juvenile leaves and leaf primordia caused chloroplast deficiencies in transplanted tsc_1 seedlings. TSC_1 encodes a noncanonical adenosine triphosphate-binding cassette（ABC） transporter homologous to At NAP_（14） and is of cyanobacterial origin. We demonstrate that TSC_1 controls plastid development in rice under dark conditions, and functions independently of light signaling.However, light rescued the tsc_1 mutant phenotype in a spectrum-independent manner. TSC_1 was upregulated following transplantation, and modulated the iron and copper levels, thereby regulating prolamellar body formation during the early P_4 stage of leaf development. Therefore, TSC_1 is indispensable for plastid development in the absence of light,and contributes to adaptation to transplantation shock.Our study provides insight into the regulation of plastid development and establishes a framework for improving recovery from transplantation shock in rice.