Summary: The functional stay‐green trait is a major goal of rice breeding. Here, we cloned OsSCE1a encoding SUMO‐conjugating enzyme from Yuanjiang common wild rice, which simultaneously regulates the functional stay‐green trait and growth duration. Low expression or knocking out OsSCE1a corresponded to increased chlorophyll content, photosynthetic competence, N use efficiency and a shortened growth period without affecting yield. A natural MITE‐transposon insertion/deletion in the OsSCE1a promoter is the functional variation that regulates these traits. OsSCE1a was selected during evolution and shows significant variation between indica and japonica rice. OsNAC2 interacts with the MITE to enhance OsSCE1a expression. Genetic manipulation of OsSCE1a revealed its potential for rice improvement. OsSCE1a‐mediated SUMOylation of OsGS2 suppresses GS (involved in N assimilation) enzyme activity. OsSCE1a also regulates growth duration by SUMOylating the transcription factor such as OsGBP1, which regulates the expression of the key heading gene Ghd7. Our findings shed light on the role of SUMOylation in crops and provide a strategy for increasing agricultural productivity.

Callus browning during tissue culture of indica rice is genotype dependent, thus limiting the application of genetic transformation for editing-assisted breeding and elucidation of gene function. Here, using 124 introgression lines (HCLs) derived from a cross between the indica rice 9311 and Chaling common wild rice and 2059 SNPs for single-point and interval analysis, we identified two major QTLs, qCBT7 on chromosome 7 and qCBT10 on chromosome 10, related to callus browning, explaining 8–13% of callus browning. Moreover, we performed RNA-seq of two introgression lines with low callus browning, HCL183 and HCL232, with Oryza. rufipogon introgression fragments on chromosomes 10 and 7, respectively. Three candidate genes (Os07g0620700, Os10g0361000, and Os10g0456800) with upregulation were identified by combining interval mapping and weighted gene coexpression network analysis using the DEGs. The qRT-PCR results of the three candidate genes were consistent with those of RNA-seq. The differentiation of indica and japonica subspecies Oryza. sativa and Oryza. rufipogon suggests that these candidate genes are possibly unique in Oryza. rufipogon. GO analyses of hub genes revealed that callus browning may be mainly associated with ethylene and hormone signaling pathways. The results lay a foundation for future cloning of qCBT7 or qCBT10 and will improve genetic transformation efficiency in rice.

Background: The genetic transformation of indicarice (Oryza sativa ssp. indica) is limited by its poor in vitro tissue culturability, especially callus browning. Elucidating the common wild rice (Oryza rufipogon Griff.) genes controlling callus browning is a literally fundamental method for improving the tissue culturability of indica rice varieties. Methods and results: In the present study, we used a population of 129 O. rufipogon (Dongxiang common wild rice; DXCWR) introgression lines in the elite cultivar GC2 (Oryza sativa ssp. indica) background and 159 simple sequence repeat (SSR) markers to identify quantitative trait loci (QTLs) associated with callus browning in rice. The callus browning phenotype was evaluated using the indices of the callus browning rate (CBR), callus browning index (CBI), and standard callus browning index (SCBI). Conclusions: We detected 30 QTLs associated with callus browning across the genotypes, which were located on chromosomes 1, 2, 3, 4, 8, 9, and 12. These were repeatedly associated with differences in CBR, CBI, and SCBI. The alleles from DXCWR had an additive effect in reducing callus browning. Especially, we identified new QTLs near RM247 an RM7003 on chromosome 12, indicating the QTLs were unique in DXCWR. Furthermore, we identified six introgression lines with significantly reduced callus browning, which is expected that these lines will be useful materials for the genetic transformation and fine mapping of the culturability trait.

Plant height and grain number are key factors influencing plant architecture and yield. Although a number of genes regulating rice plant height and grain number have been identified, further elucidation of their regulatory mechanisms remains critical for breeding high‐yield rice varieties. In this study, we show that the GRAIN NUMBER AND PLANT HEIGHT 1 ( GNH1 ) gene, which is identical to rice TRYPTOPHAN AMINOTRANSFERASE RELATED 2 ( OsTAR2 ), plays an important role in regulating both rice plant height and grain number. A natural variation located 382 bp upstream of GNH1 impairs the DNA‐binding affinity of the C ₂ H ₂ ‐type transcription factor ZFP36, increasing GNH1 transcript abundance and auxin accumulation in the indica cultivar T5 and ultimately leading to increased plant height and grain number. Haplotype analysis revealed that GNH1 has undergone differentiation between indica and japonica subspecies. Increasing the expression level of GNH1 significantly boosts rice yield in two elite rice varieties: Zhonghua 11 and Jigeng 88. Collectively, these findings not only deepen our understanding of the molecular mechanisms underlying plant architecture and yield regulation but also offer a favorable gene for rice genetic improvement.