A QTL GN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice

Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus(QTL), GRAIN NUMBER 1.1(GN1.1), which encodes a Flowering Locus T-like1(FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1^(B),derived from the Oryza indica variety, BF3-104,exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor(Arf)-GTPase-activating protein(Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1^(B)facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport(PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.

OsHAL3, a Blue Light-Responsive Protein, Interacts with the Floral Regulator Hdl to Activate Flowering in Rice

In flowering plants, photoperiodic flowering is controlled by a complicated network. Light is one of the most important environmental stimuli that control the timing of the transition from vegetative growth to reproductive development. Several photoreceptors, including PHYA, PHYB, CRY2, and FKF1 in Arabi- dopsis and their homologs （OsPHYA, OsPHYB, OsPHYC, and OsCRY2） in rice, have been identified to be related to flowering. Our previous study suggests that OsHAL3, a flavin mononucleotide-binding protein, may function as a blue-light sensor. Here, we report the identification of OsHAL3 as a positive regulator of flowering in rice. OsHAL3 overexpression lines exhibited an early flowering phenotype, whereas down- regulation of OsHAL3 expression by RNA interference delayed flowering under an inductive photoperiod （short-day conditions）. The change in flowering time was not accompanied by altered I-Idl expression but rather by reduced accumulation of Hd3a and MADS14 transcripts. OsHAL3 and Hdl colocalized in the nucleus and physically interacted in vivo under the dark, whereas their interaction was inhibited by white or blue light. Moreover, OsHAL3 directly bound to the promoter of Hd3a, especially before dawn. We conclude that OsHAL3, a novel light-responsive protein, plays an essential role in photoperiodic control of flowering time in rice, which is probably mediated by forming a complex with Hdl. Our findings open up new perspectives on the photoperiodic flowering pathway.

Translational Regulation of Plant Response to High Temperature by a Dual-Function tRNAHls Guanylyltransferase in Rice

As sessile organisms,plants have evolved numerous strategies to acclimate to changes in environmental temperature.However,the molecular basis of this acclimation remains largely unclear.In this study we identified a tRNAHis guanylyltransferase,AET1,which contributes to the modification of pre-tRNAH,s and is required for normal growth under high-temperature conditions in rice.Interestingly,AET1 possibly interacts with both RACK1A and elF3h in the endoplasmic reticulum.Notably,AET1 can directly bind to OsARF mRNAs including the uORFs of OsARF19 and OsARF23,indicating that AET1 is associated with translation regulation.Furthermore,polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant,but that the translational efficiency of OsARF19 and OsARF23 is reduced;moreover,OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature,implying that AET1 regulates auxin signaling in response to high temperature.Ourfindings provide new insights into the molecular mechanisms whereby AET1 regulates the environmental temperature response in rice by playing a dual role in tRNA modification and translational control.

Dissecting the Genetic Basis of Extremely Large Grain Shape in Rice Cultivar 'JZ1560'

Rice grain shape, grain length （GL）, width （GW）, thickness （GT） and length-to-width ratio （LWR）, are usually controlled by multiple quantitative trait locus （QTL）. To elucidate the genetic basis of extremely large grain shape, QTL analysis was performed using an F2 population derived from a cross between a japonica cuttivar ＇JZI560＇ （extremely large grain） and a contrasting indica cultivar ＇FAZI＇ （small grain）. A total number of 24 QTLs were detected on seven different chromosomes. QTLs for GL, GW, GT and LWR explained 11.6%, 95.62%, 91.5% and 89.9% of total phenotypic variation, respectively. Many QTLs pleiotropically controlled different grain traits, contributing complex traits correlation. GW2 and qSW5/GW5, which have been cloned previously to control GW, showed similar chromosomal locations with qGW2-1/qGT2-1/qLWR2-2 and qGW5-2/qLWR5-1 and should be the right candidate genes. Plants pyramiding GW2 and qSW5/GW5 showed a significant increase in GW compared with those carrying one of the two major QTLs. Furthermore, no significant QTL interaction was observed between GW2 and qSW5/GW5. These results suggested that GW2 and qSW5/GW5 might work in independent pathways to regulate grain traits. ＇JZ1560＇ alleles underlying all QTLs contributed an increase in GW and GT and the accumulation of additive effects generates the extremely large grain shape in ＇JZ1560＇.

Identification of Quantitative Trait Loci for Lipid Metabolism in Rice Seeds

Plant seed oil is important for human dietary consumption and industrial application. The oil trait is controlled by quantitative trait loci （QTLs）, but no QTLs for fatty acid composition are known in rice, the monocot model plant. QTL analysis was performed using F2 and F2：3 progeny from a cross of an indica variety and a japonica variety. Gas chroma- tography-mass spectrometry （GC-MS） analysis revealed significant differences between parental lines in fatty acid com- position of brown rice oil, and 29 associated QTLs in F2 and/or F2：3 populations were identified throughout the rice genome, except chromosomes 9 and 10. Eight QTLs were repeatedly identified in both populations across different envi- ronments. Five loci pleiotropically controlled different traits, contributing to complex interactions of oil with fatty acids and between fatty acids. Nine rice orthologs of Arabidopsis genes encoding key enzymes in lipid metabolism co-localized with 11 mapped QTLs. A strong QTL for oleic （18：1） and linoleic （18：2） acid were associated with a rice ortholog of a gene encoding acyI-CoA：diacylglycerol acyltransferase （DGAT）, and another for palmitic acid （16：0） mapped similarly to the acyl- ACP thioesterase （FatB） gene ortholog. Our approach rapidly and efficiently identified candidate genes for mapped QTLs controlling fatty acid composition and oil concentration, providing information for improving rice grain quality by marker assisted selection.

Tillering and small grain 1 dominates the tryptophan aminotransferase family required for local auxin biosynthesis in rice

Auxin is a crucial phytohormone,controlling multiple aspects of plant growth and responses to the changing environment.However,the role of local auxin biosynthesis in specific developmental programs remains unknown in crops.This study characterized the rice tillering and small grain 1(tsg1)mutant,which has more tillers but a smaller panicle and grain size resulting from a reduction in endogenous auxin.TSG1 encodes a tryptophan aminotransferase that is allelic to the FISH BONE(FIB)gene.The tsg1 mutant showed hypersensitivity to indole-3-acetic acid and the competitive inhibitor of aminotransferase,L-kynurenine.TSG1 knockout resulted in an increased tiller number but reduction in grain number and size,and decrease in height.Meanwhile,deletion of the TSG1 homologs OsTAR1,Os TARL1,and OsTARL2 caused no obvious changes,although the phenotype of the TSG1/Os TAR1 double mutant was intensified and infertile,suggesting gene redundancy in the rice tryptophan aminotransferase family.Interestingly,TSG1 and Os TAR1,but not Os TARL1 and OsTARL2,displayed marked aminotransferase activity.Meanwhile,subcellular localization was identified as the endoplasmic reticulum,while phylogenetic analysis revealed functional divergence of TSG1 and OsTAR1 from OsTARL1 and OsTARL2.These findings suggest that TSG1 dominates the tryptophan aminotransferase family,playing a prominent role in local auxin biosynthesis in rice.

Anα/βhydrolase family member negatively regulates salt tolerance but promotes flowering through three distinct functions in rice

Ongoing soil salinization drastically threatens crop growth,development,and yield worldwide.It is therefore crucial that we improve salt tolerance in rice by exploiting natural genetic variation.However,many salt-responsive genes confer undesirable phenotypes and therefore cannot be effectively applied to practical agricultural production.In this study,we identified a quantitative trait locus for salt tolerance from the African rice species Oryza glaberrima and named it as Salt Tolerance and Heading Date 1(STH1).We found that STH1 regulates fatty acid metabolic homeostasis,probably by catalyzing the hydrolytic degradation of fatty acids,which contributes to salt tolerance.Meanwhile,we demonstrated that STH1 forms a protein complex with D3 and a vital regulatory factor in salt tolerance,OsHAL3,to regulate the protein abundance of OsHAL3 via the 26S proteasome pathway.Furthermore,we revealed that STH1 also serves as a co-activator with the floral integrator gene Heading date 1 to balance the expression of the florigen gene Heading date 3a under different circumstances,thus coordinating the regulation of salt tolerance and heading date.Notably,the allele of STH1 associated with enhanced salt tolerance and high yield is found in some African rice accessions but barely in Asian cultivars.Introgression of the STH1HP46 allele from African rice into modern rice cultivars is a desirable approach for boosting grain yield under salt stress.Collectively,our discoveries not only provide conceptual advances on the mechanisms of salt tolerance and synergetic regulation between salt tolerance and flowering time but also offer potential strategies to overcome the challenges resulted from increasingly serious soil salinization that many crops are facing.