Seedling establishment is inhibited on media containing high levels (∼6%) of glucose or fructose. Genetic loci that overcome the inhibition of seedling growth on high sugar have been identified using natural variation analysis and mutant selection, providing insight into sugar signaling pathways. In this study, a quantitative trait locus (QTL) analysis was performed for seedling sensitivity to high sugar in a Col/C24 F₂ population of Arabidopsis thaliana. A glucose and fructose-sensing QTL, GSQ11, was mapped through selective genotyping and confirmed in near-isogenic lines in both Col and C24 backgrounds. Allelism tests and transgenic complementation showed that GSQ11 lies within the ANAC060 gene. The Col ANAC060 allele confers sugar insensitivity and was dominant over the sugar-sensitive C24 allele. Genomic and mRNA analyses showed that a single-nucleotide polymorphism (SNP) in Col ANAC060 affects the splicing patterns of ANAC060 such that 20 additional nucleotides are present in the mRNA. The insertion created a stop codon, resulting in a truncated ANAC60 protein lacking the transmembrane domain (TMD) that is present in the C24 ANAC060 protein. The absence of the TMD results in the nuclear localization of ANAC060. The short version of the ANAC060 protein is found in ∼12% of natural Arabidopsis accessions. Glucose induces GSQ11/ANAC060 expression in a process that requires abscisic acid (ABA) signaling. Chromatin immunoprecipitation-qPCR and transient expression analysis showed that ABI4 directly binds to the GSQ11/ANAC060 promoter to activate transcription. Interestingly, Col ANAC060 reduced ABA sensitivity and Glc-induced ABA accumulation, and ABI4 expression was also reduced in Col ANAC060 lines. Thus, the sugar-ABA signaling cascade induces ANAC060 expression, but the truncated Col ANAC060 protein attenuates ABA induction and ABA signaling. This negative feedback from nuclear ANAC060 on ABA signaling results in sugar insensitivity. In plants, sugars function as signaling molecules that control important processes such as photosynthesis, growth, carbon distribution over different organs and the production of storage compounds. Sugar signaling requires the phytohormone abscisic acid (ABA) and the ABA-induced regulatory transcription factor ABI4. In this study, a genetic analysis identified the transcription factor ANAC060 as an important component in establishing sugar sensitivity. It was found that, in natural Arabidopsis thaliana populations, the ANAC060 protein may occur as a long or a short version due to differential ANAC060 mRNA splicing caused by a single-nucleotide polymorphism (SNP). The long ANAC060 protein with an intact transmembrane domain (TMD) is excluded from the nucleus, whereas the short version lacking the TMD is always present in the nucleus, where it regulates gene expression. Functional analyses indicated that Col ANAC060 is involved in a novel negative feedback loop in the sugar-ABA signaling pathway. In this feedback loop model, ABI4 activates ANAC060 expression, but the nuclear presence of Col ANAC060 suppresses Glc-induced ABA accumulation and ABI4 expression, thereby reducing responsiveness to sugar signals.

Chloroplasts are essential for photosynthesis and play critical roles in plant development. In this study, we characterized the temperature-sensitive chlorophyll-deficient rice mutant tcd5, which develops albino leaves at low temperatures (20 °C) and normal green leaves at high temperatures (32 °C). The development of chloroplasts and etioplasts is impaired in tcd5 plants at 20 °C, and the temperature-sensitive period for the albino phenotype is the P4 stage of leaf development. The development of thylakoid membranes is arrested at the mid-P4 stage in tcd5 plants at 20 °C. We performed positional cloning of TCD5 and then complementation and knock-down experiments, and the results showed that the transcript LOC_Os05g34040.1 from the LOC_Os05g34040 gene corresponded to the tcd5 phenotype. TCD5 encodes a conserved plastid-targeted monooxygenase family protein which has not been previously reported associated with a temperature-sensitive albino phenotype in plants. TCD5 is abundantly expressed in young leaves and immature spikes, and low temperatures increased this expression. The transcription of some genes involved in plastid transcription/translation and photosynthesis varied in the tcd5 mutant. Although the phenotype and temperature dependence of the TCD5 orthologous mutant phenotype were different in rice and Arabidopsis, OsTCD5 could rescue the phenotype of the Arabidopsis mutant, suggesting that TCD5 function is conserved between monocots and dicots.

A polysaccharide acetyltransferase family gene plays a pivotal role in cell wall structure and is activated by MYC2-dependent jasmonate signaling, enhancing her

Accumulation of toxic heavy metals and metalloids (THMMs) in crop grain remarkably affects food safety and human health. Reducing the content of THMMs in grain requires the identification and manipulation of the genes regulating their accumulation. This study aimed to determine the genetic variations affecting grain THMM accumulation in rice by using association mapping. We used 276 accessions with 416 K single nucleotide polymorphisms (SNPs) and performed genome-wide association analysis of grain THMM concentrations in rice grown in heavily multi-contaminated farmlands. We detected 22, 17, and 21 quantitative trait loci (QTLs) for grain arsenic, cadmium, and lead concentrations, respectively. Both inter- and intra-subpopulation variants accounted for these QTLs. Most QTLs contained no known THMM-related genes and represented unidentified novel genes. We examined the candidate genes in qGAS1, a QTL for grain arsenic concentration with the best P-value detected for the entire population. We speculated that a transport protein of the multidrug and toxin extrusion family could be the candidate gene for this QTL. Our study suggested that the genetic regulation of grain THMM accumulation is very complex and largely unknown. The QTLs and SNPs identified in this study might help in the identification of new genes regulating THMM accumulation and aid in marker-assisted breeding of rice with low grain THMM content.

Background: Most of the rice varieties are pubescent. However, the presence of trichomes is an undesirable characteristic in rice production because trichomes can cause atmospheric pollution. The use of glabrous rice varieties represents a solution to this problem. Yunnan Nuda Rice, a glabrous cultivar that constitutes approximately 20% of rice germplasms in Yunnan can provide important recourse for breeding of glabrous rice varieties.Results: The “Nuda” phenotype in Yunnan Nuda Rice was found to be controlled by a single recessive allelic gene within the well-characterizedGL-1locus. A high-resolution genetic and physical map was constructed using 1,192 Nuda individuals from the F₂population that was delivered from the cross between the Yunnan Nuda variety HMK and the pubescent TN1 variety. TheNUDA/GL-1gene was mapped to a 28.5 kb region containing six annotated genes based on the Nipponbare genomic sequence. By comparing the sequences and expression patterns of different pubescent and glabrous varieties,LOC_Os05g02730, aWUSCHEL-like homeobox gene (OsWOX3B) was identified as the candidate gene. This hypothesis was confirmed by RNA interference (RNAi) and transgenic complementation. Trichome deficiency in RNAi lines was associated with increased efficiency of grain packaging but did not affect the main agronomic traits.Conclusion: NUDA/GL-1locus encodesOsWOX3Bgene.

Background: Pentatricopeptide repeat (PPR) proteins play essential roles in modulating the expression of organelle genes and have expanded greatly in higher plants. However, molecular mechanisms of most rice PPR genes remain unclear. Results: In this study, a new rice PPR mutant, asl3 (albino seedling lethality3) exhibits an albino lethal phenotype at the seedling stage. This albino phenotype was associated with altered photosynthetic-pigment and chloroplast development. Map-based cloning showed that ASL3 encodes a novel rice PPR protein with 10 tandem PPR motifs, which localizes to the chloroplast. ASL3 showed tissue-specific expression, as it was highly expressed in the chlorenchyma, but expressed at much lower levels in roots and panicles. RNAi of ASL3 confirmed that ASL3 plays an essential role in the early development and chloroplast development in rice. Moreover, expression analysis revealed that the asl3 mutation severely affected the transcriptional levels of important genes associated with plastid translation machinery and photosynthesis, which may impair photosynthesis and finally led to the seedling death in asl3 mutant. These results evidenced the important role of ASL3 in the early development of rice, especially chloroplast development. Conclusions: The ASL3 gene encoded a novel chloroplast-targeted PPR protein with 10 tandem PPR motifs in rice. Disruption of the ASL3 would lead to a defective chloroplast and seedling lethality, and affected expression levels of genes associated with chloroplast development and photosynthesis at early leaf stage of rice.