Leaf color and photosynthesis are important factors for rice growth and development. Hence, improving the photosynthetic rate is an effective approach for increasing rice yield. We isolated a gene, chlorophyllide-a oxygenase 1 (OsCAO1), which characterized a rice near-isogenic line named fgl (faded green leaf). Compared with its recurrent parent, Zhefu 802 (ZF802, an early-season indica rice variety), fgl had a faded green leaf color and lower chlorophyll (Chl) content, especially Chl b content. Furthermore, genetic and physiological analysis confirmed that leaf color was affected by the novel allele OsCAO1, which had a two-base pair deletion in the ninth exon. Subsequently, we over-expressed the OsCAO1 gene in ZF802. Interestingly, while OsCAO1 over-expression (OX) increased Chl b synthesis, the OX plants had a higher photosynthetic rate and heavier 1000-grain weight than ZF802. In conclusion, the novel allele OsCAO1 was involved in the positive regulation of leaf color, photosynthetic rate and rice yield.

Rice quality is influenced by many factors, viz., temperature, humidity, atmosphere and storage time. To uncover quality variations of rice after postharvest, we estimated the physicochemical properties and volatile compounds of an indica rice Zhongzheyou 8 under granary conditions (20 ºC–25 ºC in summer and 10 ºC–15 ºC in other seasons) for three years. During three-year storage, head rice rate and brown rice rate decreased from 67.02% to 61.00% and from 75.62% to 69.74%, respectively, while fissure rate increased from 4.67% to 12.33%, and the yellow rice rate grew from 0.21% to 1.58%. Increased water absorption, hardness, gumminess and chewiness, and decreased pH exhibited the degradation of rice quality in cooking and texture properties after three-year storage. Rice yellowing happened in the first year, and became stronger as time elapsed. Meanwhile, the expansion rate also gradually increased during storage. By the gas chromatography-ion mobility spectrometry (GC-IMS), aldehydes and ketones of main volatile organic compounds (VOCs) significantly increased after three-year storage, which indicated rice oxidation level aggravated. The results revealed that rice quality decline was inevitable during storage even under an appropriate condition. To get the good rice quality, rice should be kept at low or quasi low temperature, and the best storage time was within one year.

Recombinase polymerase amplification (RPA) has been emerged as an alternative to PCR due to its high specificity and sensitivity in diagnostics of animal and plant pathogens. In this study, an RPA protocol was developed and validated for detection of aroma gene in rice. We considered the functional nucleotide polymorphism (FNP) with 8 bp deletion and three single nucleotide polymorphisms (SNPs) in exon 7 of the gene Betaine Aldehyde Dehydrogenase 2 (BADH2) on chromosome 8, the key factor of fragrance in rice. Out of four designed markers, one dominant marker (Aro-RPA F1/R1) in coupling phase was identified by the RPA assay for successful differentiation between aromatic and non-aromatic rice varieties. The developed assay was highly specific and sensitive in detecting the functional mutation both from diverse aromatic rice germplasm as well as from the hybrid plants of an aromatic and non-aromatic cross (Pusa Basmati 1 × Sahbhagi Dhan). Additionally, the RPA assay was also able to detect the 8 bp-FNP from the crude leaf extracts at a dilution up to 10^-7. The time and cost involved in performing RPA were considerably lower than the conventional PCR based method. RPA can be easily done within 1 h with a minimum laboratory set up. Therefore, the developed assay can be utilized for a rapid screening of rice germplasm for the aroma gene to select parents in aromatic rice breeding programme and rice varieties by the seed industries.

Nitrogen (N) and potassium (K) are essential elements for rice growth. When N and K are in deficient rice, specific symptoms appear on the leaves that are similar and difficult to distinguish with the naked eye. To identify the category and degree of N and K nutrient stress in rice leaves as early as possible, we investigated two convolutional neural networks (CNNs) by scanned rice leaf images under nine nutrient stress degrees, including four different degrees of N stress [the concentration of N1 to N4 as 0, 28.6, 57.2 and 85.7 mg/L, respectively, with the concentration of K (K₂SO₄) as 89.3 mg/L], and four different degrees of K stress [the concentration of K1 to K4 as 0, 22.3, 44.7 and 67.0 mg/L, respectively, with the concentration of N (NH₄NO₃) as 114.3 mg/L], as well as a control group [CK, with the concentration of N (NH₄NO₃) as 114.3 mg/L and K (K₂SO₄) as 89.3 mg/L] under a normal condition. We chose the advanced EfficientNet-B0 model and the widely used Inception-V3 model, which are first trained separately by transfer learning, and then fused to form EVI (EfficientNet-V3 Integration) model to obtain more accurate results. In this study, the classification effects of the models were compared before and after transfer learning, and the effects of the two models after using transfer learning were also compared with the effects of EVI fusion model separately. The results proved that the use of transfer learning was effective, and the EVI model obtained a good accuracy of 97.1% on the category of rice leaf nutrient stress, which was 3.7% and 1.5% better than the Inception-V3 and EfficientNet-B0 models, and a good accuracy of 94.0% on the degree of rice leaf nutrient stress, which was 3.3% and 1.1% better than the Inception-V3 and EfficientNet-B0 models, respectively, effectively identifying the category and degree of nutrient stress in rice leaves.

The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD.

Peptide transport is important for plant tissues where rapid proteolysis occurs, especially during germination and senescence, to enhance redistribution of organic nitrogen (N). However, the biological role of peptide transporters is poorly investigated in rice. We characterized the function of the peptide transporter OsNPF8.1 of rice nitrate transporter 1/peptide transporter family (NPF). Ectopic expression of OsNPF8.1 in yeast revealed that OsNPF8.1 encoded a high-affinity di-/tri-peptide transporter, and the osnpf8.1 mutants had a lower uptake rate of the fluorescent-labelled dipeptide c in leaves of rice seedlings. Histochemical assays showed that OsNPF8.1 was highly expressed in mesophyll cells and vascular parenchyma cells, but not detected in root hairs and epidermises. Expression of OsNPF8.1 was induced by N deficiency, drought, NaCl and abscisic acid, and kept at a high level in senescing leaves. Under N deficiency conditions, compared with the wild type Zhonghua 11, the osnpf8.1 mutants grew slower at the seedling stage, and had lower grain yield and lower N content in the grains. In contrast, OsNPF8.1-over-expressing rice (OsNPF8.1-OE) grew faster at the seedling stage and had a higher grain yield. The osnpf8.1 seedlings were less tolerant to salt and drought stresses. These results suggested that stress-induced organic N transportation mediated by OsNPF8.1 might contribute to balance plant growth and tolerate to salt/drought stress and N-deficiency.

Zinc (Zn) is an essential mineral element for plant growth and development. Zn deficiency in crops frequently occurs in many types of soils. It is therefore crucial to identify genetic resources linking Zn acquisition traits and development of crops with improved Zn-use efficiency for sustainable crop production. In this study, we functionally identified a rice uncharacterized ABCG (ATP-binding cassette G-subfamily) gene encoding a PDR20 (pleiotropic drug resistance 20) metal transporter for mediation of rice growth, seed development and Zn accumulation. OsPDR20 was localized to the plasma membrane, but it was not transcriptionally induced under Zn deficiency, rather was sufficiently up-regulated under high level of Zn stress. Yeast (Saccharomyces cerevisiae) transformed with OsPDR20 displayed a relatively lower Zn accumulation with attenuated cellular growth, suggesting that OsPDR20 had an activity for Zn transport. Knocking-down OsPDR20 by RNA interference (RNAi) compromised rice growth with shorter plant height and decreased biomass in rice plantlets grown under hydroponic media. Zn concentration in the roots of OsPDR20 knocked-down rice lines declined under Zn deficiency, while they remained unchanged compared with the wild type under normal Zn supply. A rice lifelong field trial demonstrated that OsPDR20 mutation impaired the capacity of seed development, with shortened panicle and seed length, compromised spikelet fertility, and reduced grain number per plant or grain weight per unit area. Interestingly, OsPDR20 mutation elevated the accumulation of Zn in husk and brown rice over the wild type. Overall, this study pointed out that OsPDR20 is fundamentally required for rice growth and seed development through Zn transport and homeostasis.

Phosphorus (P) starvation in rice facilitates the reutilization of root cell wall P by enhancing the pectin content. NaCl modulates pectin content, however, it is still unknown whether NaCl is also involved in the process of pectin regulated cell wall P remobilization in rice under P starved conditions. In this study, we found that 10 mmol/L NaCl increased the shoot and root biomasses under P deficiency to a remarkable extent, in company with the elevated shoot and root soluble P contents in rice. Further analysis indicated that exogenous NaCl enhanced the root cell wall P mobilization by increasing the pectin methylesterase activity and uronic acid content in pectin suggesting the involvement of NaCl in the process of cell wall P reutilization in P starved rice roots. Additionally, exogenous NaCl up-regulated the expression of P transporter OsPT6, which was induced by P deficiency, suggesting that NaCl also facilitated the P translocation prominently from root to shoot in P starved rice. Moreover, exogenous abscisic acid (ABA) can reverse the NaCl-mediated mitigation under P deficiency, indicating the involvement of ABA in the NaCl regulated root cell wall P reutilization. Taken together, our results demonstrated that NaCl can activate the reutilization of root cell wall P in P starved rice, which is dependent on the ABA accumulation pathway.

Rice production generates a significant amount of agricultural waste. This study aimed to give results related to the existence of antioxidant phenols in agricultural waste of selected Northern Thai rice varieties. The antioxidant activities, contents of total flavonoids and phenolic compounds in the ethanolic rice husk extract were evaluated. The highest antioxidant activities were found in the variety PES1CMU, with 2,2ʹ-azinobis-3-ethyl-benzothiazoline-6-sulfonic acid and 2,2-diphenyl-1-picrylhydrazyl as 679.66 and 4.16 mmol/(L·g) trolox equivalent, respectively, ferric reducing antioxidant power as 0.87 mmol/(L·g) Fe²⁺, total phenolic content as 29.90 mmol/(L·g) gallic acid and total flavonoid content as 12.16 mg/g catechin equivalent. Polyphenol compounds were identified mainly by standard polyphenols using the liquid chromatography mass spectrometry, with the highest contents of phytic acid, o-coumaric acid, naringin and kaempferol. The non-glutenous and wetland ecotypes of rice husk samples were the richest in antioxidant activities and polyphenol contents characterized by using principal component analysis. The glutenous rice husk contained higher antioxidant activities than the rest. Interestingly, quercetin is a significant phenolic compound that positively correlated with the overall antioxidant activities of rice husk. This finding will be relevant for future application of rice husk antioxidant components in the production of functional ingredients as well as for the food and pharmaceutical industries.

Despite increasing knowledge of barnyardgrass (Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota.