Insights of Improved Aroma under Additional Nitrogen Application at Booting Stage in Fragrant Rice

Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces

Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length-width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies.

Application of Silicon Influencing Grain Yield and Some Grain Quality Features in Thai Fragrant Rice

Silicon (Si) is a beneficial nutrient that has been shown to increase rice productivity and grain quality. Fragrant rice occupies the high end of the rice market with prices at twice to more than three times those of non-fragrant rice. Thus, this study evaluated the effects of increasing Si on the yield and quality of fragrant rice. Also measured were the content of proline and the expression of the genes associated with 2AP synthesis and Si transport. The fragrant rice varieties were found to differ markedly in the effect of Si on their quality, as measured by the grain 2AP concentration, while there were only slight differences in their yield response to Si. The varieties with low 2AP when the Si supply is limited are represented by either PTT1 or BNM4 with only slight increases in 2AP when Si was increased. Si affects the gene expression levels of the genes associated with 2AP synthesis, and the accumulation of 2AP in fragrant rice mainly occurred through the upregulation of Badh2, DAO, OAT, ProDH, and P5CS genes. The findings suggest that Si is a potential micronutrient that can be utilized for improving 2AP and grain yield in further aromatic rice breeding programs.

Transcription Factor OsbZIP60-like Regulating OsP5CS1 Gene and 2-Acetyl-1-pyrroline (2-AP) Biosynthesis in Aromatic Rice

The most important volatile in determining the aroma of fragrant rice is 2-Acetyl-1-pyrroline (2-AP); however, the transcriptional regulation mechanism of 2-AP biosynthesis in fragrant rice is still unclear. In this study, Osp5cs1 knockout mutant lines and OsP5CS1 over-expression lines were constructed by the genetic transformation of the Indica rice cultivar, i.e., 'Zhonghua11', which knocks out OsBADH2 to produce fragrance in aromatic rice. The OsP5CS1 gene was also identified as a key gene in the 2-AP biosynthesis pathway of aromatic rice. The OsP5CS1 promoter was used as bait, and the OsbZIP60-like transcription factor was screened by yeast one-hybrid assays. The OsbZIP60-like transcription factor specifically bound to the OsP5CS1 gene. The dual luciferase reporting system found that the OsbZIP60-like transcription factor promoted the transcriptional activation of OsP5CS1. Compared with the wild type, OsP5CS1 gene expression was significantly down-regulated in the Osbzip60-like mutant and resulted in a substantial reduction in 2-AP biosynthesis. Moreover, the OsP5CS1 gene expression was significantly up-regulated in OsbZIP60-like over-expressed plants, and the 2-AP concentrations were also increased, whereas the Osbzip60-like mutants were found to be sensitive to Zn deficiency. Overall, the OsbZIP60-like transcription factor promoted the 2-AP accumulation. This study provides a theoretical basis for the transcriptional regulation mechanism of 2-AP biosynthesis and explores the function of the OsbZIP transcription factor in fragrant rice.