Bingyue Lu

Amomum tsao-ko is a valuable medicinal and culinary resource, yet its non-volatile terpenoid composition remains poorly characterized. This study integrated widely targeted metabolomics and transcriptomics to systematically profile non-volatile terpenoids in A. tsao-ko fruits and investigate the impacts of fruit morphotype and drying process. Using UPLC-MS/MS, 157 non-volatile terpenoids were identified, with 147 common across all samples, indicating a stable core metabolome. Fruit shape significantly influenced terpenoid accumulation, with round fruits generally exhibiting higher levels, and Caesalpin J identified as a shape-discriminatory marker. Drying induced profound alterations, promoting glycosylated forms while reducing free sesquiterpenoids and diterpenoids. Isosteviol was exclusively detected in dried fruits, serving as a drying-specific marker. Transcriptomic analysis revealed 49 shape-responsive differentially expressed genes enriched in terpenoid biosynthesis pathways. Weighted gene co-expression network analysis identified a terpenoid-associated module containing key structural genes and transcription factors. These findings provide a foundational chemical and molecular atlas for quality assessment, germplasm innovation, and optimized processing of A. tsao-ko .

Amomum tsao-ko is an important aromatic crop used in medicines and food. It can be categorized into three main types based on the fruit shape: long (L), oval (O), and round (R). However, limited information is available on the volatile substances present in differently shaped A. tsao-ko fruits. This study investigated the characteristics and biosynthesis of volatile organic compounds (VOCs) in fresh and dried A. tsao-ko fruits of different shapes using widely targeted volatilomics and transcriptome analyses. In total, 978 VOCs, primarily terpenoids, esters, and heterocyclic compounds, were detected. The number of differentially accumulated volatile organic compounds (DAVOCs) in dried fruits of various shapes was significantly higher than that in fresh fruits, with terpenoids, esters, and heterocyclic compounds accounting for approximately 50% of the total DAVOCs. Notably, α-phellandrene, identified as a shared differential accumulated terpenoid across various fruit shapes, was detected in both fresh and dried fruits. Through transcriptome analysis, 40 candidate genes implicated in the terpenoid biosynthesis pathway were screened. An integrated analysis of the metabolome and transcriptome revealed that the structural genes HMGR-2, TPS7, TPS5-10, TPS21-3, TPS21-5, TPS21-6, TPS21-7, and TPS21-9, along with 81 transcription factors (including 17 NACs, 16 MYBs, 16 AP2/ERFs, 13 WRKYs, 13 bHLHs, and 6 bZIPs), co-regulate the biosynthesis of volatile terpenoids. This study expands our understanding of the volatile metabolism profile of A. tsao-ko and provides a solid foundation for future investigations of the mechanisms governing fruit quality.

The goal of this study was to understand the effect of light intensity on the chlorogenic acid content and biosynthesis-related gene expression in Marsdenia tenacissima. In this study, M. tenacissima plants were treated with different light intensities; the chlorogenic acid content was determined by high-performance liquid chromatography; and transcriptome sequencing was performed. The amount of chlorogenic acid in the control was the highest and differed significantly from that under three different shading treatments. With a decrease in light intensity, the content of chlorogenic acid also showed a decreasing trend. A total of 1149 differentially expressed genes were identified by transcriptome sequencing, and most of the genes were down-regulated under the 90% shading treatment. A weighted gene co-expression network analysis identified the differentially expressed genes associated with light-induced chlorogenic acid biosynthesis. The different shading treatments down-regulated the expression of the chlorogenic acid biosynthesis pathway structural genes (HCTs). The MIKC family genes were the main transcription factors regulating light-induced chlorogenic acid biosynthesis, but the MYB and SBP family genes were also involved. In summary, combined physiological and transcriptome analysis, candidate structural genes, and transcription factors in the biosynthesis pathway of chlorogenic acid were identified in M. tenacissima.

The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon’s information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length–width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)—23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)—43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)—24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)—36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)—26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome.

Background: Amomum tsaokois a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from differentA. tsaokotissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.Results: A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism inA. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72A. tsaokoaccessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the sixA. tsaokopopulations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.Conclusions: Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection inA. tsaoko.

Amomum tsao-ko (Zingiberaceae) is a well-known medicinal and aromatic crop with a long history of cultivation in China. Food and pharmaceutical industries widely use its dried ripe fruit. In this study, 12 promoter anchored amplified polymorphism (PAAP) primer pairs and 12 conserved DNA-derived polymorphism (CDDP) primers were used to assess the genetic diversity and population structure of 96 A. tsao-ko accessions from eight cultivated populations. A total of 98 polymorphic loci were detected by 12 PAAP primers with 8.167 polymorphic loci per primer, and 203 polymorphic loci were observed using 12 CDDP primers with 16.92 alleles per primer. Nei’s gene diversity (PAAP, H = 0.207; CDDP, H = 0.188) and Shannon’s information index (PAAP, I = 0.329; CDDP, I = 0.305) revealed the relatively high level of genetic diversity in these populations of A. tsao-ko. The genetic differentiation coefficient (Gst) for the populations was 0.151 (PAAP) and 0.128 (CDDP), which indicated that 84.9% and 87.2%, respectively, of the genetic variation was within populations. Analysis of molecular variance (AMOVA) also revealed that genetic differentiation of the A. tsao-ko populations mainly occurred within populations (91% variation within populations for both PAAP and CDDP). Genetic identity among the investigated populations was high for PAAP (0.957) and CDDP (0.967). Cluster and principal coordinate analysis (PCoA) grouped the 96 A. tsao-ko accessions into two major groups. Accession classification was consistent with population structure analysis. Overall, these results will be useful for A. tsao-ko germplasm resource characterization, conservation, and utilization.