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Background Amomum tsaoko is 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 different A. tsaoko tissues, 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 in A. 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 72 A. tsaoko accessions. 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 six A. tsaoko populations. 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 in A. tsaoko .

Background Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored. Results In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5′ cDNA ends (5′-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development. Conclusions Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

Self-incompatibility (SI) is a reproductive protection mechanism that plants acquired during evolution to prevent self-recession. As the female determinant of SI specificity, SRK has been shown to be the only recognized gene on the stigma and plays important roles in SI response. Asteraceae is the largest family of dicotyledonous plants, many of which exhibit self-incompatibility. However, systematic studies on SRK gene family in Asteraceae are still limited due to lack of high-quality genomic data. In this study, we performed the first systematic genome-wide identification of S -locus receptor like kinases ( SRLKs ) in the self-incompatible Asteraceae species, Erigeron breviscapus , which is also a widely used perennial medicinal plant endemic to China.52 SRLK genes were identified in the E. breviscapus genome. Structural analysis revealed that the EbSRLK proteins in E. breviscapus are conserved. SRLK proteins from E. breviscapus and other SI plants are clustered into 7 clades, and the majority of the EbSRLK proteins are distributed in Clade I. Chromosomal and duplication analyses indicate that 65% of the EbSRLK genes belong to tandem repeats and could be divided into six tandem gene clusters. Gene expression patterns obtained in E. breviscapus multiple-tissue RNA-Seq data revealed differential temporal and spatial features of EbSRLK genes. Among these, two EbSRLK genes having high expression levels in tongue flowers were cloned. Subcellular localization assay demonstrated that both of their fused proteins are localized on the plasma membrane. All these results indicated that EbSRLK genes possibly involved in SI response in E. breviscapus. This comprehensive genome-wide study of the SRLK gene family in E. breviscapus provides valuable information for understanding the mechanism of SSI in Asteraceae.

The MADS-box gene family encodes transcription factors with many biological functions that extensively regulate plant growth, development and reproduction. Erigeron breviscapus is a medicinal herb used widely in traditional Chinese medicine, and is believed to improve blood circulation and ameliorate platelet coagulation. In order to gain a detailed understanding of how transcription factor expression may regulate the growth of this potentially important medicinal plant, a genome-wide analysis of the MADS-box gene family of E. breviscapus is needed. In the present study, 44 MADS-box genes were identified in E. breviscapus and categorized into five subgroups (MIKC, Mα, Mβ, Mγ and Mδ) according to their phylogenetic relationships with the Arabidopsis MADS-box genes. Additionally, the functional domain, subcellular location and motif compositions of the E. breviscapus MADS-box gene products were characterized. The expression levels for each of the E. breviscapus MADS-box (EbMADS) genes were analyzed in flower, leaf, stem and root organs, and showed that the majority of EbMADS genes were expressed in flowers. Meanwhile, some MADS genes were found to express high levels in leaf, stem and root, indicating that the MADS-box genes are involved in various aspects of the physiological and developmental processes of the E. breviscapus. The results from gene expression analysis under different pollination treatments revealed that the MADS-box genes were highly expressed after non-pollinated treatment. To the best of our knowledge, this study describes the first genome-wide analysis of the E. breviscapus MADS-box gene family, and the results provide valuable information for understanding of the classification, cloning and putative functions of the MADS-box family.

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.

Amomum tsao - ko (Zingiberaceae) is a commonly used spice and medicinal plant. Morphological variations exist in the fruits of A. tsao - ko . In this study, we compared the phenotypic traits of fruits collected from nine regions in Yunnan Province, China. Based on the mean square values of fruit weight, number of ridges, seed weight, pericarp thickness, and seed diameter, the fruits of A. tsao - ko in Yunnan were grouped into three categories, corresponding to different regions in Yunnan. A principal component analysis revealed that the number of ridges, number of seeds per fruit, and vertical fruit diameter are the most variable parameters. Considering the genetic improvement potential at the regional level, A. tsao - ko in the regions of Gongshan, Tengchong, Jinping, Lushui, and Pingbian is the most efficient for breeding new cultivars, as the plants growing in these regions have a heavier fruit weight, larger fruit diameter, larger transverse diameter, greater number of ridges, greater seed number per fruit, heavier seed weight, moderate pericarp thickness, and larger seed diameter. Based on the selected area, the nested square analysis showed that the fruit vertical diameter, fruit diameter, and the number of seeds per fruit in the region are greater than the regional mean square, and the differences reached an extremely significant level as well. Thus, these three traits can be selected as genetic materials in this region for breeding.

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.

A novel ultrasound-assisted magnetic solid-phase extraction (UA-MSPE) was developed for the separation/preconcentration of trace amounts of pyrethroids (fenpropathrin, fenvalerate, deltamethrin, and bifenthrin) in Paris polyphylla sample using carbon nanotubes based on Fe3O4 magnetic nanoparticles (Fe3O4@CNT MNPs), and high-performance liquid chromatography-UV is described. High recoveries of pyrethroids were obtained at a low MNPs concentration because sonication enhances the contact chances between magnetic nanoparticles and extractable analytes and promotes the extractability of the MSPE process. After the extraction, the adsorbent can be conveniently separated from the sample solution by an external magnet, and the adsorbed analytes were eluted from magnetic Fe3O4@CNT. The main factors influencing the extraction efficiency including the amount of the MNPs, the extraction time, the pH of sample solution, the sonicating time, and the desorption conditions were studied and optimized. Under the optimized experimental conditions, a good linearity was observed in the range of 1-100.0 ng mL−1 for all the analytes, with the correlation coefficients (r) ranging from 0.9962 to 0.9991. The limits of detection of the four pyrethroids are 0.53, 0.26, 0.47, and 0.67 ng mL−1, respectively. The recoveries of the method were in the range between 85.5% and 93.2%. This method is much faster and more effective than traditional SPE methods, and it is promising for the analysis of pyrethroids residues.

Amomum tsao-ko (Zingiberaceae) is a traditional Chinese medicine and condiment, and an important economic crop in the tropical forest of southwest China. However, few simple sequence repeat (SSR) markers are available in A. tsao-ko , which is hindering genetic research in this species. The aim of this study was to develop and characterize microsatellite markers for A. tsao-ko using restriction-site-associated DNA sequencing. A total of 115,482 microsatellites were identified using MISA software, and 13,411 SSR primer pairs were designed. 100 pairs of SSR primers were selected at random and used to evaluate polymorphisms among 4 A. tsao-ko samples. Finally, 23 pairs of SSR primers with clear bands and obvious polymorphism were selected for genetic diversity analysis of 72 A. tsao-ko accessions. The number of alleles and effective number of alleles per locus ranged from 2 to 6 and from 1.315 to 3.776, respectively. The observed heterozygosity ranged from 0.208 to 0.779, and the expected heterozygosity was from 0.239 to 0.735. The average values of the polymorphic information content were 0.454. Hardy–Weinberg equilibrium (HWE) analysis showed that 10 loci significantly deviated from HWE ( P  < 0.05). The pairwise F ST and genetic distance values revealed low levels of genetic differentiation and high genetic similarity among six A. tsao-ko populations. These microsatellite markers developed will provide a valuable tool for further germplasm characterization, genetic diversity, and breeding studies in A. tsao-ko .

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.