Optimizing DUS testing for Chimonanthus praecox using feature selection based on a genetic algorithm

Reducing costs and shortening the cetyltrimethylammonium bromide (CTAB) method to improve DNA extraction efficiency from wintersweet and some other plants

DNA extraction is a fundamental technique in molecular biology. For Chimonanthus praecox-a winter-flowering tree species-extensive and rapid DNA extraction is necessary to support genetic analyses. Currently, DNA extraction in C. praecox primarily relies on the traditional cetyltrimethylammonium bromide (CTAB) method, which is time-consuming and labor-intensive, hindering large-scale DNA extraction work. In this study, the different steps in the CTAB method are compared and evaluated to optimize the C. praecox leaf DNA extraction process. The water bath duration significantly impacts DNA extraction efficiency; the longer the water bath, the higher the DNA concentration. However, a 10-min water bath is sufficient to yield DNA of ideal concentration and purity. Additionally, a single extraction step is appropriate, with a 10-min precipitation at - 20 °C yielding high-quality DNA. Additionally, the pre-treatment step was modified by using a frozen pipette tip to crush samples directly in a centrifuge tube, reducing operational complexity and minimizing liquid nitrogen and sample consumption. Only 25 mg of sample is required, and high-quality DNA from C. praecox leaves can be extracted within 1 h. The amounts of required sample and liquid nitrogen were reduced by 75% and 90%, respectively. Moreover, the time required for the simplified extraction step was reduced by 77.14%. The applicability of the simplified scheme was evaluated using different C. praecox tissues, Calycanthaceae family members, and species of other families. The simplified scheme extracted DNA from the tepals and leaves of C. praecox with higher concentration purity. However, this protocol was biased toward the Chimonanthus family, Nicotiana tabacum, Populus tomentosa, and Lilium brownii. The proposed method enables the rapid and efficient extraction of high-quality DNA from 25 mg of plant leaves and is suitable for multiple species. This method reduces sample and liquid nitrogen consumption, lowering costs while significantly shortening the procedure time and enhancing extraction efficiency. This method is highly suitable for applications involving the extraction of large amounts of low-concentration DNA across various plant species.

Metabolomic and transcriptomic analyses jointly reveal the mechanism underlying the reddening of Chimonanthus praecox stamens

Introduction

Flower characteristics are crucial ornamental and reproductive traits in Chimonanthus praecox. Over its long cultivation history, variations have been observed in the floral organs, primarily in the petals, with limited reports on stamen traits. Stamen variation, integral to the mating system, can enhance the plant's ornamental value and directly impact its reproductive success.

Methods

This study is the first to report the phenomenon of red coloration in C. praecox stamens. Using UPLC-MS/MS, we analyzed the types and quantities of major metabolites in stamens of different colors.

Results

Our results indicated that the red coloration was primarily due to the accumulation 42 on of high levels of anthocyanins, specifically cyanidin 3-O-rutinoside and cyanidin 3-O-glucoside. Transcriptomic sequencing identified 63 differentially expressed genes (DEGs) related to the anthocyanin biosynthetic pathway, most showing peak expression during the bud stage. The results of the metabolite analysis and transcriptomic sequencing were similar to those of previous studies on petal reddening, suggesting a close relationship between the mechanisms of stamen and petal reddening.

Discussion

This study elucidated the mechanism of stamen reddening in C. praecox, expanding the species' genetic resources and offering insights into color changes across floral tissue..

Establishment of Novel Simple Sequence Repeat (SSR) Markers from Chimonanthus praecox Transcriptome Data and Their Application in the Identification of Varieties

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag-simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.

Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox

Floral color and scent profiles vary across species, geographical locations, and developmental stages. The exclusive floral color and fragrance of Chimonanthus praecox is contributed by a range of endogenous chemicals that distinguish it from other flowers and present amazing ornamental value. This comprehensive review explores the intricate interplay of environmental factors, chemicals and genes shaping the flower color and fragrance of Chimonanthus praecox. Genetic and physiological factors control morpho-anatomical attributes as well as pigment synthesis, while environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Specific genes control pigment synthesis, and environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Physiological processes including plant hormone contribute to flower color and fragrance. Hormones, notably ethylene, exert a profound influence on varioustraits. Pigment investigations have spotlighted specific flavonoids, including kaempferol 3-O-rutinoside, quercetin, and rutin. Red tepals exhibit unique composition with cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside being distinctive components. Elucidating the molecular basis of tepal color variation, particularly in red and yellow varieties, involves the identification of crucial regulatory genes. In conclusion, this review unravels the mysteries of Chimonanthus praecox, providing a holistic understanding of its flower color and fragrance for landscape applications. This comprehensive review uniquely explores the genetic intricacies, chemical and environmental influences that govern the mesmerizing flower color and fragrance of Chimonanthus praecox, providing valuable insights for its landscape applications. This review article is designed for a diverse audience, including plant geneticists, horticulturists, environmental scientists, urban planners, and students, offering understandings into the genetic intricacies, ecological significance, and practical applications of Chimonanthus praecox across various disciplines. Its appeal extends to professionals and enthusiasts interested in plant biology, conservation, and industries dependent on unique floral characteristics.