Pepper is an important condiment, and its aroma affects its commercial value. In this study, transcriptome sequencing and combined headspace solid-phase microextraction and gas chromatography–mass spectrometry (HS-SPME-GC-MS) were used to analyze the differentially expressed genes and volatile organic compounds in spicy and non-spicy pepper fruits. Compared with non-spicy fruits, there were 27 up-regulated volatile organic compounds (VOCs) and 3353 up-regulated genes (Up-DEGs) in spicy fruits. The results of KEGG enrichment analysis of the Up-DEGs combined with differential VOCs analysis showed that fatty acid biosynthesis and terpenoid biosynthesis may be the main metabolic pathways for aroma differences between non-spicy and spicy pepper fruits. The expression levels of the fatty acid biosynthesis-related genes FAD, LOX1, LOX5, HPL, and ADH and the key terpene synthesis gene TPS in spicy pepper fruits were significantly higher than those in non-spicy pepper fruits. The differential expression of these genes may be the reason for the different aroma. The results can provide reference for the development and utilization of high-aroma pepper germplasm resources and the breeding of new varieties.

Capsicum annuum L. is extensively cultivated in subtropical and temperate regions globally, respectively, when grown in a medium with 8 holding significant economic importance. Despite the availability of genome sequences and editing tools, gene editing in peppers is limited by the lack of a stable regeneration and transformation method. This study assessed regeneration and transformation protocols in seven chili pepper varieties, including CM334, Zunla-1, Zhongjiao6 (ZJ6), 0818, 0819, 297, and 348, in order to enhance genetic improvement efforts. Several explants, media compositions, and hormonal combinations were systematically evaluated to optimize the in vitro regeneration process across different chili pepper varieties. The optimal concentrations for shoot formation, shoot elongation, and rooting in regeneration experiments were determined as 5 mg/L of 6-Benzylaminopurine (BAP) with 5 mg/L of silver nitrate (AgNO₃), 0.5 mg/L of Gibberellic acid (GA₃), and 1 mg/L of Indole-3-butyric acid (IBA), respectively. The highest regeneration rate of 41% was observed from CM334 cotyledon explants. Transformation optimization established 300 mg/L of cefotaxime for bacterial control, with a 72-h co-cultivation period at OD₆₀₀ = 0.1. This study optimizes the protocols for chili pepper regeneration and transformation, thereby contributing to genetic improvement efforts.

Capsicum frutescens (C. frutescens) has rich germplasm resources, but there have been no reports on its genetic diversity analysis alone using simplified genome sequencing technology (GBS). To provide a basis for the breeding of new pepper varieties and the later development of C. frutescens SNP molecular markers, this study used GBS technology to sequence 65 collected pepper germplasm resources. A total of 1,399,391 SNP sites were obtained by GBS simplified genome sequencing, and there were 1,465,897 SNP variant sites. Through population genetic structure analysis, the population structure and phylogenetic tree of 65 C. frutescens germplasms were constructed. The GBS method is also suitable for the genetic relationship analysis of C. frutescens, and it also shows that there is an obvious separation of materials from different origins, and there is also a certain degree of genetic exchange. Most of C. frutescens varieties from Fujian Province and its surrounding areas are clustered together; C. frutescens varieties from western China are also clustered together. We selected T62 and T60 with a genetic distance of 0.2796 and a spiciness level of nine as the female and male parent combinations, respectively, and bred a new high-yield C. frutescens combination, ‘Mingjiao 308’. C. frutescens varieties from the same geographical origin are usually clustered together. These germplasms may contain the ancestry of multiple varieties. This result can also provide basic data for the later construction of an SNP fingerprint database.

Lotus seeds, which are renowned for their unique flavor and medicinal value, have become an important economic crop. Determining the optimal harvesting period is crucial for obtaining high-quality lotus seeds. From the perspectives of appearance and nutritional composition, we described the variations in lotus seeds “Jianxuan 30” during different developmental stages. Furthermore, we employed headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS–SPME–GC–MS) and a transcriptomic analysis to identify the characteristic volatile metabolites and differentially expressed genes in mature lotus seeds. Our findings revealed that the morphological development of lotus seeds is not synchronized with the accumulation of nutrients. During the 15–20-day developmental period, although the rate of morphological change slows, the contents and weights of nutrients increase rapidly. Upon maturation, hexadecanoic acid methyl ester, 1-butanol, 3-methylbutanal, and methylparinarate are released, and their biosynthesis is attributed to the transcriptional activation of lipoxygenase (LOX), alcohol dehydrogenase (ADH), and aldehyde dehydrogenase (ALDH). Consequently, relying on visual appearance to assess the ripeness of lotus seeds is inaccurate. We elucidated the key volatile metabolites produced during the maturation of lotus seeds and the marker genes that promote their biosynthesis, laying a molecular foundation for future applications of Odor scanner to determine the optimal harvesting period for lotus seeds.