A minimal two-amino-acid deletion in SmMYB1 converts an activator into a dominant repressor, reshaping global eggplant anthocyanin pigmentation during domestication.

LsMYB3, an R2R3-MYB repressor without canonical repression motifs, negatively regulates anthocyanin biosynthesis in lettuce.

Anthocyanins contribute to pigmentation, nutritional quality, and stress responses in plants. Although red spines are a characteristic trait of wild lettuce (Lactuca serriola), the genetic basis underlying spine pigmentation remains unclear. Here, we identified LsMYB3, a gene controlling spine color variation in wild lettuce. LsMYB3 encodes an R2R3-MYB transcription factor lacking a canonical repression motif but functioning as a negative regulator of anthocyanin biosynthesis. CRISPR/Cas9-mediated knockout of LsMYB3 enhanced anthocyanin accumulation, whereas overexpression suppressed pigmentation and converted red spines to green. Sequence analysis revealed that the natural Lsmyb3 allele carries a conserved Cys-to-Ser substitution within the R2 domain and a 1-bp deletion causing premature protein truncation, indicating loss of function. Yeast one-hybrid and dual-luciferase assays demonstrated that LsMYB3 directly represses LsDFR, a key anthocyanin biosynthetic gene. Notably, the effects of LsMYB3 disruption were tissue-specific and varied among genetic backgrounds, resulting in increased anthocyanin accumulation in wild lettuce spines and cultivated lettuce leaves. In addition, LsMYB3 physically interacted with the bHLH regulator RLL1, suggesting its involvement in the lettuce MBW regulatory network. Together, our findings identify LsMYB3 as a key negative regulator of anthocyanin biosynthesis and provide new insights into the evolution and diversification of pigmentation traits in lettuce.

CRISPR/Cas12a-mediated allele engineering of SmAPRR2 and SmGLK2 reveals complementary control of fruit peel and flesh chlorophyll pigmentation in eggplant

A multiplex CRISPR/Cas12a system is established in eggplant accession MEL3, representing, to the authors' knowledge, the first application of this nuclease for genome editing in eggplant and demonstrating the potential of Cas12a for functional genomics, allele engineering, and precision breeding in eggplant.

From genome to gene module: decoding the BsAlfin2-BsTT2 regulatory network controlling low temperature-induced anthocyanin biosynthesis in Begonia semperflorens

Begonia semperflorens is an important ornamental plant worldwide, but its practical application is severely limited by low temperature sensitivity. However, the molecular regulatory mechanisms underlying low temperature-induced anthocyanin biosynthesis remain unclear. In this study, we assembled a high-quality chromosome-level B. semperflorens genome. Through genomic and MYB gene family analysis, we identified a key transcription factor BsTT2, which directly binds to the BsDFR promoter and enhances its activity, thereby driving anthocyanin accumulation in B. semperflorens. Furthermore, using BsTT2 as bait, we identified its interacting protein BsAlfin2. Under low temperature-induced reactive oxygen species (ROS) signaling, BsAlfin2 undergoes nuclear translocation and forms a complex with BsTT2, synergistically enhancing the activation of the BsDFR promoter and significantly improving anthocyanin production efficiency. Based on these results, we propose a previously uncharacterized BsAlfin2/BsTT2-BsDFR regulatory module, which reveals a molecular links low-temperature ROS signaling to anthocyanin biosynthesis in B. semperflorens. In summary, this study not only provides chromosome-level genomic resources for B. semperflorens research but also elucidates a key molecular module in low temperature-induced anthocyanin biosynthesis regulatory pathway, laying a theoretical and data foundation for future studies on leaf color improvement and stress resistance breeding in Begonia.

Natural variation in the PmbHLH162 promoter regulates anthocyanin biosynthesis and accumulation in Prunus mume.

Comparative genomics and time-course transcriptomics uncover homoeologous exchange events reshaping glucosinolate metabolism in Brassica napus

Improving glucosinolate (GSL) profiles in rapeseed (Brassica napus)—high in leaves for pathogen resistance but low in seeds for meal quality—is a key breeding goal, yet its genetic basis remains unclear. Here, we present a chromosome-level genome assembly for ZY821, an elite high-GSL variety, generated using long-read sequencing and Hi-C scaffolding. Comparative analysis with the low-GSL variety ZS11 identified three major homoeologous exchange (HE) events and extensive structural variation. Notably, an A09–C09 HE event replaced the low-expression BnaC09.MYB28 allele with the high-expression BnaA09.MYB28 allele, resulting in elevated MYB28s expression and thereby increased GSL accumulation in ZY821, whereas a deletion of BnaA09.MYB28 in ZS11 significantly reduced the expression of multiple putative downstream targets in the GSL biosynthesis pathway, leading to a reduction in GSL content. This mechanism was supported by population-level HE analysis and time-course transcriptomes across 116 RNA-Seq samples. Furthermore, joint differential expression and co-expression network analyses uncovered several novel candidate genes implicated in GSL metabolism. Collectively, our study provides new mechanistic insights into the genetic control of GSL accumulation, with significant implications for breeding optimized GSL profiles.

Strictosidine Synthase-like Gene NMS1 Is Required for Male Fertility in Rice by Regulating Tapetal Degradation

Background: Male sterility is a critical trait for large-scale hybrid rice seed production, yet the genetic and molecular regulatory networks governing tapetal degradation during anther development remain incompletely understood. This study aimed to clone the causal gene underlying a novel rice non-pollen male sterility mutant and elucidate its role in tapetal development and microsporogenesis. Methods: The nms1 (non-pollen male sterility 1) sterile mutant was screened from the ethyl methanesulfonate (EMS)-mutagenized progeny of the elite indica restorer line Shuhui 498 (R498). Map-based cloning and whole-genome resequencing-assisted bulked segregant analysis were used to identify the causal variant. Gene function was verified via cytological observation, genetic complementation testing, RNA sequencing, and quantitative real-time PCR (qRT-PCR) to profile sterility-associated transcriptional changes. Results: Gene mapping identified a T635A single-nucleotide substitution within OsR498G0305626400.01 on chromosome 3, which encodes a strictosidine synthase-like protein. This nucleotide alteration causes a Val212Glu amino acid change and is associated with delayed tapetal degradation and pollen abortion. Transgenic complementation experiments verified that functional NMS1 restores fertility in nms1 mutant plants. Spatiotemporal expression analysis showed predominant NMS1 expression in late-developing spikelets. Furthermore, combined RNA sequencing and qRT-PCR analyses demonstrated that loss of NMS1 function leads to significant transcriptional dysregulation of key regulators of programmed cell death (PCD) in the tapetum (PTC2, TIP2) and pollen wall biosynthesis genes (TIP3, OsMS2). Conclusions: This study demonstrates that NMS1 plays a crucial role in coordinating tapetal degradation and microspore development in rice. The discovered functional SNP of NMS1 provides a novel theoretical foundation and a valuable sterile genetic resource for hybrid rice breeding.