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Abstract Background The brown planthopper (BPH) is an economically significant pest of rice. Bph3 is a key BPH resistance gene. However, the proteomic response of rice to BPH infestation, both in the presence and absence of Bph3, remains largely unexplored. Results In this study, we employed tandem mass tag labeling in conjunction with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins (DEPs) in rice samples. We detected 265 and 125 DEPs via comparison of samples infected with BPH for 2 and 4 days with untreated samples of the BPH-sensitive line R582. For the Bph3 introgression line R373, we identified 29 and 94 DEPs in the same comparisons. Bioinformatic analysis revealed that Bph3 significantly influences the abundance of proteins associated with metabolic pathways, secondary metabolite biosynthesis, microbial metabolism in diverse environments, and phenylpropanoid biosynthesis. Moreover, Bph3 regulates the activity of proteins involved in the calcium signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signal transduction. Conclusions Our results indicate that Bph3 enhances the resistance of rice to BPH mainly by inhibiting the down-regulation of proteins associated with metabolic pathways; calcium signaling, the MAPK signaling pathway, and plant hormone signal transduction might also be involved in BPH resistance induced by Bph3.

Abstract Maize (Zea mays L.), a staple food and significant economic crop, is enriched with riboflavin, micronutrients and other compounds that are beneficial for human health. As emphasis on the nutritional quality of crops increases maize research has expanded to focus on both yield and quality. This study exploreed the genetic factors influencing micronutrient levels in maize kernels through a comprehensive genome-wide association study (GWAS). We utilized a diverse panel of 244 inbred maize lines and approximately 3 million single nucleotide polymorphisms (SNPs) to investigate the accumulation of essential and trace elements including cadmium (Cd), cobalt (Co), copper (Cu), nickel (Ni), selenium (Se) and zinc (Zn). Our analysis identified 842 quantitative trait loci (QTLs), with 12 QTLs shared across multiple elements and pinpointed 524 potential genes within a 100 kb radius of these QTLs. Notably ZmHMA3 has emerged as a key candidate gene previously reported to influence the Cd accumulation. We highlighted ten pivotal genes associated with trace element transport including those encoding heavy metal ATPases, MYB transcription factors, ABC transporters and other crucial proteins involved in metal handling. Additionally, haplotype analysis revealed that eight inbred linesaccumulated relatively high levels of beneficial elements while harmful elements were minimized. These findings elucidate the genetic mechanisms underlying trace element accumulation in maize kernels and provide a foundation for the breeding of nutritionally enhanced maize varieties.

Abstract Background Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene expression vital for the growth and development of plants. Despite this, the role of lncRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) pollen development and male fertility remains poorly understood. Results In this study, we characterized a recessive genic male sterile mutant (366–2 S), where the delayed degradation of tapetum and the failure of tetrad separation primarily led to the inability to form single microspores, resulting in male sterility. To analyze the role of lncRNAs in pollen development, we conducted a comparative lncRNA sequencing using anthers from the male sterile mutant line (366–2 S) and the wild-type male fertile line (366–2 F). We identified 385 differentially expressed lncRNAs between the 366–2 F and 366–2 S lines, with 172 of them potentially associated with target genes. To further understand the alterations in mRNA expression and explore potential lncRNA-target genes (mRNAs), we performed comparative mRNA transcriptome analysis in the anthers of 366–2 S and 366–2 F at two stages. We identified 1,176 differentially expressed mRNAs. Remarkably, GO analysis revealed significant enrichment in five GO terms, most notably involving mRNAs annotated as pectinesterase and polygalacturonase, which play roles in cell wall degradation. The considerable downregulation of these genes might contribute to the delayed degradation of tapetum in 366–2 S. Furthermore, we identified 15 lncRNA-mRNA modules through Venn diagram analysis. Among them, MSTRG.9997-BraA04g004630.3 C (β-1,3-glucanase) is associated with callose degradation and tetrad separation. Additionally, MSTRG.5212-BraA02g040020.3 C (pectinesterase) and MSTRG.13,532-BraA05g030320.3 C (pectinesterase) are associated with cell wall degradation of the tapetum, indicating that these three candidate lncRNA-mRNA modules potentially regulate pollen development. Conclusion This study lays the foundation for understanding the roles of lncRNAs in pollen development and for elucidating their molecular mechanisms in regulating male sterility in Chinese cabbage.

Abstract Background Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. Results We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. Conclusions The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.

Abstract Maize (Zea mays L.) is an important food and feed crop worldwide and serves as a a vital source of biological trace elements, which are important breeding targets. In this study, 170 maize materials were used to detect QTNs related to the content of Mn, Fe and Mo in maize grains through two GWAS models, namely MLM_Q + K and MLM_PCA + K. The results identified 87 (Mn), 205 (Fe), and 310 (Mo) QTNs using both methods in the three environments. Considering comprehensive factors such as co-location across multiple environments, strict significance threshold, and phenotypic value in multiple environments, 8 QTNs related to Mn, 10 QTNs related to Fe, and 26 QTNs related to Mo were used to identify 44 superior alleles. Consequently, three cross combinations with higher Mn element, two combinations with higher Fe element, six combinations with higher Mo element, and two combinations with multiple element (Mn/Fe/Mo) were predicted to yield offspring with higher numbers of superior alleles, thereby increasing the likelihood of enriching the corresponding elements. Additionally, the candidate genes identified 100 kb downstream and upstream the QTNs featured function and pathways related to maize elemental transport and accumulation. These results are expected to facilitate the screening and development of high-quality maize varieties enriched with trace elements, establish an important theoretical foundation for molecular marker assisted breeding and contribute to a better understanding of the regulatory network governing trace elements in maize.

Abstract Background Plants have remarkable diversity in petal colour through the biosynthesis and accumulation of various pigments. To better understand the mechanisms regulating petal pigmentation in Lonicera japonica, we used multiple approaches to investigate the changes in carotenoids, anthocyanins, endogenous hormones and gene expression dynamics during petal colour transitions, i.e., green bud petals (GB_Pe), white flower petals (WF_Pe) and yellow flower petals (YF_Pe). Results Metabolome analysis showed that YF_Pe contained a much higher content of carotenoids than GB_Pe and WF_Pe, with α-carotene, zeaxanthin, violaxanthin and γ-carotene identified as the major carotenoid compounds in YF_Pe. Comparative transcriptome analysis revealed that the key differentially expressed genes (DEGs) involved in carotenoid biosynthesis, such as phytoene synthase, phytoene desaturase and ζ-carotene desaturase, were significantly upregulated in YF_Pe. The results indicated that upregulated carotenoid concentrations and carotenoid biosynthesis-related genes predominantly promote colour transition. Meanwhile, two anthocyanins (pelargonidin and cyanidin) were significantly increased in YF_Pe, and the expression level of an anthocyanidin synthase gene was significantly upregulated, suggesting that anthocyanins may contribute to vivid yellow colour in YF_Pe. Furthermore, analyses of changes in indoleacetic acid, zeatin riboside, gibberellic acid, brassinosteroid (BR), methyl jasmonate and abscisic acid (ABA) levels indicated that colour transitions are regulated by endogenous hormones. The DEGs involved in the auxin, cytokinin, gibberellin, BR, jasmonic acid and ABA signalling pathways were enriched and associated with petal colour transitions. Conclusion Our results provide global insight into the pigment accumulation and the regulatory mechanisms underlying petal colour transitions during the flower development process in L. japonica.

Abstract Background Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12–4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12–4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12–4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.