Map-based cloning and gene editing confirmed that ClChlH was the causal gene controlling yellow rind color in watermelon. Fruit rind color is a crucial agronomic trait influencing the commercial quality of watermelon (Citrullus lanatus). Although yellow rind is an important phenotype, its underlying molecular mechanisms remain poorly understood. In this study, genetic analysis using two mapping populations derived from crosses between a yellow rind line (W-21-4-2) and two green rind lines (W-21-301 and W-21-129) indicated that the yellow rind trait is controlled by a single dominant locus, ClYR. By combining BSA and KASP genotyping, we initially mapped ClYR to a 6.5 Mb region on chromosome 4. Subsequent fine mapping with 1345 F2:3 individuals narrowed the candidate interval to 325.37 Kb, which contains 10 annotated genes. Among these, ClChlH (Cla97C04G068530) emerged as the most promising candidate gene due to multiple insertions/deletions (InDels) in its promoter region that distinguish the yellow and green rind lines. Expression analysis revealed significantly reduced ClChlH transcript levels in the yellow rind line W-21-4-2. Promoter activity assays further demonstrated that these structural variations suppress transcriptional activation of ClChlH. Haplotype analysis confirmed that these promoter InDels were correlated with yellow rind phenotype. Functional validation via CRISPR/Cas9-mediated mutagenesis generated mutants exhibiting yellow-green or sectored (half-green-half-yellow) pigmentation in both rind and leaf tissues. Collectively, our findings elucidate a key genetic regulator of rind coloration and provide valuable molecular resources for future watermelon breeding programs.

Continuous watermelon cropping leads to increases in soil-borne diseases, which negatively affect plant growth. We investigated the impact of continuous watermelon cropping on soil biochemical properties, enzyme activities, microbial biomass, occurrence of Fusarium wilt, diversity and structure of bacterial and fungal communities, as well as the relationship among these factors with plant growth. The results showed significant decreases in soil pH, OM, AN, AP, and AK contents (p < 0.05), while UA, APA, and DA were reduced, along with declines in MBC and MBN in the rhizosphere soil of continuous watermelon cropping (p < 0.05). The population of FON and Fusarium wilt incidence increased significantly after continuous cropping (p < 0.05). High-throughput sequencing analysis revealed that the richness and diversity of soil bacterial and fungal communities significantly decreased (p < 0.05). There were significant differences in bacterial and fungal community composition between the continuous cropping and control groups. Besides, the Pearson correlation analysis of plant growth and environmental factors revealed that soil parameters, including pH, SOM, AN, AP, UA, APA, DA, MBC, and the richness and diversity of bacterial and fungal communities all had significant effects on plant growth. Additionally, the incidence of Fusarium wilt and the population of FON negatively affected growth. In conclusion, we hypothesize that soil acidification, deterioration of biochemical properties, an increase in Fusarium wilt, and changes in microbial community structure are causes of poor watermelon growth.

Leaf color affects the efficiency of photosynthesis, and leaf color mutants are important genetic materials for studying the mechanisms of photosynthesis, chlorophyll biosynthesis, and chloroplast development in rice. In this study, a white-striped leaf mutant, wst1 , was obtained from the mutant population of the indica restorer line ‘Chuanhui 907’ (R907) when treated with 60 Co-γ radiation. Compared to the wild-type, the wst1 mutant showed normal leaf color before tillering and white stripes on the leaf and leaf sheaths after tillering. The chlorophyll and carotenoid contents were significantly reduced, and the thylakoids of chloroplasts developed abnormalities in wst1 plants in the tillering stage. The results of agronomic trait analysis showed that the number of effective panicles, plant height, seed setting rate, and 1000-grain weight of the wst1 mutant were significantly lower than those of the wild-type. Genetic analysis revealed that the phenotype of the wst1 mutant is controlled by a pair of recessive nuclear genes. The candidate gene was mapped to a 72 kb region between the InDel markers M6 and M12 on the short arm of chromosome 1 using molecular marker linkage analysis. Candidate genes were sequenced on the interval, and a G base was replaced by A at the 6972nd position on the 16th exon of LOC_Os01g01920 , which encoded a previously reported protein containing the HD domain, WSF3/WFSL1, leading to alternative splicing, causing a 104 bp deletion in the coding region, and resulting in mistranslation after the 490 amino acid of the encoded protein translation in wst1 . RT-qPCR analysis showed that the expression levels of most genes related to chlorophyll synthesis and chloroplast development were significantly altered in wst1 plants. Our study identified a novel allele of wsf3 and wfsl1 mutant and provided a new genetic resource and theoretical basis for further understanding of the molecular mechanism of WST1 gene regulation of white-striped leaves in rice.

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon’s ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene’s expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Nicotianamine (NA) plays a crucial role in transporting metal ions, including iron (Fe), in plants; therefore, NICOTIANAMINE SYNTHASE (NAS) genes, which control NA synthesis, are tightly regulated at the transcriptional level. However, the transcriptional regulatory mechanisms of NAS genes require further investigations. In this study, we determined the role of bZIP44 in mediating plant response to Fe deficiency stress by conducting transformation experiments and assays. bZIP44 positively regulated the response of Arabidopsis to Fe deficiency stress by interacting with MYB10 and MYB72 to enhance their abilities to bind at NAS2 and NAS4 promoters, thereby increasing NAS2 and NAS4 transcriptional levels and promote NA synthesis. In summary, the transcription activities of bZIP44, MYB10, and MYB72 were induced in response to Fe deficiency stress, which enhanced the interaction between bZIP44 and MYB10 or MYB72 proteins, synergistically activated the transcriptional activity of NAS2 and NAS4, promoted NA synthesis, and improved Fe transport, thereby enhancing plant tolerance to Fe deficiency stress.

Golden2-like (GLK) genes positively regulate chloroplast development, increase crop yields, and improve fruit quality. However, there has been no comprehensive identification and characterization of GLKs in watermelon. In this study, a total of 48 ClGLKs were identified in the watermelon genome. Based on phylogenetic analysis, they were divided into five groups. ClGLKs within the same group showed a similar gene structure and conserved motif compositions. Promoter analysis indicated that cis-elements responsive to light were the most abundant, though cis-elements associated with hormones, stress, and developmental regulation were also identified in ClGLKs promoters. Expression analysis indicated significant responses of some ClGLKs to drought and CGMMV stress, suggesting that these genes may participate in responses to biotic and abiotic stresses. Phenotypic analyses revealed enhanced chloroplast development and increased thylakoid density and chlorophyll content in the pericarp of a "dark green" watermelon cultivar. ClGLK8 was identified as the homolog of GLK1-2, the genes that promote chloroplast development and chlorophyll biosynthesis in fruits, and showed significantly increased expression in accordance with chloroplast development and chlorophyll accumulation. Our results provide detailed knowledge of the ClGLKs, which will enhance efforts to further improve the fruit quality of watermelon.

Wheat intercropping in watermelon could provide relief from the occurrence of Fusarium wilting of watermelon, a severe soil-borne disease caused by the fungus Fusarium oxysporum f. sp. niveum (FON). The current study aims to investigate the effect of root exudates from three wheat cultivars and one watermelon cultivar on the growth of FON and the responses of Fusarium wilt in watermelon to intercropping with wheat. The results revealed the contrasting effects of root exudates on the mycelial growth of FON; the wheat root exudates inhibited the mycelial growth of FON, and watermelon root exudates promoted the mycelial growth of FON. Watermelon plants suffered less Fusarium wilt in the intercropping system than in the monocropping system. Wheat intercropping reduced the incidence of Fusarium wilt in watermelon, and this effect was associated with the role of wheat root exudates that inhibited the growth of FON. Malondialdehyde (MDA) contents decreased in the intercropping system compared with the monocropping system after FON inoculation. The catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and polyphenol oxidase (PPO) activities, and total phenolics and flavonoid contents in the roots of watermelon in the intercropping system were significantly higher than those in the monocropping system. Real-time PCR analysis showed that ClCAT, ClSOD, ClAPX, and ClPPO defensive enzymes and ClPDF2.1 and ClPDF2.4 defensin-like gene expression were significantly induced during the early stage after FON inoculation in the intercropping system compared to the monocropping system, while peroxidases did not show a significant response to FON infection. It is suggested that intercropping with wheat alleviates Fusarium wilt of watermelon by reducing the population of FON in rhizospheric soil and activating physiological responses and defense gene expression to protect watermelon from FON infection and improve the resistance of watermelon to FON in the intercropping system.

As one of the important traits, hull color is the morphological marker of rice, which plays an important role in the mechanized color selection of hybrid rice seed production but lacks good application. Here, we obtained a reddish-brown hull 1 (rbh1) mutant from an Indica maintainer material H9808 by aerospace mutagenesi. In the rbh1 mutant, the hull color was reddish brown, and the grain width and 1000-grain weight decreased significantly, but the other agronomic traits did not change significantly. Furthermore, the total flavonoids and anthocyanin content in the rbh1 hulls deposition was remarkably higher than WT, and the lignin level in the rbh1 hull was reduced. Genetic analysis indicated that the reddish-brown hull trait was controlled by a pair of recessive nuclear genes. Map-based cloning indicated that RBH1 was located within the physical distance of 48 kb on the short arm of chromosome 2. The comparative analysis of genome DNA sequence between rbh1 and WT found that a substitution from T to C (+ 1001) occurred in the fourth exon of LOC_Os02g09490 in rbh1 mutant. Genetic complementation experiments indicate that RBH1 is an allele of the previously reported GH2, which encoding a cinnamyl alcohol dehydrogenase protein involving in lignin biosynthesis. qRT-PCR showed that the relative expression of lignin and flavonoid-related genes in the hulls of rbh1 mutant was significantly upregulated, confirming that GH2/RBH1 is an important gene in the metabolism of lignin and flavonoids; and provides material basis for further studying the mechanism of GH2/RBH1 regulating the rice hull color.. In addition, the hybrid F-1 combination analysis indicated that the rbh1 mutation site did not affect the agronomic traits and yield of the hybrid rice, which was to cultivate the rbh1 locus into a new sterile line or restorer line with reddish-brown hulls and rice breeding application of rbh1 locus on mechanized seed production of hybrid rice provides a theoretical basis.

Fruit cracking in watermelon (Citrullus lanatus) causes a great economic loss. To understand the molecular mechanisms underlying watermelon fruit cracking, the differentially expressed genes (DEGs) between resistant and susceptible-cracking watermelon were analyzed using transcriptome sequencing. We selected the parent inbred W11 (resistant-cracking) and W13 (susceptible-cracking), and Near-Isogenic Lines W96 (resistant cracking) and W85 (susceptible-cracking) as materials. Differentially expressed genes (DEGs) analysis showed that 290 DEGs had detectable in "W11" VS "W13", while 165 DEGs had detectable in "W96" VS "W85". There were 56 DEGs between the four samples. Additionally, 14 DEGs related to fruit cracking were identified from the transcriptome. Only 8 DEGs among them, were involved in 14 KEGG pathway. The expression patterns of the 14 DEGs related to fruit cracking were analyzed by qRT-PCR to explore their putative functions. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of fruit cracking and contribute to watermelon breeding..

Brassica campestris L. subsp. chinensis var. rosularis Tsen is one of important vegetables grown in Yangtze river basin in winter. "Heixinwu" and "Huangxinwu" were two major varieties, and the carotenoid content of "Huangxinwu" was much richer than "Heixinwu". In this study, we used transcriptome sequencing to identify the repertoire of genes expressed between "Heixinwu" and "Huangxinwu", aiming to delineate the molecular mechanisms of carotenoid biosynthesis. A total of 19.02 gigabase pairs (Gbp) of data with 18,920,370 high quality reads were obtained, and 55,076 unigenes with average length of 775.96 base pairs were identified by de novo assembly. Of these, 39,454 unigenes (71.64%) were further annotated by comparison to public protein databases. A total of 13,018 (33.00%) unigenes were mapped into 122 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEGs) analysis identified 1184 DEGs from the comparison of "Heixinwu" and "Huangxinwu", including 610 up-regulated and 574 down-regulated genes. Additionally, 14 carotenoid synthase genes were identified from the transcriptome. The expression patterns of the 14 genes related to carotenoid biosynthesis were analyzed by qRT-PCR to explore their putative functions. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of carotenoid formation and contribute to future artificial production and applications.