Yanzhou Wang

Ramie (Boehmeria nivea) is renowned for its superior fiber strength, length, and unique properties, yet its genetic improvement has lagged behind other fiber crops. This review synthesizes recent advances in ramie fiber development at the genetic, genomic, and molecular levels. Population genomic analyses have uncovered distinct domestication, improvement, and feralization signatures, identifying numerous fiber-related genes under selection. Parallel genetic and molecular studies have mapped scores of loci and genes governing fiber formation, laying the foundation for molecular breeding. However, despite the availability of genetic transformation systems, the need for methodological improvements remains a major challenge for engineering fiber traits via transgenic approaches. Overall, a solid research foundation has been established. Future progress in establishing marker-assisted and genomic selection breeding systems, optimizing transformation protocols, and developing efficient gene-editing methods holds promise for realizing molecular breeding to enhance fiber quality and yield in ramie.

Chloro-organophosphate ester (Cl-OPE) accumulation in soil and aquatic environments, and their potential hazard to crops, has attracted widespread attention. However, little is known about the potential adverse effects of Cl-OPEs on plants. Green onions are a specialty vegetable worldwide, and the heavy application of pesticides during their growth period has led to increasingly severe soil contamination in cultivation areas. We evaluated the toxic effects of Cl-OPEs on green onions and examined their toxicity mechanism. After 20 days of treatment, physiological parameters were measured across five biological replicates per treatment. Results indicated that as Cl-OPE concentrations increased, green onion leaf malondialdehyde (MDA) content and reactive oxygen species (ROS) levels rose significantly. Concurrently, the activities of the antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly enhanced. However, leaf chlorophyll content and net photosynthetic rate (Pn) decreased significantly, indicating that Cl-OPE-induced oxidative stress inhibited photosynthesis. Meanwhile, the nutrient content of green onions gradually decreased as the concentration of Cl-OPEs increased. In conclusion, Cl-OPEs can damage chloroplasts by promoting ROS accumulation, which results in the yellowing of green onion leaves. The resulting decrease in Pn reduced the plant’s ability to assimilate nutrients.

Ramie is one of the most important fiber crops in China, with fibers extracted from stem barks having been used as textile materials for thousands of years. DNA methylation is an important epigenetic modification involved in plant growth and development. However, the role of methylation in ramie fiber growth remains poorly understood. In the present study, we investigated the DNA methylation landscape of the nuclear genome in bark sections taken from the top (TPS) and the middle (MPS) of the stems of ramie plants, which represent different stages of fiber growth, using whole-genome bisulfite sequencing. We detected 7,709,555 and 8,508,326 5-methylcytosines in the TPS and MPS genomes, respectively. The distribution of methylation across three sequence contexts, CG, CHG, and CHH, varied greatly among gene elements, with methylation at CHH being the most prevalent. Comparison of methylation levels between the TPS and MPS genomes revealed 23.162 Mb of differentially methylated genomic regions, encompassing 9485 genes. Among these differentially methylated genes, 841 exhibited altered expression in the MPS genome. Notably, an SND2 ortholog Bni05G006779 showed a negative correlation between its expression and methylation levels. Overexpression of Bni05G006779 in Arabidopsis dramatically increased the number of xylem fibers and the secondary wall thickness of the fibers in the stems of transgenic plants. These findings provide important insights into the involvement of DNA methylation in regulating ramie fiber growth.

The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.

The KNOX transcription factor plays crucial roles in regulating fiber growth in plants. Although the genome of ramie, an important fiber crop in China, is available, knotted related homeobox (KNOX) genes have not been systematically explored in this crop. In this study, seven members of the KNOX gene from the ramie genome were identified and assigned to two groups, Class I and II. The intron–exon structure, conserved domain architecture, cis-regulating elements, and expression pattern showed distinct differences among the seven KNOX regulators. One of the genes, Bnt07G011994, encodes an ortholog of Arabidopsis fiber-growth-related KNAT7, and is differentially expressed among barks undergoing different stages of fiber growth. The overexpression of Bnt07G011994 dramatically decreases the fiber number in transgenic Arabidopsis, indicating a negative role played by this gene in modulating fiber growth. Further transcriptome analysis of transgenic Arabidopsis revealed that the overexpression of Bnt07G011994 resulted in an expression change in 14 pectin biosynthesis-/metabolism-related genes. These findings provide a useful foundation for further investigating the function of KNOX genes in ramie, and provide an important insight into the involvement of the ramie KNOX gene in fiber growth.

NAM, ATAF, and CUC (NAC) proteins are plant-specific transcription factors that play crucial roles in fiber growth by regulating the secondary wall thickening. In this study, a systematical investigation of NAC genes was performed in the genome of ramie, an important fiber crop, resulting in a total of 60 ramie NAC genes identified. Phylogenetic analysis of these 60 NAC members in conjunction with 111 Arabidopsis NAC proteins identified 11 subfamilies, three of which showed considerable contraction in the ramie genome. Ten ramie NAC genes were identified to encode the orthologs of Arabidopsis NAC regulators involved in the control of secondary wall biosynthesis. Of these ten genes, most showed relatively high expression in the stems, and eight displayed a differential expression between the barks from the top and middle section of the stems where fiber growth is under different stages. Furthermore, the overexpression of three of these ten NAC genes significantly promoted fiber growth in transgenic Arabidopsis. These results indicated that these ten NAC genes were associated with the fiber growth of ramie. This study provided an important basis for researching the regulatory mechanism of fiber growth.

Ramie (Boehmeria nivea L.) is a perennial plant with vigorously vegetative growth and high nutritive value that is an excellent source of green feed in China. Crude protein and fiber content are the most important traits associated with ramie forage quality; however, their genetic basis remains largely unknown. In this study, we investigated the genetic architecture of these two traits using an F₂ population derived from cultivated Zhongsizhu 1 (ZSZ1) and wild Boehmeria nivea var. tenacissima (tenacissima). Linkage mapping identified eight quantitative trait loci (QTLs) in crude fiber and one QTL in crude protein. Of these, five were further validated by association analysis. Then, two major QTLs for crude fiber content, CF7 and CF13, were further identified using bulked segregant analysis (BSA) sequencing, and their exact physical intervals were determined via genotype analysis of F₂ progenies with extremely low crude fiber content. In total, 10 genes in the CF7 and CF13 regions showed differential expression in ZSZ1 and tenacissima leaves, including an MYB gene whole_GLEAN_10016511 from the CF13 region. Wide variation was observed in the promoter regions of whole_GLEAN_10016511, likely responsible for its downregulated expression in tenacissima. Interestingly, more fiber cells were observed in Arabidopsis with overexpression of whole_GLEAN_10016511, indicating that the downregulated expression of this gene could have an association with the relatively low fiber content in wild tenacissima. These results provided evidence that whole_GLEAN_10016511 is a logical candidate for CF13. This study provides important insights into the genetic basis underlying ramie crude protein and fiber content, and it presents genetic loci for improving the forage quality of ramie using marker-assisted selection.

Mediterranean buffalo (Bubalus bubalis Linnaeus, 1758 breed Mediterranean, MEB) is one of the best milk-producing breeds in river-type buffaloes in the world. It is the first time that the complete mitochondrial genome sequence of the MEB was reported. The total length of the mtDNA is 16,357 bp, It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region). The overall composition of the mtDNA was estimated to be 33.10% for A, 26.44% for T, 26.57% for C and 13.89% for G, in the order A > C > T > G feature occurs in the MEB. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 18 ruminantia species are divided into four major clades: Bovidae, Cervidae, Giraffidae and Atilocapridae. In addition, our work confirmed that MEB and Nili-Ravi buffalo (NRB) have a close genetic relationship with fellow tribal members Murrah buffalo. Meanwhile, we also found that MEB and NRB have highly similar genetic relationship.

Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie.

19 DNA binding with one finger (Dof) transcription factor genes were identified from genome and transcriptome data of ramie (Boehmeria nivea L. Gaud). Chemical character, subnuclear localization, motif analysis, phylogenetic analysis, and tissue-specific analysis were performed. To select BnDof genes participating in nitrogen metabolism, we analyzed the expression patterns of BnDof genes in different nitrogen conditions (N0, N4, N8, and N12) in different tissues. As a result, eight BnDof genes were identified. BnDof07 (stem) and BnDof14 (root) had higher expression levels in N0 and N4, and BnDof15 (stem and leaves) and BnDof18 (stem) both exhibited the highest expression level in N0, suggesting that these four genes may take part in nitrogen stress. In the leaves, BnDof01, BnDof06, BnDof09, and BnDof19 expression levels were higher in N8 and N12 but lower in N0 and N4. The present findings provide insights into nitrogen metabolism in ramie highlighting the need to investigate this aspect in further detail in future studies.