A fasciclin-like arabinogalactan protein, GhFLA1, is involved in fiber initiation and elongation of cotton

Simultaneous improvement of fiber yield and quality in upland cotton (Gossypium hirsutum L.) by integration of auxin transport and synthesis

Cotton is a widely planted commercial crop in the world. Enhancing fiber yield and quality is a long-term goal for cotton breeders. Our previous work has demonstrated that fine promotion of auxin biosynthesis in ovule epidermis, by overexpressing FBP7pro::iaaM, has a significant improvement on lint yield and fiber fineness. Lately, transgenic cottons overexpressing GhROP6 variants modify mature fiber length by controlling GhPIN3a-mediated polar auxin transport in ovules. Here, this study showed that all these GhROP6-related cottons displayed unsatisfactory agronomic performance in field conditions. Yet extra auxin supply could promote their fiber development, suggesting inadequate auxin supply in the ovules. Thus, these cottons were integrated with enhanced auxin synthesis by crossing with FBP7pro::iaaM cotton. All the transgene-stacked cottons exhibited synergetic effects on cotton yield (seedcotton yield, lint yield, and lint percentage) and quality (length, strength, and micronaire). Notably, comparing to the FBP7pro::iaaM background, the transgene-stacked cotton co-expressing FBP7pro::iaaM and CA-ghrop6 (constitutively active GhROP6) exhibited a 12.6% increase in seedcotton yield and a 19.0% increase in lint yield over a three-year field trial, and simultaneously resulted in further improvement on fiber length, strength, and micronaire. Collectively, our data provide a potential strategy for genetic improvement on cotton fiber yield and quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01500-w.

The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger

Cotton is globally known for its high-priority cellulose-rich natural fiber. In addition to providing fiber for the textile industry, it is an important source material for edible oil, livestock feed, and fuel products. Global warming and the growing population are the major challenges to the world's agriculture and the potential risks to food security. In this context, improving output traits in cotton is necessary to achieve sustainable cotton production. During the last few years, high throughput omics techniques have aided in identifying crucial genes associated with traits of cotton fiber, seed, and plant architecture which could be targeted with more precision and efficiency through the CIRPSR/Cas-mediated genome editing technique. The various CRISPR/Cas systems such as CRISPR/Cas9, CRISPR/nCas9, and CRISPR/Cas12a have been employed to edit cotton genes associated with a wide range of traits including fiber length, flowering, leaf colour, rooting, seed oil, plant architecture, gossypol content, somatic embryogenesis, and biotic and abiotic stresses tolerance, highlighting its effectiveness in editing the cotton genome. Thus, CRISPR/Cas-mediated genome editing has emerged as a technique of choice to tailor crop phenotypes for better yield potential and environmental resilience. The review covers a comprehensive analysis of cotton phenotypic traits and their improvement with the help of the latest genome editing tools to improve fiber, food, feed, and fuel-associated genes of cotton to ensure food security.

GhWRKY40 Interacts with an Asparaginase GhAPD6 Involved in Fiber Development in Upland Cotton (Gossypium hirsutum L.)

Fiber quality improvement is a primary goal in cotton breeding. Identification of fiber quality-related genes and understanding the underlying molecular mechanisms are essential prerequisites. Previously, studies determined that silencing the gene GhWRKY40 resulted in longer cotton fibers; however, both the underlying mechanisms and whether this transcription factor is additionally involved in the regulation of cotton fiber strength/fineness are unknown. In the current study, we verified that GhWRKY40 influences the fiber strength, fiber fineness, and fiber surface structure by using virus-induced gene silencing (VIGS). Potential proteins that may interact with the nucleus-localized GhWRKY40 were screened in a yeast two-hybrid (Y2H) nuclear-system cDNA library constructed from fibers at 0, 10, and 25 days post-anthesis (DPA) in two near-isogenic lines differing in fiber length and strength. An aspartyl protease/asparaginase-related protein, GhAPD6, was identified and confirmed by Y2H and split-luciferase complementation assays. The expression of GhAPD6 was approximately 30-fold higher in the GhWRKY40-VIGS lines at 10 DPA and aspartyl protease activity was significantly upregulated in the GhWRKY40-VIGS lines at 10-20 DPA. This study suggested that GhWRKY40 may interact with GhAPD6 to regulate fiber development in cotton. The results provide a theoretical reference for the selection and breeding of high-quality cotton fibers assisted by molecular technology.

The dehydration-responsive protein PpFAS1.3 in moss Physcomitrium patens plays a regulatory role in lipid metabolism

Moss plants appear in the early stages of land colonization and possess varying degrees of dehydration tolerance. In this study, a protein called PpFAS1.3 was identified, which contains a fasciclin 1-like domain and is essential for the moss Physcomitrium patens' response to short-term rapid dehydration. When the FAS1.3 protein was knocked out, leafyshoots showed a significant decrease in tolerance to rapid dehydration, resulting in accelerated water loss and increased membrane leakage. Phylogenetic analysis suggests that PpFAS1.3 and its homologous proteins may have originated from bacteria and are specifically found in non-vascular plants like mosses and liverworts. As a dehydration-related protein, FAS1.3 plays a significant role in regulating lipid metabolism, particularly in the synthesis of free fatty acids (FFA) and the metabolism of two phospholipids, PC and PA. This discovery highlights the close connection between PpFAS1.3 and lipid metabolism, providing new insights into the molecular mechanisms underlying plant adaptation to stresses.

Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening

Carotenoids are important pigmented nutrients synthesized by tomato fruits during ripening. To reveal the molecular mechanism underlying carotenoid synthesis during tomato fruit ripening, we analyzed carotenoid metabolites and transcriptomes in six development stages of tomato fruits. A total of thirty different carotenoids were detected and quantified in tomato fruits from 10 to 60 DPA. Based on differential gene expression profiles and WGCNA, we explored several genes that were highly significant and negatively correlated with lycopene, all of which encode fasciclin-like arabinogalactan proteins (FLAs). The FLAs are involved in plant signal transduction, however the functional role of these proteins has not been studied in tomato. Genome-wide analysis revealed that cultivated and wild tomato species contained 18 to 22 FLA family members, clustered into four groups, and mainly evolved by means of segmental duplication. The functional characterization of FLAs showed that silencing of SlFLA1, 5, and 13 were found to contribute to the early coloration of tomato fruits, and the expression of carotenoid synthesis-related genes was up-regulated in fruits that changed phenotypically, especially in SlFLA13-silenced plants. Furthermore, the content of multiple carotenoids (including (E/Z)-phytoene, lycopene, γ-carotene, and α-carotene) was significantly increased in SlFLA13-silenced fruits, suggesting that SlFLA13 has a potential inhibitory function in regulating carotenoid synthesis in tomato fruits. The results of the present study broaden the idea of analyzing the biological functions of tomato FLAs and preliminary evidence for the inhibitory role of SlFLA13 in carotenoid synthesis in fruit, providing the theoretical basis and a candidate for improving tomato fruit quality.

Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development

INTRODUCTION

Upland cotton is an important allotetrapolyploid crop providing natural fibers for textile industry. Under the present high-level breeding and production conditions, further simultaneous improvement of fiber quality and yield is facing unprecedented challenges due to their complex negative correlations.

OBJECTIVES

The study was to adequately identify quantitative trait loci (QTLs) and dissect how they orchestrate the formation of fiber quality and yield.

METHODS

A high-density genetic map (HDGM) based on an intraspecific recombinant inbred line (RIL) population consisting of 231 individuals was used to identify QTLs and QTL clusters of fiber quality and yield traits. The weighted gene correlation network analysis (WGCNA) package in R software was utilized to identify WGCNA network and hub genes related to fiber development. Gene functions were verified via virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 strategies.

RESULTS

An HDGM consisting of 8045 markers was constructed spanning 4943.01 cM of cotton genome. A total of 295 QTLs were identified based on multi-environmental phenotypes. Among 139 stable QTLs, including 35 newly identified ones, seventy five were of fiber quality and 64 yield traits. A total of 33 QTL clusters harboring 74 QTLs were identified. Eleven candidate hub genes were identified via WGCNA using genes in all stable QTLs and QTL clusters. The relative expression profiles of these hub genes revealed their correlations with fiber development. VIGS and CRISPR/Cas9 edition revealed that the hub gene cellulose synthase 4 (GhCesA4, GH_D07G2262) positively regulate fiber length and fiber strength formation and negatively lint percentage.

CONCLUSION

Multiple analyses demonstrate that the hub genes harbored in the QTLs orchestrate the fiber development. The hub gene GhCesA4 has opposite pleiotropic effects in regulating trait formation of fiber quality and yield. The results facilitate understanding the genetic basis of negative correlation between cotton fiber quality and yield.

Systematically and Comprehensively Understanding the Regulation of Cotton Fiber Initiation: A Review

Cotton fibers provide an important source of raw materials for the textile industry worldwide. Cotton fiber is a kind of single cell that differentiates from the epidermis of the ovule and provides a perfect research model for the differentiation and elongation of plant cells. Cotton fiber initiation is the first stage throughout the entire developmental process. The number of fiber cell initials on the seed ovule epidermis decides the final fiber yield. Thus, it is of great significance to clarify the mechanism underlying cotton fiber initiation. Fiber cell initiation is controlled by complex and interrelated regulatory networks. Plant phytohormones, transcription factors, sugar signals, small signal molecules, functional genes, non-coding RNAs, and histone modification play important roles during this process. Here, we not only summarize the different kinds of factors involved in fiber cell initiation but also discuss the mechanisms of these factors that act together to regulate cotton fiber initiation. Our aim is to synthesize a systematic and comprehensive review of different factors during fiber initiation that will provide the basics for further illustrating these mechanisms and offer theoretical guidance for improving fiber yield in future molecular breeding work.

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits

In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP-trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

BACKGROUND

The epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood.

RESULTS

Here, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells.

CONCLUSIONS

We uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.

Marsdenia tenacissima genome reveals calcium adaptation and tenacissoside biosynthesis

Marsdenia tenacissima is a medicinal plant widely distributed in the calcium-rich karst regions of southwest China. However, the lack of a reference genome has hampered the implementation of molecular techniques in its breeding, pharmacology and domestication. We generated the chromosome-level genome assembly in Apocynaceae using combined SMRT sequencing and Hi-C. The genome length was 381.76 Mb, with 98.9% of it found on 11 chromosomes. The genome contained 222.63 Mb of repetitive sequences and 21 899 predicted gene models, with a contig N50 of 6.57 Mb. Phylogenetic analysis revealed that M. tenacissima diverged from Calotropis gigantea at least 13.43 million years ago. Comparative genomics showed that M. tenacissima underwent ancient shared whole-genome duplication. This event, together with tandem duplication, contributed to 70.71% of gene-family expansion. Both pseudogene analysis and selective pressure calculations suggested calcium-related adaptive evolution in the M. tenacissima genome. Calcium-induced differentially expressed genes (DEGs) were mainly enriched in cell-wall-related processes. Domains (e.g. Fasciclin and Amb_all) and cis-elements (e.g. MYB and MYC) frequently occurred in the coding and promoter regions of cell-wall DEGs, respectively, and the expression levels of these genes correlated significantly with those of calcium-signal-related transcription factors. Moreover, calcium addition increased tenacissoside I, G and H contents. The availability of this high-quality genome provides valuable genomic information for genetic breeding and molecular design, and lends insights into the calcium adaptation of M. tenacissima in karst areas.

Weighted Gene Co-Expression Network Analysis Reveals Hub Genes for Fuzz Development in Gossypium hirsutum

Fuzzless Gossypium hirsutum mutants are ideal materials for investigating cotton fiber initiation and development. In this study, we used the fuzzless G. hirsutum mutant Xinluzao 50 FLM as the research material and combined it with other fuzzless materials for verification by RNA sequencing to explore the gene expression patterns and differences between genes in upland cotton during the fuzz period. A gene ontology (GO) enrichment analysis showed that differentially expressed genes (DEGs) were mainly enriched in the metabolic process, microtubule binding, and other pathways. A weighted gene co-expression network analysis (WGCNA) showed that two modules of Xinluzao 50 and Xinluzao 50 FLM and four modules of CSS386 and Sicala V-2 were highly correlated with fuzz. We selected the hub gene with the highest KME value among the six modules and constructed an interaction network. In addition, we selected some genes with high KME values from the six modules that were highly associated with fuzz in the four materials and found 19 common differential genes produced by the four materials. These 19 genes are likely involved in the formation of fuzz in upland cotton. Several hub genes belong to the arabinogalactan protein and GDSL lipase, which play important roles in fiber development. According to the differences in expression level, 4 genes were selected from the 19 genes and tested for their expression level in some fuzzless materials. The modules, hub genes, and common genes identified in this study can provide new insights into the formation of fiber and fuzz, and provide a reference for molecular design breeding for the genetic improvement of cotton fiber.

Phenomics and transcriptomics analyses reveal deposition of suberin and lignin in the short fiber cell walls produced from a wild cotton species and two mutants

Fiber length is one of the major properties determining the quality and commercial value of cotton. To understand the mechanisms regulating fiber length, genetic variations of cotton species and mutants producing short fibers have been compared with cultivated cottons generating long and normal fibers. However, their phenomic variation other than fiber length has not been well characterized. Therefore, we compared physical and chemical properties of the short fibers with the long fibers. Fiber characteristics were compared in two sets: 1) wild diploid Gossypium raimondii Ulbrich (short fibers) with cultivated diploid G. arboreum L and tetraploid G. hirsutum L. (long fibers); 2) G. hirsutum short fiber mutants, Ligon-lintless 1 (Li1) and 2 (Li2) with their near isogenic line (NIL), DP-5690 (long fibers). Chemical analyses showed that the short fibers commonly consisted of greater non-cellulosic components, including lignin and suberin, than the long fibers. Transcriptomic analyses also identified up-regulation of the genes related to suberin and lignin biosynthesis in the short fibers. Our results may provide insight on how high levels of suberin and lignin in cell walls can affect cotton fiber length. The approaches combining phenomic and transcriptomic analyses of multiple sets of cotton fibers sharing a common phenotype would facilitate identifying genes and common pathways that significantly influence cotton fiber properties.

High-resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets

Structural variations (SVs) are critical factors affecting genome evolution and important traits. However, identification results and functional analyses of SVs in upland cotton are rare. Here, based on the genetic relationships, breeding history and cumulative planting area of upland cotton in China, nine predominant cultivars from the past 60 years (1950s-2010s) were selected for long read sequencing to uncover genic variations and breeding improvement targets for this crop. Based on the ZM24 reference genome, 0.88-1.47 × 10⁴ SVs per cultivar were identified, and an SV set was constructed. SVs affected the expression of a large number of genes during fiber elongation, and a transposable element insertion resulted in the glandless phenotype in upland cotton. Six widespread inversions were identified based on nine draft genomes and high-throughput chromosome conformation capture data. Multiple haplotype blocks that were always associated with aggregated SVs were demonstrated to play a pivotal role in the agronomic traits of upland cotton and drove its adaptation to the northern planting region. Exotic introgression was the source of these haplotype blocks and increased the genetic diversity of upland cotton. Our results enrich the genome resources of upland cotton, and the identified SVs will promote genetic and breeding research in cotton.

Cas9/gRNA-Mediated Mutations in PtrFLA40 and PtrFLA45 Reveal Redundant Roles in Modulating Wood Cell Size and SCW Synthesis in Poplar

Fasciclin-like arabinogalactan proteins (FLAs) play an important role in plant development and adaptation to the environment. However, the roles of FLAs in wood formation remain poorly understood. Here, we identified a total of 50 PtrFLA genes in poplar. They were classified into four groups: A to D, among which group A was the largest group with 28 members clustered into four branches. Most PtrFLAs of group A were dominantly expressed in developing xylem based on microarray and RT-qPCR data. The roles of PtrFLA40 and PtrFLA45 in group A were investigated via the Cas9/gRNA-induced mutation lines. Loss of PtrFLA40 and PtrFLA45 increased stem length and diameter in ptrfla40ptrfla45 double mutants, but not in ptrfla40 or ptrfla45 single mutants. Further, our findings indicated that the ptrfla40ptrfla45 mutants enlarged the cell size of xylem fibers and vessels, suggesting a negative modulation in stem xylem cell size. In addition, wood lignin content in the ptrfla40fla45 mutants was increased by nearly 9%, and the lignin biosynthesis-related genes were significantly up-regulated in the ptrfla40fla45 mutants, in agreement with the increase in wood lignin content. Overall, Cas9/gRNA-mediated mutations in PtrFLA40 and PtrFLA45 reveal redundant roles in modulating wood cell size and secondary cell wall (SCW) synthesis in poplar.

Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton

Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056-1255 ENAs showed transgressive expression in fibres at 5-15 dpa (days post-anthesis) of some BILs, 520 of which were located in FL-quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL-QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR-cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

Seeing the unseen: a trifoliate (MYB117) mutant allele fortifies folate and carotenoids in tomato fruits

In tomato (Solanum lycopersicum), mutations in the gene encoding the R2R3-MYB117 transcription factor elicit trifoliate leaves and initiate the formation of axillary meristems; however, their effects on fruit ripening remain unexplored. The fruits of a new trifoliate (tf) mutant (tf-5) were firmer and had higher °Brix values and higher folate and carotenoid contents. The transcriptome, proteome, and metabolome profiling of tf-5 reflected a broad-spectrum change in cellular homeostasis. The tf-5 allele enhanced the fruit firmness by suppressing cell wall softening-related proteins. tf-5 fruit displayed a substantial increase in amino acids, particularly γ-aminobutyric acid, with a parallel reduction in aminoacyl-tRNA synthases. The increased lipoxygenase protein and transcript levels seemingly elevated jasmonic acid levels. In addition, increased abscisic acid hydrolase transcript levels coupled with reduced precursor supply lowered abscisic acid levels. The upregulation of carotenoids was mediated by modulation of methylerythreitol and plastoquinone pathways and increased the levels of carotenoid isomerization proteins. The upregulation of folate in tf-5 was connoted by the increase in the precursor p-aminobenzoic acid and transcript levels of several folate biosynthesis genes. The reduction in pterin-6-carboxylate levels and γ-glutamyl hydrolase activity indicated that reduced folate degradation in tf-5 increased folate levels. Our study delineates that in addition to leaf development, MYB117 also influences fruit metabolism. The tf-5 allele can be used to increase γ-aminobutyric acid, carotenoid, and folate levels in tomato.

Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development

N6-methyladenosine (m⁶A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m⁶A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m⁶A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m⁶A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.

Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes

MAIN CONCLUSION

Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an F_ST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait.

Arabinogalactan Proteins: Focus on the Role in Cellulose Synthesis and Deposition during Plant Cell Wall Biogenesis

Arabinogalactan proteins (AGPs) belong to a family of glycoproteins that are widely present in plants. AGPs are mostly composed of a protein backbone decorated with complex carbohydrate side chains and are usually anchored to the plasma membrane or secreted extracellularly. A trickle of compelling biochemical and genetic evidence has demonstrated that AGPs make exciting candidates for a multitude of vital activities related to plant growth and development. However, because of the diversity of AGPs, functional redundancy of AGP family members, and blunt-force research tools, the precise functions of AGPs and their mechanisms of action remain elusive. In this review, we put together the current knowledge about the characteristics, classification, and identification of AGPs and make a summary of the biological functions of AGPs in multiple phases of plant reproduction and developmental processes. In addition, we especially discuss deeply the potential mechanisms for AGP action in different biological processes via their impacts on cellulose synthesis and deposition based on previous studies. Particularly, five hypothetical models that may explain the AGP involvement in cellulose synthesis and deposition during plant cell wall biogenesis are proposed. AGPs open a new avenue for understanding cellulose synthesis and deposition in plants.

Water Stress Differentially Modulates the Expression of Tomato Cell Wall Metabolism-Related Genes in Meloidogyne incognita Feeding Sites

Microscopic observations and transcriptomic RNA-Seq analyses were applied to investigate the effect of water stress during the formation of tomato galls formation 1 and 2 weeks after inoculation with the root-knot nematode Meloidogyne incognita. Water stress affected root growth and the nematode ability to mount an efficient parasitism. The effects of water stress on the feeding site development were already observed at 1 week after nematode inoculation, with smaller giant cells, delayed development, and thinner cell walls. These features suggested changes in the expression levels of genes involved in the feeding site formation and maintenance. Gene Ontology (GO) enrichment and expression patterns were used to characterize differentially expressed genes. Water stress modified the expression profile of genes involved in the synthesis, degradation, and remodeling of the cell wall during the development of nematode feeding site. A comparison of gene expression with unstressed galls revealed that water stress intensified the up or downregulation of most genes. However, it particularly influenced the expression pattern of expansin A11 (Solyc04g081870.4.1), expansin-like B1(Solyc08g077910.3.1), a pectin acetylesterase (Solyc08g005800.4.1), and the pectin methylesterase pmeu1 (Solyc03g123630.4.1) which were upregulated in unstressed galls and repressed by water stress, at both sampling times. The expression of most members of the genes involved in cell wall metabolism, i.e., those coding for Csl, fasciclin, and COBRA proteins, were negatively influenced. Interestingly, alteration in the expression profiles of most dirigent protein genes (DIRs) and upregulation of five gene coding for Casparian strip domain protein (CASP)-like proteins were found. Gene expression analysis of galls from water stressed plants allowed us to better understand the molecular basis of M. incognita parasitism in tomato. Specific genes, including those involved in regulation of cellulose synthesis and lignification process, require further study to develop defense strategies against root-knot nematodes.

OsFLA1 encodes a fasciclin-like arabinogalactan protein and affects pollen exine development in rice

OsFLA1 positively regulates pollen exine development, and locates in the cellular membrane. Arabinogalactan proteins are a type of hydroxyproline-rich glycoprotein that are present in all plant tissues and cells and play important roles in plant growth and development. Little information is available on the participation of fasciclin-like arabinogalactan proteins in sexual reproduction in rice. In this study, a rice male-sterile mutant, osfla1, was isolated from an ethylmethanesulfonate-induced mutant library. The osfla1 mutant produced withered, shrunken, and abortive pollen. The gene OsFLA1 encoded a FLA protein and was expressed strongly in the anthers in rice. Subcellular localization showed that OsFLA1 was located in the cellular membrane. In the osfla1 mutant, abnormal Ubisch bodies and a discontinuous nexine layer of the microspore wall were observed, which resulted in pollen abortion and ultimately in male sterility. The results show the important role that OsFLA1 plays in male reproductive development in rice.

Glucose regulates cotton fiber elongation by interacting with brassinosteroid

In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.

Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

Cotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

Phosphorylation of WRKY16 by MPK3-1 is essential for its transcriptional activity during fiber initiation and elongation in cotton (Gossypium hirsutum)

Cotton, one of the most important crops in the world, produces natural fiber materials for the textile industry. WRKY transcription factors play important roles in plant development and stress responses. However, little is known about whether and how WRKY transcription factors regulate fiber development of cotton so far. In this study, we show that a fiber-preferential WRKY transcription factor, GhWRKY16, positively regulates fiber initiation and elongation. GhWRKY16-silenced transgenic cotton displayed a remarkably reduced number of fiber protrusions on the ovule and shorter fibers compared to the wild-type. During early fiber development, GhWRKY16 directly binds to the promoters of GhHOX3, GhMYB109, GhCesA6D-D11, and GhMYB25 to induce their expression, thereby promoting fiber initiation and elongation. Moreover, GhWRKY16 is phosphorylated by the mitogen-activated protein kinase GhMPK3-1 at residues T-130 and S-260. Phosphorylated GhWRKY16 directly activates the transcription of GhMYB25, GhHOX3, GhMYB109, and GhCesA6D-D11 for early fiber development. Thus, our data demonstrate that GhWRKY16 plays a crucial role in fiber initiation and elongation, and that GhWRKY16 phosphorylation by GhMPK3-1 is essential for the transcriptional activation on downstream genes during the fiber development of cotton.

Genome-Wide Association Mapping of Mixed Linkage (1,3;1,4)-β-Glucan and Starch Contents in Rice Whole Grain

The glucan content of rice is a key factor defining its nutritional and economic value. Starch and its derivatives have many industrial applications such as in fuel and material production. Non-starch glucans such as (1,3;1,4)-β-D-glucan (mixed-linkage β-glucan, MLG) have many benefits in human health, including lowering cholesterol, boosting the immune system, and modulating the gut microbiome. In this study, the genetic variability of MLG and starch contents were analyzed in rice (Oryza sativa L.) whole grain, by performing a new quantitative analysis of the polysaccharide content of rice grains. The 197 rice accessions investigated had an average MLG content of 252 μg/mg, which was negatively correlated with the grain starch content. A new genome-wide association study revealed seven significant quantitative trait loci (QTLs) associated with the MLG content and two QTLs associated with the starch content in rice whole grain. Novel genes associated with the MLG content were a hexose transporter and anthocyanidin 5,3-O-glucosyltransferase. Also, the novel gene associated with the starch content was a nodulin-like domain. The data pave the way for a better understanding of the genes involved in determining both MLG and starch contents in rice grains and should facilitate future plant breeding programs.

Arabinogalactan glycoprotein dynamics during the progamic phase in the tomato pistil

Pistil AGPs display dynamic localization patterns in response to fertilization in tomato. SlyFLA9 (Solyc07g065540.1) is a chimeric Fasciclin-like AGP with enriched expression in the ovary, suggesting a potential function during pollen-pistil interaction. During fertilization, the male gametes are delivered by pollen tubes to receptive ovules, deeply embedded in the sporophytic tissues of the pistil. Arabinogalactan glycoproteins (AGPs) are a diverse family of highly glycosylated, secreted proteins which have been widely implicated in plant reproduction, particularly within the pistil. Though tomato (Solanum lycopersicum) is an important crop requiring successful fertilization for production, the molecular basis of this event remains understudied. Here we explore the spatiotemporal localization of AGPs in the mature tomato pistil before and after fertilization. Using histological techniques to detect AGP sugar moieties, we found that accumulation of AGPs correlated with the maturation of the stigma and we identified an AGP subpopulation restricted to the micropyle that was no longer visible upon fertilization. To identify candidate pistil AGP genes, we used an RNA-sequencing approach to catalog gene expression in functionally distinct subsections of the mature tomato pistil (the stigma, apical and basal style and ovary) as well as pollen and pollen tubes. Of 161 predicted AGP and AGP-like proteins encoded in the tomato genome, we identified four genes with specifically enriched expression in reproductive tissues. We further validated expression of two of these, a Fasciclin-like AGP (SlyFLA9, Solyc07g065540.1) and a novel hybrid AGP (SlyHAE, Solyc09g075580.1). Using in situ hybridization, we also found SlyFLA9 was expressed in the integuments of the ovule and the pericarp. Additionally, differential expression analyses of the pistil transcriptome revealed previously unreported genes with enriched expression in each subsection of the mature pistil, setting the foundation for future functional studies.

Weighted Gene Co-Expression Network Analysis Reveals Hub Genes Contributing to Fuzz Development in Gossypium arboreum

Fuzzless mutants are ideal materials to decipher the regulatory network and mechanism underlying fuzz initiation and formation. In this study, we utilized two Gossypium arboreum accessions differing in fuzz characteristics to explore expression pattern differences and discriminate genes involved in fuzz development using RNA sequencing. Gene ontology (GO) analysis was conducted and found that DEGs were mainly enriched in the regulation of transcription, metabolic processes and oxidation–reduction-related processes. Weighted gene co-expression network analysis discerned the MEmagenta module highly associated with a fuzz/fuzzless trait, which included a total of 50 hub genes differentially expressed between two materials. GaFZ, which negatively regulates trichome and fuzz formation, was found involved in MEmagenta cluster1. In addition, twenty-eight hub genes in MEmagenta cluster1 were significantly up-regulated and expressed in fuzzless mutant DPL972. It is noteworthy that Ga04G1219 and Ga04G1240, which, respectively, encode Fasciclin-like arabinogalactan protein 18(FLA18) and transport protein, showed remarkable differences of expression level and implied that they may be involved in protein glycosylation to regulate fuzz formation and development. This module and hub genes identified in this study will provide new insights on fiber and fuzz formation and be useful for the molecular design breeding of cotton genetic improvement.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BACKGROUND

Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.

RESULTS

Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.

CONCLUSION

Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

Family-Wide Evaluation of Multiple C2 Domain and Transmembrane Region Protein in Gossypium hirsutum

Multiple C2 domain and transmembrane region proteins (MCTPs) are a group of evolutionarily conserved proteins and show emerging roles in mediating protein trafficking and signaling transduction. Although, several studies showed that MCTPs play important roles during plant growth and development, their biological functions in cotton remain largely unknown. Here, we identify and characterize 33 GhMCTP genes from upland cotton (Gossypium hirsutum) and reveal the diverse expression patterns of GhMCTPs in various tissues. We also find that GhMCTP7, GhMCTP12, and GhMCTP17 are highly expressed in the main stem apex, suggesting their possible roles in shoot development. Through analyzing different cotton species, we discover plant heights are closely related to the expression levels of GhMCTP7, GhMCTP12, and GhMCTP17. Furthermore, we silence the expression of GhMCTP genes using virus-induced gene silencing (VIGS) system in cotton and find that GhMCTP7, GhMCTP12, and GhMCTP17 play an essential role in shoot meristem development. GhMCTPs interact with GhKNAT1 and GhKNAT2 and regulate meristem development through integrating multiple signal pathways. Taken together, our results demonstrate functional redundancy of GhMCTPs in cotton shoot meristem development and provide a valuable resource to further study various functions of GhMCTPs in plant growth and development.

Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis

The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.

The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality

The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective manipulation of technical fiber quality. A key step was to identify genes with tissue and stage-specific pattern of expression in the developing fibers. In the current study, we investigated the relationship between gene expression evaluated in bast fibers of developing flax plants and the quality parameters of technical fibers measured after plant harvesting. Based on previously published transcriptomic data, two sets of genes that are upregulated in fibers during intrusive growth and tertiary cell wall deposition were selected. The expression level of the selected genes and fiber quality parameters were measured in fiber flax, linseed (oil flax) cultivars, and wild species that differ in type of yield and fiber quality parameters. Based on gene expression data, linear regression models for technical stem length, fiber tensile strength, and fiber flexibility were constructed, resulting in the identification of genes that have high potential for manipulating fiber quality. Chromosomal localization and single nucleotide polymorphism distribution in the selected genes were characterized for the efficacy of their use in conventional breeding and genome editing programs. Transcriptome-based selection is a highly targeted functional approach that could be used during the development of new cultivars of various crops.

Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation

Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.

Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise

Water limitation represents the main environmental constraint affecting crop yield worldwide. Photosynthesis is a primary drought target, resulting in over-reduction of the photosynthetic electron transport chain and increased production of reactive oxygen species in plastids. Manipulation of chloroplast electron distribution by introducing alternative electron transport sinks has been shown to increase plant tolerance to multiple environmental challenges including hydric stress, suggesting that a similar strategy could be used to improve drought tolerance in crops. We show herein that the expression of the cyanobacterial electron shuttle flavodoxin in potato chloroplasts protected photosynthetic activities even at a pre-symptomatic stage of drought. Transcriptional and metabolic profiling revealed an attenuated response to the adverse condition in flavodoxin-expressing plants, correlating with their increased stress tolerance. Interestingly, 5-6% of leaf-expressed genes were affected by flavodoxin in the absence of drought, representing pathways modulated by chloroplast redox status during normal growth. About 300 of these genes potentially contribute to stress acclimation as their modulation by flavodoxin proceeds in the same direction as their drought response in wild-type plants. Tuber yield losses under chronic water limitation were mitigated in flavodoxin-expressing plants, indicating that the flavoprotein has the potential to improve major agronomic traits in potato.

Identification of Hydroxyproline-Containing Proteins and Hydroxylation of Proline Residues in Rice

The hydroxyproline-containing proteins (HCPs) among secretory and vacuolar proteins play important roles in growth and development of higher plants. Many hydroxyproline-rich glycoproteins (HRGPs), including Arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs), are identified as HCPs by bioinformatics approaches. The experimental evidence for validation of novel proline hydroxylation sites is vital for understanding their functional roles. In this study, the 62 HCPs containing 114 hydroxyproline (O, Hyp) residues were identified, and it was found that hydroxylation of proline residues in the HCPs could either constitute attachment sites for glycans or have other biological function in rice. The glycomodules of AO, OA, OG, VO, LO, and OE were abundant in the 62 HCPs. Further analysis showed that the 22 of 62 HCPs contained both signal peptides and transmembrane domains, and the 19 HCPs only contained transmembrane domains, while 21 HCPs contained neither. This study indicated the feasibility of mass spectrometry-based proteomics combined with bioinformatics approaches for the large-scale characterization of Hyp sites from complex protein digest mixtures. Furthermore, the expression of AGPs in rice was detected by using β-GlcY reagent and JIM13 antibody. The results displayed that the AGPs were widely distributed in different tissues and organs of rice, especially expressed highly in lateral root, pollen and embryo. In conclusion, our study revealed that the HCPs and Hyp residues in rice were ubiquitous and that these Hyps could be candidates for linking to glycans, which laid the foundation for further studying the functions of HCPs and hydroxylation of proline residues in rice.

The Rice BZ1 Locus Is Required for Glycosylation of Arabinogalactan Proteins and Galactolipid and Plays a Role in both Mechanical Strength and Leaf Color

BACKGROUND

The cell wall and chloroplast are two fundamental structures determining plant mechanical strength and grain yield. Therefore, understanding mechanisms that improve plants' ability to develop a robust cell wall and well-developed chloroplast is of utmost importance for agricultural activities.

RESULTS

In this study, we report the functional characterization of a novel rice mutant, brittle stem and zebra leaf (bz1), which displays altered cell wall composition and collapsed chloroplast membrane. Molecular and biochemical analysis revealed that BZ1 encodes a functional UDP-galactose/glucose epimerase (UGE) and is ubiquitously expressed with higher expression in stem and leaf tissues. Multiple techniques analyses, including immunoblots, immuno-gold, and cryogenic scanning electron microscopy, demonstrated a significantly impaired glycosylation of arabinogalactan proteins (AGPs) and disordered cellulose microfibril deposition in bz1. Lipid profiling assay showed that the amount of monogalactosyldiacylglycerols (MGDG), a major chloroplast membrane glycolipid, was significantly decreased in bz1. Taken together, these results strongly demonstrate that BZ1 participates in UDP-galactose supply for the sugar chains biosynthesis of AGPs and MGDG, which thereby, respectively, results in altered cell wall and abnormal chloroplast development. Due to inferior mechanical strength and reduced photosynthesis, bz1 plants displayed detrimental agronomic traits, whereas BZ1 overexpressing lines showed enhanced plant growth. Transcriptome analysis of stems and leaves further showed that numerous key genes involved in AGPs biosynthesis and photosynthesis metabolism were substantially suppressed in bz1.

CONCLUSIONS

Our finding identifies BZ1 as a dual-targeting UGE protein for glycosylation of AGPs and MGDG and suggests a strategy for breeding robust elite crops.

Genome-wide analyses of banana fasciclin-like AGP genes and their differential expression under low-temperature stress in chilling sensitive and tolerant cultivars

Thirty MaFLAs vary in their molecular features. MaFLA14/18/27/29 are likely to be involved in banana chilling tolerance by facilitating the cold signaling pathway and enhancing the cell wall biosynthesis. Although several studies have identified the molecular functions of individual fasciclin-like arabinogalactan protein (FLA) genes in plant growth and development, little information is available on their involvement in plant tolerance to low-temperature (LT) stress, and the related underlying mechanism is far from clear. In this study, the different expression of FLAs of banana (Musa acuminata) (MaFLAs) in the chilling-sensitive (CS) and chilling-tolerant (CT) banana cultivars under natural LT was investigated. Based on the latest banana genome database, a genome-wide identification of this gene family was done and the molecular features were analyzed. Thirty MaFLAs were distributed in 10 out of 11 chromosomes and these clustered into four major phylogenetic groups based on shared gene structure. Twenty-four MaFLAs contained N-terminal signal, 19 possessed predicted glycosylphosphatidylinositol (GPI), while 16 had both. Most MaFLAs were downregulated by LT stress. However, MaFLA14/18/29 were upregulated by LT in both cultivars with higher expression level recorded in the CT cultivar. Interestingly, MaFLA27 was significantly upregulated in the CT cultivar, but the opposite occurred for the CS cultivar. MaFLA27 possessed only N-terminal signal, MaFLA18 contained only GPI anchor, MaFLA29 possessed both, while MaFLA14 had neither. Thus, it was suggested that the accumulation of these FLAs in banana under LT could improve banana chilling tolerance through facilitating cold signal pathway and thereafter enhancing biosynthesis of plant cell wall components. The results provide background information of MaFLAs, suggest their involvement in plant chilling tolerance and their potential as candidate genes to be targeted when breeding CT banana.

Overexpression of a Monocot Acyl-CoA-Binding Protein Confers Broad-Spectrum Pathogen Protection in a Dicot

Plants are continuously infected by various pathogens throughout their lifecycle. Previous studies have reported that the expression of Class III acyl-CoA-binding proteins (ACBPs) such as the Arabidopsis ACBP3 and rice ACBP5 were induced by pathogen infection. Transgenic Arabidopsis AtACBP3-overexpressors (AtACBP3-OEs) displayed enhanced protection against the bacterial biotroph, Pseudomonas syringae, although they became susceptible to the fungal necrotroph Botrytis cinerea. A Class III ACBP from a monocot, rice (Oryza sativa) OsACBP5 was overexpressed in the dicot Arabidopsis. The resultant transgenic Arabidopsis lines conferred resistance not only to the bacterial biotroph P. syringae but to fungal necrotrophs (Rhizoctonia solani, B. cinerea, Alternaria brassicicola) and a hemibiotroph (Colletotrichum siamense). Changes in protein expression in R. solani-infected Arabidopsis OsACBP5-overexpressors (OsACBP5-OEs) were demonstrated using proteomic analysis. Biotic stress-related proteins including cell wall-related proteins such as FASCILIN-LIKE ARABINOGALACTAN-PROTEIN10, LEUCINE-RICH REPEAT EXTENSIN-LIKE PROTEINS, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE PROTEIN4, and PECTINESTERASE INHIBITOR18; proteins associated with glucosinolate degradation including GDSL-LIKE LIPASE23, EPITHIOSPECIFIER MODIFIER1, MYROSINASE1, MYROSINASE2, and NITRILASE1; as well as a protein involved in jasmonate biosynthesis, ALLENE OXIDE CYCLASE2, were induced in OsACBP5-OEs upon R. solani infection. These results indicated that upregulation of these proteins in OsACBP5-OEs conferred protection against various plant pathogens.

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)

Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.

Pectate lyase-like Gene GhPEL76 regulates organ elongation in Arabidopsis and fiber elongation in cotton

Pectate lyases (PELs) play important roles in plant growth and development, mainly by degrading the pectin in primary cell walls. However, the role of PELs in cotton fiber elongation, which also involves changes in cellular structure and components, is poorly understood. Therefore, we aimed to isolate and characterize GhPEL76, as we suspected it to contribute to the regulation of fiber elongation. Expression analysis (qRT-PCR) revealed that GhPEL76 is predominately expressed in cotton fiber, with significantly different expression levels in long- and short-fiber cultivars, and that GhPEL76 expression is responsive to gibberellic acid and indoleacetic acid treatment. Furthermore, GhPEL76 promoter-driven β-glucuronidase activity was detected in the roots, hypocotyls, and leaves of transgenic Arabidopsis plants, and the overexpression of GhPEL76 in transgenic Arabidopsis promoted the elongation of several organs, including petioles, hypocotyls, primary roots, and trichomes. Additionally, the virus-induced silencing of GhPEL76 in cotton reduced fiber length, and both yeast one-hybrid and transient dual-luciferase assays suggested that GhbHLH13, a bHLH transcription factor that is up-regulated during fiber elongation, activates GhPEL76 expression by binding to the G-box of the GhPEL76 promoter region. Therefore, these results suggest GhPEL76 positively regulates fiber elongation and provide a basis for future studies of cotton fiber development.

In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development

KEY MESSAGE

The fasciclin-like arabinogalactan proteins organization into four groups is conserved and may be related to specific roles in developmental processes across angiosperms. Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs), which contain fasciclin-like domains in addition to typical AGP domains. FLAs are present across all embryophytes, and despite their low overall sequence similarity, conserved regions that define the fasciclin functional domain (FAS) have been identified, suggesting that the cell adhesion property is also conserved. FLAs in Arabidopsis have been organized into four subgroups according to the number and distribution of functional domains. Recent studies associated FLAs with cell wall-related processes where domain organization seemed to be related to functional roles. In Arabidopsis, FLAs containing a single FAS domain were found to be important for the integrity and elasticity of the plant cell wall matrix, and FLAs with two FAS domains and two AGP domains were found to be involved in maintaining proper cell expansion under salt stress conditions. The main purpose of the present work was to elucidate the expression pattern of selected FLA genes during embryo and seed development using RT-qPCR. AtFLA8 and AtFLA10, two Arabidopsis genes that stood out in previous microarray studies of embryo development, were further examined using promoter-driven gene reporter analyses. We also studied the expression of cork oak FLA genes and found that their expression partially parallels the expression patterns of the putative AtFLA orthologs. We propose that the functional organization of FLAs is conserved and may be related to fundamental aspects of embryogenesis and seed development across angiosperms. Phylogenetic studies were performed, and we show that the same basic four-subgroup organization described for Arabidopsis FLA gene classification is valid for most Arabidopsis FLA orthologs of several plant species, namely poplar, corn and cork oak.

Cell wall composition and transcriptomics in stem tissues of stinging nettle (Urtica dioica L.): Spotlight on a neglected fibre crop

Stinging nettle (Urtica dioica L.) produces silky cellulosic fibres, as well as bioactive molecules. To improve the knowledge on nettle and enhance its opportunities of exploitation, a draft transcriptome of the "clone 13" (a fibre clone) is here presented. The transcriptome of whole internodes sampled at the top and middle of the stem is then compared with the core and cortical tissues sampled at the bottom. Young internodes show an enrichment in genes involved in the biosynthesis of phytohormones (auxins and jasmonic acid) and secondary metabolites (flavonoids). The core of internodes collected at the bottom of the stem is enriched in genes partaking in different aspects of secondary cell wall formation (cellulose, hemicellulose, lignin biosynthesis), while the cortical tissues reveal the presence of a C starvation signal probably due to the UDP-glucose demand necessary for the thickening phase of bast fibres. Cell wall analysis indicates a difference in rhamnogalacturonan structure/composition of mature bast fibres, as evidenced by the higher levels of galactose measured, as well as the occurrence of more water-soluble pectins in elongating internodes. The targeted quantification of phenolics shows that the middle internode and the cortical tissues at the bottom have higher contents than top internodes. Ultrastructural analyses reveal the presence of a gelatinous layer in bast fibres with a lamellar structure. The data presented will be an important resource and reference for future molecular studies on a neglected fibre crop.

Arabinogalactan Proteins and the Extracellular Matrix of Charophytes: A Sticky Business

Charophytes represent the group of green algae whose ancestors invaded land and ultimately gave rise to land plants 450 million years ago. While Zygnematophyceae are believed to be the direct sister lineage to embryophytes, different members of this group (Penium, Spirogyra, Zygnema) and the advanced thallus forming Coleochaete as well as the sarcinoid basal streptophyte Chlorokybus were investigated concerning their vegetative extracellular matrix (ECM) properties. Many taxa exhibit adhesion phenomena that are critical for affixing to a substrate or keeping cells together in a thallus, however, there is a great variety in possible reactions to e.g., wounding. In this study an analysis of adhesion mechanisms revealed that arabinogalactan proteins (AGPs) are most likely key adhesion molecules. Through use of monoclonal antibodies (JIM13) or the Yariv reagent, AGPs were located in cell surface sheaths and cell walls that were parts of the adhesion focal zones on substrates including wound induced rhizoid formation. JIM5, detecting highly methyl-esterfied homoglacturonan and JIM8, an antibody detecting AGP glycan and LM6 detecting arabinans were also tested and a colocalization was found in several examples (e.g., Zygnema) suggesting an interplay between these components. AGPs have been described in this study to perform both, cell to cell adhesion in algae forming thalli and cell to surface adhesion in the filamentous forms. These findings enable a broader evolutionary understanding of the function of AGPs in charophyte green algae.

Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application

Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.

The cotton XLIM protein (GhXLIM6) is required for fiber development via maintaining dynamic F-actin cytoskeleton and modulating cellulose biosynthesis

LIM domain proteins are cysteine-rich proteins, and are often considered as actin bundlers and transcription factors in plants. However, the roles of XLIM proteins in plants (especially in cotton) remain unexplored in detail so far. In this study, we identified a cotton XLIM protein (GhXLIM6) that is preferentially expressed in cotton fiber during whole elongation stage and early secondary cell wall (SCW) synthesis stage. The GhXLIM6-silenced transgenic cotton produces shorter fibers with thinner cell walls, compared with wild-type (WT). GhXLIM6 protein could directly bind F-actin and promote actin polymerization both in vitro and in vivo. It also acts as a transcription factor to suppress GhKNL1 expression through binding the PAL-box element of GhKNL1 promoter, and subsequently regulate the expression of CesA genes related to cellulose biosynthesis and deposition in SCWs of cotton fibers. The cellulose content in fibers of GhXLIM6RNAi cotton is lower than that in WT. Taken together, these data reveal the dual roles of GhXLIM6 in fiber development. On one hand, GhXLIM6 functions in fiber elongation through binding to F-actin to maintain the dynamic F-actin cytoskeleton. On the other hand, GhXLIM6 fine-tunes fiber SCW formation, probably through directly suppressing transcription of GhKNL1 to promote cellulose biosynthesis.

Hitting the Wall-Sensing and Signaling Pathways Involved in Plant Cell Wall Remodeling in Response to Abiotic Stress

Plant cells are surrounded by highly dynamic cell walls that play important roles regulating aspects of plant development. Recent advances in visualization and measurement of cell wall properties have enabled accumulation of new data about wall architecture and biomechanics. This has resulted in greater understanding of the dynamics of cell wall deposition and remodeling. The cell wall is the first line of defense against different adverse abiotic and biotic environmental influences. Different abiotic stress conditions such as salinity, drought, and frost trigger production of Reactive Oxygen Species (ROS) which act as important signaling molecules in stress activated cellular responses. Detection of ROS by still-elusive receptors triggers numerous signaling events that result in production of different protective compounds or even cell death, but most notably in stress-induced cell wall remodeling. This is mediated by different plant hormones, of which the most studied are jasmonic acid and brassinosteroids. In this review we highlight key factors involved in sensing, signal transduction, and response(s) to abiotic stress and how these mechanisms are related to cell wall-associated stress acclimatization. ROS, plant hormones, cell wall remodeling enzymes and different wall mechanosensors act coordinately during abiotic stress, resulting in abiotic stress wall acclimatization, enabling plants to survive adverse environmental conditions.

Molecular Background of Pi Deficiency-Induced Root Hair Growth in Brassica carinata - A Fasciclin-Like Arabinogalactan Protein Is Involved

Formation of longer root hairs under limiting phosphate (P) conditions can increase the inorganic P (Pi) uptake. Here, regulatory candidate genes for Pi deficiency-induced root hair growth were identified by comparison of massive analysis of cDNA ends (MACE) provided expression profiles of two Brassica carinata cultivars (cv.) differing in their root hair response to Pi deficiency: cv. Bale develops longer root hairs under Pi deficiency, but not cv. Bacho. A split-root experiment was conducted for the differentiation between locally and systemically regulated genes. Furthermore, plants were exposed to nitrogen and potassium deficiency to identify P-specific reacting genes. The latter were knocked out by CRISPR/Cas9 and the effect on the root hair length was determined. About 500 genes were differentially expressed under Pi deficiency in cv. Bale, while these genes did not respond to the low P supply in cv. Bacho. Thirty-three candidate genes with a potential regulatory role were selected and the transcriptional regulation of 30 genes was confirmed by quantitative PCR. Only five candidate genes seemed to be either exclusively regulated locally (two) or systemically (three), whereas 25 genes seemed to be involved in both local and systemic signaling pathways. Potassium deficiency affected neither the root hair length nor the expression of the 30 candidate genes. By contrast, both P and nitrogen deficiency increased the root hair length, and both affected the transcript levels in 26 cases. However, four genes reacted specifically to Pi starvation. These genes and, additionally, INORGANIC PHOSPHATE TRANSPORTER 1 (BcPHT1) were targeted by CRISPR/Cas9. However, even if the transcript levels of five of these genes were clearly decreased, FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 1 (BcFLA1) was the only gene whose downregulation reduced the root hair length in transgenic hairy roots under Pi-deficient conditions. To the best of our knowledge, this is the first study describing a fasciclin-like arabinogalactan protein with a predicted role in the Pi deficiency-induced root hair elongation.