Genome-wide identification of expansin genes in Brachypodium distachyon and functional characterization of BdEXPA27

GW9 determines grain size and floral organ identity in rice

Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zinc finger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.

Overexpression of ZmEXPA5 reduces anthesis-silking interval and increases grain yield under drought and well-watered conditions in maize

Drought is one of the major abiotic stresses affecting the maize production worldwide. As a cross-pollination crop, maize is sensitive to water stress at flowering stage. Drought at this stage leads to asynchronous development of male and female flower organ and increased interval between anthesis and silking, which finally causes failure of pollination and grain yield loss. In the present study, the expansin gene ZmEXPA5 was cloned and its function in drought tolerance was characterized. An indel variant in promoter of ZmEXPA5 is significantly associated with natural variation in drought-induced anthesis-silking interval. The drought susceptible haplotypes showed lower expression level of ZmEXPA5 than tolerant haplotypes and lost the cis-regulatory activity of ZmDOF29. Increasing ZmEXPA5 expression in transgenic maize decreases anthesis-silking interval and improves grain yield under both drought and well-watered environments. In addition, the expression pattern of ZmEXPA5 was analyzed. These findings provide insights into the genetic basis of drought tolerance and a promising gene for drought improvement in maize breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01432-x.

Regulation of drought tolerance in Arabidopsis involves the PLATZ4-mediated transcriptional repression of plasma membrane aquaporin PIP2;8

Plant A/T-rich protein and zinc-binding protein (PLATZ) transcription factors play important roles in plant growth, development and abiotic stress responses. However, how PLATZ influences plant drought tolerance remains poorly understood. The present study showed that PLATZ4 increased drought tolerance in Arabidopsis thaliana by causing stomatal closure. Transcriptional profiling analysis revealed that PLATZ4 affected the expression of a set of genes involved in water and ion transport, antioxidant metabolism, small peptides and abscisic acid (ABA) signaling. Among these genes, the direct binding of PLATZ4 to the A/T-rich sequences in the plasma membrane intrinsic protein 2;8 (PIP2;8) promoter was identified. PIP2;8 consistently reduced drought tolerance in Arabidopsis through inhibiting stomatal closure. PIP2;8 was localized in the plasma membrane, exhibited water channel activity in Xenopus laevis oocytes and acted epistatically to PLATZ4 in regulating the drought stress response in Arabidopsis. PLATZ4 increased ABA sensitivity through upregulating the expression of ABSCISIC ACID INSENSITIVE 3 (ABI3), ABI4 and ABI5. The transcripts of PLATZ4 were induced to high levels in vegetative seedlings under drought and ABA treatments within 6 and 3 h, respectively. Collectively, these findings reveal that PLATZ4 positively influences plant drought tolerance through regulating the expression of PIP2;8 and genes involved in ABA signaling.

Genome-wide association studies and transcriptome sequencing analysis reveal novel genes associated with Al tolerance in wheat

Aluminum (Al) toxicity is a major threat to the productivity and quality of wheat on acid soil. Identifying novel Al tolerance genes is crucial for breeders to pyramid different tolerance mechanisms thus leading to greater Al tolerance. We aim to identify novel quantitative trait loci (QTL) and key candidate genes associated with Al tolerance in wheat. Herein, we investigated the genotypic variation in Al tolerance among 334 wheat varieties using an acid soil assay. Genome-wide association study (GWAS) and transcriptome were carried out to identify key genes for Al tolerance. GWAS identified several QTL associated with acid soil tolerance including one major QTL on chromosome 1A, in addition to the QTL on 4D where TaALMT1 is located. The four significant markers around the newly identified QTL explained 27.2% of the phenotypic variation. With the existence of reported markers for TaALMT1, more than 97% of the genotypes showed tolerance to Al. For those genotypes with the existence of the novel QTL on 1A but without TaALMT1, more than 90% of genotypes showed medium or high tolerance to Al, confirming the existence of the Al tolerance gene(s) on chromosome 1A. By combining GWAS and RNA-seq analysis, we identified 11 candidate genes associated with Al tolerance. The results provide new insights into the genetic basis of Al tolerance in wheat. The identified genes can be used for the breeding of Al tolerant accessions.

Overexpression of the GmEXPA1 gene reduces plant susceptibility to Meloidogyne incognita

The overexpression of the soybean GmEXPA1 gene reduces plant susceptibility to M. incognita by the increase of root lignification. Plant expansins are enzymes that act in a pH-dependent manner in the plant cell wall loosening and are associated with improved tolerance or resistance to abiotic or biotic stresses. Plant-parasitic nematodes (PPN) can alter the expression profile of several expansin genes in infected root cells. Studies have shown that overexpression or downregulation of particular expansin genes can reduce plant susceptibility to PPNs. Root-knot nematodes (RKN) are obligate sedentary endoparasites of the genus Meloidogyne spp. of which M. incognita is one of the most reported species. Herein, using a transcriptome dataset and real-time PCR assays were identified an expansin A gene (GmEXPA1; Glyma.02G109100) that is upregulated in the soybean nematode-resistant genotype PI595099 compared to the susceptible cultivar BRS133 during plant parasitism by M. incognita. To understand the role of the GmEXPA1 gene during the interaction between soybean plant and M. incognita were generated stable A. thaliana and N. tabacum transgenic lines. Remarkably, both A. thaliana and N. tabacum transgenic lines overexpressing the GmEXPA1 gene showed reduced susceptibility to M. incognita. Furthermore, plant growth, biomass accumulation, and seed yield were not affected in these transgenic lines. Interestingly, significant upregulation of the NtACC oxidase and NtEFE26 genes, involved in ethylene biosynthesis, and NtCCR and Nt4CL genes, involved in lignin biosynthesis, was observed in roots of the N. tabacum transgenic lines, which also showed higher lignin content. These data suggested a possible link between GmEXPA1 gene expression and increased lignification of the root cell wall. Therefore, these data support that engineering of the GmEXPA1 gene in soybean offers a powerful biotechnology tool to assist in RKN management.

Genome-wide identification, expression analyses of Wuschel-related homeobox (WOX) genes in Brachypodium distachyon and functional characterization of BdWOX12

As one kind of plant-specific transcription factors (TFs), WOX (Wuschel-related homeobox) plays an essential role in plant growth and development. In this study, 21 WOX TFs were identified in Brachypodium distachyon. They were divided into ancient, intermediate, and WUS clades based on phylogenetic analysis. These 21 BdWOX genes are mapped on 5 chromosomes unevenly. In the promoters, the most abundant cis-elements are ABRE, TGACG-motif, and G-box. qRT-PCR results showed that most BdWOX genes are expressed in vegetative and reproductive organs. Meanwhile, the expression of 14, 12, and 15 BdWOX genes are up-regulated by exogenous 6-BA, NAA, and GA, respectively. These results indicated that BdWOX genes participate in hormone signaling and regulate plant growth and development. Overexpression of BdWOX12 in Arabidopsis improved the root system, further indicating the functions of BdWOX genes in growth and development. This study provided a basis for the functional elucidation of BdWOX genes.

Genome-Wide Identification of Expansin Genes in Wild Soybean (Glycine soja) and Functional Characterization of Expansin B1 (GsEXPB1) in Soybean Hair Root

Wild soybean, the progenitor and close relative of cultivated soybean, has an excellent environmental adaptation ability and abundant resistance genes. Expansins, as a class of cell wall relaxation proteins, have important functions in regulating plant growth and stress resistance. In the present study, we identified a total of 75 members of the expansin family on the basis of recent genomic data published for wild soybean. The predicted results of promoter elements structure showed that wild soybean expansin may be associated with plant hormones, stress responses, and growth. Basal transcriptome data of vegetative organs suggest that the transcription of expansin members has some organ specificity. Meanwhile, the transcripts of some members had strong responses to salt, low temperature and drought stress. We screened and obtained an expansin gene, GsEXPB1, which is transcribed specifically in roots and actively responds to salt stress. The results of A. tumefaciens transient transfection showed that this protein was localized in the cell wall of onion epidermal cells. We initially analyzed the function of GsEXPB1 by a soybean hairy root transformation assay and found that overexpression of GsEXPB1 significantly increased the number of hairy roots, root length, root weight, and the tolerance to salt stress. This research provides a foundation for subsequent studies of expansins in wild soybean.

Elastic and collapsible: current understanding of cell walls in succulent plants

Succulent plants represent a large functional group of drought-resistant plants that store water in specialized tissues. Several co-adaptive traits accompany this water-storage capacity to constitute the succulent syndrome. A widely reported anatomical adaptation of cell walls in succulent tissues allows them to fold in a regular fashion during extended drought, thus preventing irreversible damage and permitting reversible volume changes. Although ongoing research on crop and model species continuously reports the importance of cell walls and their dynamics in drought resistance, the cell walls of succulent plants have received relatively little attention to date, despite the potential of succulents as natural capital to mitigate the effects of climate change. In this review, we summarize current knowledge of cell walls in drought-avoiding succulents and their effects on tissue biomechanics, water relations, and photosynthesis. We also highlight the existing knowledge gaps and propose a hypothetical model for regulated cell wall folding in succulent tissues upon dehydration. Future perspectives of methodological development in succulent cell wall characterization, including the latest technological advances in molecular and imaging techniques, are also presented.

Transcriptome profiling to identify tepal cell enlargement and pigmentation genes and the function of LtEXLB1 in Lilium tsingtauense

To understand the molecular mechanism underlying tepal development and pigmentation in Lilium tsingtauense Gilg, we performed whole-transcriptome profiles from closed buds at the greenish tepal stage (CBS), the full-bloom with un-horizontal tepal stage (UFS), and the completely opened bud with reflected tepal stage (RFS) of L. tsingtauense. More than 95699 transcripts were generated using a de novo assembly approach. Gene ontology and pathway analysis of the assembled transcripts revealed carbon metabolism is involved in tepal development and pigmentation. In total, 8171 differentially expression genes (DEGs) in three tepal stages were identified. Among these DEGs, ~994 genes putatively encoded transcription factors (TFs), whereas 693 putatively encoded protein kinases. Regarding hormone pathways, 51 DEGs involved in auxin biosynthesis and signalling and 10 DEGs involved in ethylene biosynthesis and signalling. We also isolated seven LtEXPANSINs, including four EXPAs, one EXPB, one EXLA and one EXLB. LtEXLB1 (GenBank: MN856627) was expressed at higher levels in UFS and RFS, compared with CBS. Silencing LtEXLB1 in leaf discs and tepals by virus-induced gene silencing significantly decreased cell expansion under rehydration conditions. Further analysis revealed that more cell numbers were existed in the abaxial and adaxial subepidermis in the silenced LtEXLB1 samples. As the first transcriptome of L. tsingtauense, the unigenes are a valuable resource for future studies on tepal development, and LtEXLB1 functions in cell expansion.

Genome-Wide Identification of the Expansin Gene Family and Its Potential Association with Drought Stress in Moso Bamboo

Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.