Further characterization of a rice AGL12 group MADS-box gene, OsMADS26

Omics approaches to understand the MADS-box gene family in common bean (Phaseolus vulgaris L.) against drought stress

MADS-box genes are known to play important roles in diverse aspects of growth/devolopment and stress response in several plant species. However, no study has yet examined about MADS-box genes in P. vulgaris. In this study, a total of 79 PvMADS genes were identified and classified as type I and type II according to the phylogenetic analysis. While both type I and type II PvMADS classes were found to contain the MADS domain, the K domain was found to be present only in type II PvMADS proteins, in agreement with the literature. All chromosomes of the common bean were discovered to contain PvMADS genes and 17 paralogous gene pairs were identified. Only two of them were tandemly duplicated gene pairs (PvMADS-19/PvMADS-23 and PvMADS-20/PvMADS-24), and the remaining 15 paralogous gene pairs were segmentally duplicated genes. These duplications were found to play an important role in the expansion of type II PvMADS genes. Moreover, the RNAseq and RT-qPCR analyses showed the importance of PvMADS genes in response to drought stress in P. vulgaris.

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

A SEPALLATA MADS-Box Transcription Factor, SlMBP21, Functions as a Negative Regulator of Flower Number and Fruit Yields in Tomato

MADS-box transcription factors act as the crucial regulators in plant organ differentiation. Crop yields are highly influenced by the flower number and fruit growth. However, flower identification is a very complex biological process, which involves many cascade regulations. The molecular mechanisms underlying the genetic regulation of flower identification in cultivated plants, such as tomato, are intricate and require further exploration. In this study, we investigated the vital function of a SEPALLATA (SEP) MADS-box gene, SlMBP21, in tomato sympodial inflorescence meristem (SIM) development for the conversion from SIMs to floral meristems (FMs). SlMBP21 transcripts were primarily accumulated in young inflorescence meristem, flowers, sepals, and abscission zones. The Ailsa Craig (AC++) tomato plants with suppressed SlMBP21 mRNA levels using RNAi exhibited a large increase in flower number and fruit yields in addition to enlarged sepals and inhibited abscission zone development. Scanning electron microscopy (SEM) revealed that the maturation of inflorescence meristems (IMs) was repressed in SlMBP21-RNAi lines. RNA-seq and qRT-PCR analyses showed that numerous genes related to the flower development, plant hormone signal transduction, cell cycle, and cell proliferation et al. were dramatically changed in SlMBP21-RNAi lines. Yeast two-hybrid assay exhibited that SlMBP21 can respectively interact with SlCMB1, SFT, JOINTLESS, and MC, which play key roles in inflorescence meristems or FM development. In summary, our data demonstrate that SlMBP21 functions as a key regulator in SIM development and the conversion from SIMs to FMs, through interacting with other regulatory proteins to control the expression of related genes.

Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time

KEY MESSAGE

111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

Two SEPALLATA MADS-Box Genes, SlMBP21 and SlMADS1, Have Cooperative Functions Required for Sepal Development in Tomato

MADS-box transcription factors have crucial functions in numerous physiological and biochemical processes during plant growth and development. Previous studies have reported that two MADS-box genes, SlMBP21 and SlMADS1, play important regulatory roles in the sepal development of tomato, respectively. However, the functional relationships between these two genes are still unknown. In order to investigate this, we simultaneously studied these two genes in tomato. Phylogenetic analysis showed that they were classified into the same branch of the SEPALLATA (SEP) clade. qRT-PCR displayed that both SlMBP21 and SlMADS1 transcripts are preferentially accumulated in sepals, and are increased with flower development. During sepal development, SlMBP21 is increased but SlMADS1 is decreased. Using the RNAi, tomato plants with reduced SlMBP21 mRNA generated enlarged and fused sepals, while simultaneous inhibition of SlMBP21 and SlMADS1 led to larger (longer and wider) and fused sepals than that in SlMBP21-RNAi lines. qRT-PCR results exhibited that the transcripts of genes relating to sepal development, ethylene, auxin and cell expansion were dramatically changed in SlMBP21-RNAi sepals, especially in SlMBP21-SlMADS1-RNAi sepals. Yeast two-hybrid assay displayed that SlMBP21 can interact with SlMBP21, SlAP2a, TAGL1 and RIN, and SlMADS1 can interact with SlAP2a and RIN, respectively. In conclusion, SlMBP21 and SlMADS1 cooperatively regulate sepal development in tomato by impacting the expression or activities of other related regulators or via interactions with other regulatory proteins.

Genome-wide identification and expression analysis of the C2H2-zinc finger transcription factor gene family and screening of candidate genes involved in floral development in Coptis teeta Wall. (Ranunculaceae)

Background: C2H2-zinc finger transcription factors comprise one of the largest and most diverse gene superfamilies and are involved in the transcriptional regulation of flowering. Although a large number of C2H2 zinc-finger proteins (C2H2-ZFPs) have been well characterized in a number of model plant species, little is known about their expression and function in Coptis teeta. C. teeta displays two floral phenotypes (herkogamy phenotypes). It has been proposed that the C2H2-zinc finger transcription factor family may play a crucial role in the formation of floral development and herkogamy observed in C. teeta. As such, we performed a genome-wide analysis of the C2H2-ZFP gene family in C. teeta. Results: The complexity and diversity of C. teeta C2H2 zinc finger proteins were established by evaluation of their physicochemical properties, phylogenetic relationships, exon-intron structure, and conserved motifs. Chromosome localization showed that 95 members of the C2H2 zinc-finger genes were unevenly distributed across the nine chromosomes of C. teeta, and that these genes were replicated in tandem and segmentally and had undergone purifying selection. Analysis of cis-acting regulatory elements revealed a possible involvement of C2H2 zinc-finger proteins in the regulation of phytohormones. Transcriptome data was then used to compare the expression levels of these genes during the growth and development of the two floral phenotypes (F-type and M-type). These data demonstrate that in groups A and B, the expression levels of 23 genes were higher in F-type flowers, while 15 genes showed higher expressions in M-type flowers. qRT-PCR analysis further revealed that the relative expression was highly consistent with the transcriptome data. Conclusion: These data provide a solid basis for further in-depth studies of the C2H2 zinc finger transcription factor gene family in this species and provide preliminary information on which to base further research into the role of the C2H2 ZFPs gene family in floral development in C. teeta.

Uncovering Novel QTLs and Candidate Genes for Salt Tolerance at the Bud Burst Stage in Rice through Genome-Wide Association Study

Salt stress is one of the most important factors limiting rice growth and yield increase. Salt tolerance of rice at the bud burst (STB) stage determines whether germinated seeds can grow normally under salt stress, which is very important for direct seeding. However, reports on quantitative trait loci (QTLs) and candidate genes for STB in rice are very limited. In this study, a natural population of 130 indica and 81 japonica rice accessions was used to identify STB-related QTLs and candidate genes using a genome-wide association study (GWAS). Nine QTLs, including five for relative shoot length (RSL), two for relative root length (RRL), and two for relative root number (RRN), were identified. Five of these STB-related QTLs are located at the same site as the characterized salt tolerance genes, such as OsMDH1, OsSRFP1, and OsCDPK7. However, an important QTL related to RSL, qRSL1-2, has not been previously identified and was detected on chromosome 1. The candidate region for qRSL1-2 was identified by linkage disequilibrium analysis, 18 genes were found to have altered expression levels under salt stress through the RNA-seq database, and 10 of them were found to be highly expressed in the shoot. It was also found that, eight candidate genes (LOC_Os01g62980, LOC_Os01g63190, LOC_Os01g63230, LOC_Os01g63280, LOC_Os01g63400, LOC_Os01g63460, and LOC_Os01g63580) for qRSL1-2 carry different haplotypes between indica and japonica rice, which exactly corresponds to the significant difference in RSL values between indica and japonica rice in this study. Most of the accessions with elite haplotypes were indica rice, which had higher RSL values. These genes with indica-japonica specific haplotypes were identified as candidate genes. Rice accessions with elite haplotypes could be used as important resources for direct seeding. This study also provides new insights into the genetic mechanism of STB.

Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis

The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.

Comparative transcriptome analysis of dioecious floral development in Trachycarpus fortunei using Illumina and PacBio SMRT sequencing

BACKGROUND

Trachycarpus fortunei is a plant with significant economic and ornamental value. Both male and female flowers of T. fortunei originate as bisexual flowers, and selective abortion occurs during floral development. However, the regulatory mechanisms underlying this process remain unclear in T. fortunei. In this study, transcriptome sequencing with Illumina and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) platforms were used to investigate gene expression differences between male and female T. fortunei plants.

RESULTS

A total of 833,137 full-length non-chimeric (FLNC) reads were obtained, and 726,846 high-quality full-length transcripts were identified. A total of 159 genes were differentially expressed between male and female flowers at all development stages. Some of the differentially expressed genes (DEGs) showed male bias, including serine/threonine-protein kinase (STPK), THUMP1 homolog and other genes. Through single-nucleotide polymorphisms(SNPs) identification, 28 genes were considered as potential sex-associated SNPs. Time-Ordered Gene Co-expression Network (TO-GCN) analysis revealed that MADS2 and MADS26 may play important roles in the development of female and male flowers T. fortune plants, respectively.

CONCLUSIONS

These findings provide a genetic basis for flower development and differentiation in T. fortunei, and improve our understanding of the mechanisms underlying sexual differentiation in T. fortunei.

Drought stress-induced the formation of heteromorphic leaves of Populus euphratica Oliv: evidence from gene transcriptome

Populus euphratica Oliv., a dominant species of arid desert community, grows heteromorphic leaves at different crown positions. Whether heteromorphic leaves are a strategy of plant adaptation to drought stress is rarely reported. This study sequenced the transcriptome of three typical heteromorphic leaves (lanceolate, ovate and broad-ovate leaves) of P. euphratica, and measured their drought stress. We wanted to reveal the molecular mechanisms underlying the formation of heteromorphic leaves. Drought stress was increased significantly from lanceolate to ovate to broad-ovate leaves. Gene ontology (GO) and KEGG enrichment analysis showed that the MADs-box gene regulated the expression of peroxidase (POD) in the phenylpropane biosynthetic pathway. The up-regulated expression of the chalcone synthase (CHS) gene in broad-ovate leaves significantly activated the flavonoid biosynthetic pathway. In the process of leaf shape change, the different expressions of homeodomain leucine zipper (HD-ZIP) among the three heteromorphic leaves had potential interactions on the AUX and ABA pathways. The expression of Sucrose phosphate synthase (SPS) and sucrose synthase (SUS) increased from lanceolate to broad-ovate leaves, resulting in a consistent change in starch and sucrose content. We concluded that these resistance-related pathways are expressed in parallel with leaf formation genes, thereby inducing the formation of heteromorphic leaves. Our work provided a new insights for desert plants to adapt to drought stress.

Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome

KEY MESSAGE

Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.

Gene Structural Specificity and Expression of MADS-Box Gene Family in Camellia chekiangoleosa

MADS-box genes encode transcription factors that affect plant growth and development. Camellia chekiangoleosa is an oil tree species with ornamental value, but there have been few molecular biological studies on the developmental regulation of this species. To explore their possible role in C. chekiangoleosa and lay a foundation for subsequent research, 89 MADS-box genes were identified across the whole genome of C. chekiangoleosa for the first time. These genes were present on all the chromosomes and were found to have expanded by tandem duplication and fragment duplication. Based on the results of a phylogenetic analysis, the 89 MADS-box genes could be divided into either type I (38) or type II (51). Both the number and proportion of the type II genes were significantly greater than those of Camellia sinensis and Arabidopsis thaliana, indicating that C. chekiangoleosa type II genes experienced a higher duplication rate or a lower loss rate. The results of both a sequence alignment and a conserved motif analysis suggest that the type II genes are more conserved, meaning that they may have originated and differentiated earlier than the type I genes did. At the same time, the presence of extra-long amino acid sequences may be an important feature of C. chekiangoleosa. Gene structure analysis revealed the number of introns of MADS-box genes: twenty-one type I genes had no introns, and 13 type I genes contained only 1~2 introns. The type II genes have far more introns and longer introns than the type I genes do. Some MIKC^C genes have super large introns (≥15 kb), which are rare in other species. The super large introns of these MIKC^C genes may indicate richer gene expression. Moreover, the results of a qPCR expression analysis of the roots, flowers, leaves and seeds of C. chekiangoleosa showed that the MADS-box genes were expressed in all those tissues. Overall, compared with that of the type I genes, the expression of the type II genes was significantly higher. The CchMADS31 and CchMADS58 genes (type II) were highly expressed specifically in the flowers, which may in turn regulate the size of the flower meristem and petals. CchMADS55 was expressed specifically in the seeds, which might affect seed development. This study provides additional information for the functional characterization of the MADS-box gene family and lays an important foundation for in-depth study of related genes, such as those involved in the development of the reproductive organs of C. chekiangoleosa.

Genome-wide identification of MADS-box gene family in orchardgrass and the positive role of DgMADS114 and DgMADS115 under different abiotic stress

Abiotic stress, a major factor limit growth and productivity of major crops. Orchardgrass is one of the most important cool-season forage grasses in the world, and it is highly tolerant to abiotic stress. The MADS-box transcription factor family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, MADS-box transcription factors in orchardgrass, especially those involved in abiotic stress, have not yet been elucidated. Here, 123 DgMADS-box members were identified in orchardgrass and a detailed overview has been presented. Syntenic analysis indicated that the expansion of the DgMADS-box genes in orchardgrass is mainly dependent on tandem duplication events. Some DgMADS-box genes were induced by multiple abiotic stresses, indicating that these genes may play critical regulatory roles in orchardgrass response to various abiotic stresses. Heterologous expression showed that DgMADS114 and DgMADS115 could enhance stress tolerance of transgenic Arabidopsis, as revealed by longer root length or higher survival rates under PEG, NaCl, ABA, and heat stress. The results of this study provide a scientific basis for clarifying the functional characterization of MADS-box genes in orchardgrass in response to environmental stress can be further used to improve forages and crops via breeding programs.

Controlled Induction of Parthenogenesis in Transgenic Rice via Post-translational Activation of PsASGR-BBML

Modern plant breeding programs rely heavily on the generation of homozygous lines, with the traditional process requiring the inbreeding of a heterozygous cross for five to six generations. Doubled haploid (DH) technology, a process of generating haploid plants from an initial heterozygote, followed by chromosome doubling, reduces the process to two generations. Currently established in vitro methods of haploid induction include androgenesis and gynogenesis, while in vivo methods are based on uni-parental genome elimination. Parthenogenesis, embryogenesis from unfertilized egg cells, presents another potential method of haploid induction. PsASGR-BABY BOOM-like, an AP2 transcription factor, induces parthenogenesis in a natural apomictic species, Pennisetum squamulatum (Cenchrus squamulatus) and PsASGR-BBML transgenes promote parthenogenesis in several crop plants, including rice, maize, and pearl millet. The dominant nature of PsASGR-BBML transgenes impedes their use in DH technology. Using a glucocorticoid-based post-translational regulation system and watering with a 100 μM DEX solution before anthesis, PsASGR-BBML can be regulated at the flowering stage to promote parthenogenesis. Conditional expression presents a novel opportunity to use parthenogenetic genes in DH production technology and to elucidate the molecular mechanism underlying parthenogenetic embryogenesis.

Tissue-specific enhancement of OsRNS1 with root-preferred expression is required for the increase of crop yield

INTRODUCTION

Root development is a fundamental process that supports plant survival and crop productivity. One of the essential factors to consider when developing biotechnology crops is the selection of a promoter that can optimize the spatial-temporal expression of introduced genes. However, there are insufficient cases of suitable promoters in crop plants, including rice.

OBJECTIVES

This study aimed to verify the usefulness of a new rice root-preferred promoter to optimize the function of a target gene with root-preferred expression in rice.

METHODS

osrns1 mutant had defects in root development based on T-DNA insertional mutant screening and CRISPR technology. To optimize the function of OsRNS1, we generated OsRNS1-overexpression plants under two different promoters: a whole-plant expression promoter and a novel root-preferred expression promoter. Root growth, yield-related agronomic traits, RNA-seq, and reactive oxygen species (ROS) accumulation were analyzed for comparison.

RESULTS

OsRNS1 was found to be involved in root development through T-DNA insertional mutant analysis and gene editing mutant analysis. To understand the gain of function of OsRNS1, pUbi1::OsRNS1 was generated for the whole-plant expression, and both root growth defects and overall growth defects were found. To overcome this problem, a root-preferential overexpression line using Os1-CysPrxB promoter (Per) was generated and showed an increase in root length, plant height, and grain yield compared to wild-type (WT). RNA-seq analysis revealed that the response to oxidative stress-related genes was significantly up-regulated in both overexpression lines but was more obvious in pPer::OsRNS1. Furthermore, ROS levels in the roots were drastically decreased in pPer::OsRNS1 but were increased in the osrns1 mutants compared to WT.

CONCLUSION

The results demonstrated that the use of a root-preferred promoter effectively optimizes the function of OsRNS1 and is a useful strategy for improving root-related agronomic traits as well as ROS regulation.

The MADS transcription factor GhFYF is involved in abiotic stress responses in upland cotton (Gossypium hirsutum L.)

Cotton is an important textile industry raw material crops, which plays a critical role in the development of society. MADS transcription factors (TFs) play a key role about the flowering time, flower development, and abiotic stress responses in plants, but little is known about their functions on abiotic stress in cotton. In this study, a MIKC^C subfamily gene from cotton, GhFYF (FOREVER YOUNG FLOWER), was isolated and characterized. Our data showed that GhFYF localized to the nucleus. A β-glucuronidase (GUS) activity assay revealed that the promoter of GhFYF was mainly expressed in the flower and seed of ProGhFYF::GUS transgenic A. thaliana plants. The GUS staining of flowers and seeds was deepened after drought, salt treatment, and the expression level of the GUS gene and corresponding stress genes AtERD10, AtAnnexin1 are up-regulated in the inflorescence. Overexpression GhFYF in A. thaliana could promote the seed germination and growth under different salt concentrations, and determin the proline content. Yeast two-hybrid (Y2H) assays showed that GhFYF interacted with the HAD-like protein GhGPP2, which has responds to abiotic stress. Our findings indicate that GhFYF is involved in abiotic stress responses, especially for salt stress. This work establishes a solid foundation for further functional analysis of the GhFYF gene in cotton.

Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress

Background

Alfalfa, the “queen of forage”, is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa.

Results

In the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mβ, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses.

Conclusions

In this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding.

Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07911-9.

Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response

MADS-box transcription factors play vital roles in multiple biological processes in plants. At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.) has not been reported. In this study, we identified 72 MADS-box genes in the foxtail millet genome and give an overview of the phylogeny, chromosomal location, gene structures, and potential functions of the proteins encoded by these genes. We also found that the expression of 10 MIKC-type MADS-box genes was induced by abiotic stresses (PEG-6000 and NaCl) and exogenous hormones (ABA and GA), which suggests that these genes may play important regulatory roles in response to different stresses. Further studies showed that transgenic Arabidopsis and rice (Oryza sativa L.) plants overexpressing SiMADS51 had reduced drought stress tolerance as revealed by lower survival rates and poorer growth performance under drought stress conditions, which demonstrated that SiMADS51 is a negative regulator of drought stress tolerance in plants. Moreover, expression of some stress-related genes were down-regulated in the SiMADS51-overexpressing plants. The results of our study provide an overall picture of the MADS-box gene family in foxtail millet and establish a foundation for further research on the mechanisms of action of MADS-box proteins with respect to abiotic stresses.

Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress

Water deficits are a major constraint on maize growth and yield, and deep roots are one of the major mechanisms of drought tolerance. In this study, four root and shoot traits were evaluated within an association panel consisting of 209 diverse maize accessions under well-watered (WW) and water-stressed (WS) conditions. A significant positive correlation was observed between seminal root length (SRL) under WS treatment and the drought tolerance index (DI) of maize seedlings. The transcriptome profiles of maize seminal roots were compared between four drought-tolerant lines and four drought-sensitive lines under both water conditions to identify genes associated with the drought stress response. After drought stress, 343 and 177 common differentially expressed genes (DEGs) were identified in the drought-tolerant group and drought-sensitive group, respectively. In parallel, a coexpression network underlying SRL was constructed on the basis of transcriptome data, and 10 hub genes involved in two significant associated modules were identified. Additionally, a genome-wide association study (GWAS) of the SRL revealed 62 loci for the two water treatments. By integrating the results of the GWAS, the common DEGs and the coexpression network analysis, 7 promising candidate genes were prioritized for further research. Together, our results provide a foundation for the enhanced understanding of seminal root changes in response to drought stress in maize.

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.

MADS-box genes underground becoming mainstream: plant root developmental mechanisms

Plant growth is largely post-embryonic and depends on meristems that are active throughout the lifespan of an individual. Developmental patterns rely on the coordinated spatio-temporal expression of different genes, and the activity of transcription factors is particularly important during most morphogenetic processes. MADS-box genes constitute a transcription factor family in eukaryotes. In Arabidopsis, their proteins participate in all major aspects of shoot development, but their role in root development is still not well characterized. In this review we synthetize current knowledge pertaining to the function of MADS-box genes highly expressed in roots: XAL1, XAL2, ANR1 and AGL21, as well as available data for other MADS-box genes expressed in this organ. The role of Trithorax group and Polycomb group complexes on MADS-box genes' epigenetic regulation is also discussed. We argue that understanding the role of MADS-box genes in root development of species with contrasting architectures is still a challenge. Finally, we propose that MADS-box genes are key components of the gene regulatory networks that underlie various gene expression patterns, each one associated with the distinct developmental fates observed in the root. In the case of XAL1 and XAL2, their role within these networks could be mediated by regulatory feedbacks with auxin.

Overexpression of SlGRAS7 Affects Multiple Behaviors Leading to Confer Abiotic Stresses Tolerance and Impacts Gibberellin and Auxin Signaling in Tomato

Abiotic stresses remain the key environmental issues that reduce plant development and therefore affect crop production. Transcription factors, such as the GRAS family, are involved in various functions of abiotic stresses and plant growth. The GRAS family of tomato (Solanum lycopersicum), SlGRAS7, is described in this study. We produced overexpressing SlGARS7 plants to learn more about the GRAS transcription factors. Plants overexpressing SlGARS7 (SlGRAS7-OE) showed multiple phenotypes related to many behaviors, including plant height, root and shoot length, and flowering time. We observed that many genes in the SlGRAS7-OE seedlings that are associated with auxin and gibberellin (GA) are downregulated and have altered sensitivity to GA₃/IAA. SlGRAS7 was upregulated during abiotic stresses following treatment with sodium chloride (NaCl) and D-mannitol in the wild-type (WT) tomato. Tomato plants overexpressing SlGRAS7 showed more resistance to drought and salt stress comparison with WT. Our study of SlGRAS7 in tomato demonstrates how GRAS showed an integrative role, improving resistance to abiotic stresses and enhancing gibberellin/auxin signaling through reproductive as well as vegetative processes.

CaMADS, a MADS-box transcription factor from pepper, plays an important role in the response to cold, salt, and osmotic stress

MADS-box family transcription factors play essential roles in the growth and development of plants, and some MADS-box genes have also been found to participate in the stress-response. At present, little information regarding stress-related MADS-box genes is available in pepper. We isolated a MADS-box transcription factor gene from Capsicum annuum, which we named CaMADS. CaMADS expression is induced by low and high temperature, salt, and osmotic stress, and also by abscisic acid (ABA), salicylic acid (SA), methyl-jasmonic acid (MeJA), and CaCl_2. To understand the function of CaMADS in the abiotic stress response, we generated pepper plants in which CaMADS expression was down-regulated using VIGS (Virus-induced Gene Silencing), and also transgenic Arabidopsis plants overexpressing CaMADS. We found that CaMADS-down-regulated seedlings were more seriously injured than WT after cold, NaCl, and mannitol treatment, and showed increased electrolyte leakage, malondialdehyde (MDA) levels, and lower chlorophyll content. CaMADS-overexpressing Arabidopsis plants were more tolerant to these stresses than WT, and showed significantly high survival rates and lower H₂O₂ and super oxide radical contents after cold treatment. CaMADS-overexpressing plants had higher germination rates and percentages of green cotyledons following NaCl and mannitol treatment. Root lengths and fresh weight in CaMADS-overexpressing plants were also significantly longer and higher, respectively, than in WT plants. Taken together, our results suggest that CaMADS functions as a positive stress-responsive transcription factor in the cold, salt, and osmotic stress signaling pathways.

Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.)

Estimation of phytoene, lycopene, β-carotene, lutein, and zeaxanthin in grains of white, brown and purple cultivars of rice revealed marked differences in the levels of these carotenoid intermediates amongst the cultivars. Grains of white rice did not show any significant accumulation of carotenoid intermediates at any stage of development. On the other hand, grains of the purple cultivar accumulated 49.16 ± 5 µg of β-carotene, 28.89 ± 3.2 µg of lutein and 34.65 ± 4.6 µg of zeaxanthin per gm of grain fresh weight. In addition to PSY1, higher expression of βLCY than εLCY appears to be an important factor in determining the flux of pathway towards synthesis of β-β branch carotenoids in purple rice. This cultivar showed a higher fold change in carotenoid precursors during transition from milky to doughing stages and an enhanced flux of lycopene towards β-carotene during grain maturation. Our results indicate that higher level of carotenoids in purple rice is a consequence of higher expression of genes involved in pyruvate metabolism as well as those involved in carotenoid biosynthesis such as PSY1, PDS and β-LCY. Co-expression networking revealed a strong positive relationship between the expression profiles of genes involved in carotenoid biosynthesis and genes coding for geranylgeranyl transferase type II, glutathione S-transferase, DnaJ and SET domain containing proteins as well as MADS26 and R2R3MYB family of transcription factors.

MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants

Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition. Despite the fact that several studies have started to identify various members of the MADS-box gene family as important molecular components involved in different types of stress responses, we still lack an integrated view of their role in these processes. In this review, we analyze the function and regulation of MADS-box gene family members in response to drought, salt, cold, heat, and oxidative stress conditions in different developmental processes of several plants. In addition, we suggest that MADS-box genes are key components of gene regulatory networks involved in plant responses to stress and plant developmental plasticity in response to seasonal changes in environmental conditions.

Molecular cloning, characterization and expression analysis of MADS-box genes associated with reproductive development in Momordica dioica Roxb

The repertoire and functions of MADS-box family transcription factors (TFs) largely remains unexplored with respect to floral organogenesis of Momordica dioica Roxb. Degenerative PCR followed by rapid amplification of cDNA ends was employed in the present study to clone and characterize 17 MADS-box genes (designated as MdMADS01 to MdMADS17) from the floral buds of M. dioica. The cloned genes were clustered into three subgroups (11 MIKC^C, 4 MIKC* and 2 Mα) based on phylogenetic relationships with the MADS-box genes from Cucumis sativus, Cucumis melo and Arabidopsis thaliana. Southern hybridization showed that all the isolated genes were represented by single copy locus in the M. dioica genome. Gene structure analysis revealed 1-8 exons in MdMADS-box genes with the number of exons in MIKC greatly exceeding from that in M-type genes. Motif elicitation of the MdMADS-box genes indicated the presence of additional domains with MIKC type, suggesting that they had more complex structures. Expression analysis of MdMADS genes in six M. dioica transcriptome suggested that, 11 MIKC^C-type genes are associated with floral homeotic functions, 4 MIKC*-type genes (MdMADS12 to MdMADS15) controlled the growth of male gametophyte, while the two M-type genes (MdMADS16 and MdMADS17) played significant role in female gametogenesis and seed development. Overall, these are the first set of MADS-box genes from M. dioica exhibiting a differential expression pattern during floral development. The results from this study will provide valuable information for further functional studies of candidate MADS-box genes in the sexual dimorphism of this economically important dioecious cucurbit.

Regulation of plant height in rice by the Polycomb group genes OsEMF2b, OsFIE2 and OsCLF

An ideal plant height is essential for crop yield. Some Polycomb group (PcG) genes mutants exhibit a dwarf phenotype in rice. To determine how PcG genes regulate plant height, we investigated the phenotypes of the emf2b mutant and OsEMF2b, OsFIE2 and OsCLF RNAi transgenic plants; they all exhibited dwarf phenotype. Further analyses indicated that stem elongation at jointing stage was seriously inhibited in emf2b and RNAi transgenic plants. Reduced cell expansion and cell division of stem caused significant reduction of stem length during mature period of OsEMF2b, OsFIE2 and OsCLF RNAi transgenic plants. Transcription analysis revealed that cell division, cell expansion and plant hormones related genes differentially expressed between emf2b and WT. In addition, PcG genes mutants weakened GA signal and GA concentration and leaded to suppresseion of plant height. Analysis of differentially expressed genes revealed that 109 up-regulated and 19 down-regulated genes were identified in both emf2b and fie2. H3K27me3-modified sites were observed in 95 of the 109 up-regulated genes, and some of them were up-regulated in OsFIE2, OsCLF and OsEMF2b RNAi transgenic plants, and their H3K27me3 levels were reduced in emf2b. Moreover, OsEMF2b interacted with OsCLF. Therefore, we speculated that these PcG genes, OsFIE2, OsCLF and OsEMF2b, may work as a PRC2 to regulate rice height.

Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato

MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2-4 days compared with that of the wild-type (WT). The accumulation of carotenoids and biosynthesis of ethylene in fruits were decreased in SlMBP15-silenced tomato. Genes related to carotenoid and ethylene biosynthesis were greatly repressed. SlMBP15 can interact with RIN, a MADS-box regulator affecting the carotenoid accumulation and ethylene biosynthesis in tomato. In addition, SlMBP15-silenced tomato produced dark green leaves, and its plant height was reduced. The gibberellin (GA) content of transgenic plants was lower than that of the WT and GA biosynthesis genes were repressed. These results demonstrated that SlMBP15 not only positively regulated tomato fruit ripening but also affected the morphogenesis of the vegetative organs.

OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice

Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant.

A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

BACKGROUND

MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes.

RESULTS

We identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 and FLC lineages in woody perennial species.

CONCLUSIONS

Most Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.

Post-translational regulation of rice MADS29 function: homodimerization or binary interactions with other seed-expressed MADS proteins modulate its translocation into the nucleus

OsMADS29 is a seed-specific MADS-box transcription factor that affects embryo development and grain filling by maintaining hormone homeostasis and degradation of cells in the nucellus and nucellar projection. Although it has a bipartite nuclear localization signal (NLS) sequence, the transiently expressed OsMADS29 monomer does not localize specifically in the nucleus. Dimerization of the monomers alters the intracellular localization fate of the resulting OsMADS29 homodimer, which then translocates into the nucleus. By generating domain-specific deletions/mutations, we show that two conserved amino acids (lysine(23) and arginine(24)) in the NLS are important for nuclear localization of the OsMADS29 homodimer. Furthermore, the analyses involving interaction of OsMADS29 with 30 seed-expressed rice MADS proteins revealed 19 more MADS-box proteins, including five E-class proteins, which interacted with OsMADS29. Eleven of these complexes were observed to be localized in the nucleus. Deletion analysis revealed that the KC region (K-box and C-terminal domain) plays a pivotal role in homodimerization. These data suggest that the biological function of OsMADS29 may not only be regulated at the level of transcription and translation as reported earlier, but also at the post-translational level by way of the interaction between OsMADS29 monomers, and between OsMADS29 and other MADS-box proteins.

Fine mapping of the tomato yellow leaf curl virus resistance gene Ty-2 on chromosome 11 of tomato

Resistances to begomoviruses, including bipartite tomato mottle virus and monopartite tomato yellow leaf curl virus (TYLCV), have been introgressed to cultivated tomato (Solanum lycopersicum) from wild tomato accessions. A major gene, Ty-2 from S. habrochaites f. glabratum accession "B6013," that confers resistance to TYLCV was previously mapped to a 19-cM region on the long arm of chromosome 11. In the present study, approximately 11,000 plants were screened and nearly 157 recombination events were identified between the flanking markers C2_At1g07960 (82.5 cM, physical distance 51.387 Mb) and T0302 (89 cM, 51.878 Mb). Molecular marker analysis of recombinants and TYLCV evaluation of progeny from these recombinants localized Ty-2 to an approximately 300,000-bp interval between markers UP8 (51.344 Mb) and M1 (51.645 Mb). No recombinants were identified between TG36 and C2_At3g52090, a region of at least 115 kb, indicating severe recombination suppression in this region. Due to the small interval, fluorescence in situ hybridization analysis failed to clarify whether recombination suppression is caused by chromosomal rearrangements. Candidate genes predicted based on tomato genome annotation were analyzed by RT-PCR and virus-induced gene silencing. Results indicate that the NBS gene family present in the Ty-2 region is likely not responsible for the Ty-2-conferred resistance and that two candidate genes might play a role in the Ty-2-conferred resistance. Several markers very tightly linked to the Ty-2 locus are presented and useful for marker-assisted selection in breeding programs to introgress Ty-2 for begomovirus resistance.

A MADS-box gene is specifically expressed in fibers of cotton (Gossypium hirsutum) and influences plant growth of transgenic Arabidopsis in a GA-dependent manner

In this study, a cDNA, GhMADS14, encoding a typical MADS-box protein with 223 amino acids was isolated from a cotton cDNA library. Fluorescent microscopy indicated that the GhMADS14 protein was localized in the cell nucleus. GhMADS14 was specifically expressed in the elongating fibers, and its expression was gradually enhanced at early stages of fiber elongation and reached its peak in 9-10 DPA fibers. Overexpression of GhMADS14 in Arabidopsis hindered plant growth. Measurement and statistical analysis revealed that hypocotyl length of GhMADS14 transgenic seedlings was significantly reduced, and the height of the mature transgenic plants was remarkably less than that of the wild type. Furthermore, expression of GA 20-oxidase (AtGA20ox1 and AtGA20ox2) and GA 3-oxidase (AtGA3ox1 and AtGA3ox2) genes was remarkably reduced, whereas AtGA2ox1 and AtGA2ox8 were dramatically up-regulated in the transgenic plants, compared with the wild type. These results suggested that overexpression of GhMADS14 in Arabidopsis may alter expression levels of the genes related to GA biosynthetic and metabolic pathways, resulting in the reduction of endogenous GA amounts in cells. As a result, the transgenic plants grew slowly and display a GA-deficient phenotype.

Fine mapping of the tomato yellow leaf curl virus resistance gene Ty-2 on chromosome 11 of tomato

Resistances to begomoviruses, including bipartite tomato mottle virus and monopartite tomato yellow leaf curl virus (TYLCV), have been introgressed to cultivated tomato (Solanum lycopersicum) from wild tomato accessions. A major gene, Ty-2 from S. habrochaites f. glabratum accession "B6013," that confers resistance to TYLCV was previously mapped to a 19-cM region on the long arm of chromosome 11. In the present study, approximately 11,000 plants were screened and nearly 157 recombination events were identified between the flanking markers C2_At1g07960 (82.5 cM, physical distance 51.387 Mb) and T0302 (89 cM, 51.878 Mb). Molecular marker analysis of recombinants and TYLCV evaluation of progeny from these recombinants localized Ty-2 to an approximately 300,000-bp interval between markers UP8 (51.344 Mb) and M1 (51.645 Mb). No recombinants were identified between TG36 and C2_At3g52090, a region of at least 115 kb, indicating severe recombination suppression in this region. Due to the small interval, fluorescence in situ hybridization analysis failed to clarify whether recombination suppression is caused by chromosomal rearrangements. Candidate genes predicted based on tomato genome annotation were analyzed by RT-PCR and virus-induced gene silencing. Results indicate that the NBS gene family present in the Ty-2 region is likely not responsible for the Ty-2-conferred resistance and that two candidate genes might play a role in the Ty-2-conferred resistance. Several markers very tightly linked to the Ty-2 locus are presented and useful for marker-assisted selection in breeding programs to introgress Ty-2 for begomovirus resistance.

Rice male development under drought stress: phenotypic changes and stage-dependent transcriptomic reprogramming

Drought affects rice reproduction and results in severe yield loss. The developmental defects and changes of gene regulation network in reproductive tissues under drought stress are largely unknown. In this study, rice plants subjected to reproductive stage drought stress were examined for floral development and transcriptomic changes. The results showed that male fertility was dramatically affected, with differing pollen viability in flowers of the same panicle due to aberrant anther development under water stress. Examination of local starch distribution revealed that starch accumulated abnormally in terms of position and abundance in anthers of water-stressed plants. Microarray analysis using florets of different sizes identified >1000 drought-responsive genes, most of which were specifically regulated in only one or two particular sizes of florets, suggesting developmental stage-dependent responses to drought. Genes known to be involved in tapetum and/or microspore development, cell wall formation or expansion, and starch synthesis were found more frequently among the genes affected by drought than genome average, while meiosis and MADS-box genes were less frequently affected. In addition, pathways related to gibberellin acid signaling and abscisic acid catabolism were reprogrammed by drought. Our results strongly suggest interactions between reproductive development, phytohormone signaling, and carbohydrate metabolism in water-stressed plants.

Transcriptomic and physiological variations of three Arabidopsis ecotypes in response to salt stress

Salt stress is one of the major abiotic stresses in agriculture worldwide. Analysis of natural genetic variation in Arabidopsis is an effective approach to characterize candidate salt responsive genes. Differences in salt tolerance of three Arabidopsis ecotypes were compared in this study based on their responses to salt treatments at two developmental stages: seed germination and later growth. The Sha ecotype had higher germination rates, longer roots and less accumulation of superoxide radical and hydrogen peroxide than the Ler and Col ecotypes after short term salt treatment. With long term salt treatment, Sha exhibited higher survival rates and lower electrolyte leakage. Transcriptome analysis revealed that many genes involved in cell wall, photosynthesis, and redox were mainly down-regulated by salinity effects, while transposable element genes, microRNA and biotic stress related genes were significantly changed in comparisons of Sha vs. Ler and Sha vs. Col. Several pathways involved in tricarboxylic acid cycle, hormone metabolism and development, and the Gene Ontology terms involved in response to stress and defense response were enriched after salt treatment, and between Sha and other two ecotypes. Collectively, these results suggest that the Sha ecotype is preconditioned to withstand abiotic stress. Further studies about detailed gene function are needed. These comparative transcriptomic and analytical results also provide insight into the complexity of salt stress tolerance mechanisms.

Proteins linked to drought tolerance revealed by DIGE analysis of drought resistant and susceptible barley varieties

Drought is a major threat to world agriculture. In order to identify proteins associated with plant drought tolerance, barley varieties bred in the UK (Golden Promise) and Iraq (Basrah) were compared. The variety Basrah showed physiological adaptations to drought when compared to Golden Promise, for example relative water content of roots and shoots after 1 week of drought was much higher for Basrah than for Golden Promise. DIGE analysis was carried out on proteins from roots and leaves under control and drought conditions. Twenty-four leaf and 45 root proteins were identified by MALDI-TOF MS. The relative expression patterns of the identified proteins fell into a number of distinct classes. The variety Basrah is characterised by constitutive expression or higher drought-induced expression levels of proteins regulating ROS production and protein folding. Photosynthetic enzymes, by contrast, were downregulated in Basrah. Enzyme assays showed a good correlation between DIGE-derived protein abundance estimates and enzyme activity in extracts. Overall, this study shows that the enhanced drought tolerance of variety Basrah is driven by an enhanced regulation of ROS under drought.

Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice

In plants, MADS-box transcription factors are key regulators of floral and fruit development, organ dehiscence and stress responses. Nevertheless, the functions of most of them are still unknown. In Arabidopsis thaliana, the AGL17-like clade of MADS-box transcription factors comprises four members. AGL17 is involved in floral induction, whereas AGL44/ANR1 is involved in the adaptive development of roots in response to nitrate. AGL21 is primarily expressed in the roots and AGL16 in the leaves, suggesting that these transcription factors may be involved in the control of vegetative development. In Oryza sativa, the AGL17-like clade comprises five members, OsMADS23, OsMADS25, OsMADS27, OsMADS57 and OsMADS61. In a first attempt to characterize their functions, we used promoter::Gus reporter gene fusions and RT-qPCR to study the expression patterns of these genes and their regulation by different external stimuli. The OsMADS23, OsMADS25, OsMADS27 and OsMADS57 promoters were active in the root's central cylinder. In addition, the OsMADS57 promoter was active in leaves, whereas the OsMADS61 promoter was only active in the leaf tips and the stem base. OsMADS25 and OsMADS27 transcripts accumulated in response to osmotic stress, whereas the expression levels of OsMADS25, OsMADS27 and OsMADS57 were slightly induced by nitrate. Each of these five genes was responsive to various hormonal treatments. These distinct expression patterns indicate that these five genes have specific and non-redundant functions that likely differs from those of their A. thaliana homologs.

The OitaAG and OitaSTK genes of the orchid Orchis italica: a comparative analysis with other C- and D-class MADS-box genes

According to the ABCDE model of flower development, the C- and D- class MADS box genes are involved in the formation of male and female reproductive organs (fused to form the column in orchids) and in ovule maturation (triggered by fertilization in orchids). In the present study, we report the isolation of the Orchis italica genes OitaAG and OitaSTK, homologs of the C-class AGAMOUS and the D-class SEEDSTICK genes of Arabidopsis, respectively. Analysis of their expression profiles reveals high levels of mRNA in columns and ovaries, particularly after pollination. However, weak expression is also detectable in the inner tepals (OitaAG) and the lip and root (OitaSTK). This expression profile is only partially overlapping with those reported in other orchid species and may be the consequence of a different evolutionary history of these functional gene classes in orchids. The genomic characterization of the OitaAG and OitaSTK genes shows that a high number of traces of mobile elements are present in introns and could have contributed to the size expansion of some of them (e.g., intron 2 and 3 of OitaAG and intron 3, 4 and 5 of OitaSTK). Nucleotide sequences of intron 1 of the OitaSTK gene and other STK-like genes do not share regulatory motifs, whereas sequence comparison of intron 2 of the OitaAG gene with that of intron 2 of other AG-like genes reveals, for the first time in an orchid species, the presence of conserved cis-regulatory boxes and binding sites for transcription factors that positively (e.g., LEAFY and WUSCHEL) or negatively (e.g., BELLRINGER) regulate the expression of the AG homologs in dicots and monocots.

Genome-wide association study (GWAS) of resistance to head smut in maize

Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a devastating global disease in maize, leading to severe quality and yield loss each year. The present study is the first to conduct a genome-wide association study (GWAS) of head smut resistance using the Illumina MaizeSNP50 array. Out of 45,868 single nucleotide polymorphisms in a panel of 144 inbred lines, 18 novel candidate genes were associated with head smut resistance in maize. These candidate genes were classified into three groups, namely, resistance genes, disease response genes, and other genes with possible plant disease resistance functions. The data suggested a complicated molecular mechanism of maize resistance against S. reiliana. This study also suggested that GWAS is a useful approach for identifying causal genetic factors for head smut resistance in maize.

Agave tequilana MADS genes show novel expression patterns in meristems, developing bulbils and floral organs

Agave tequilana is a monocarpic perennial species that flowers after 5-8 years of vegetative growth signaling the end of the plant's life cycle. When fertilization is unsuccessful, vegetative bulbils are induced on the umbels of the inflorescence near the bracteoles from newly formed meristems. Although the regulation of inflorescence and flower development has been described in detail for monocarpic annuals and polycarpic species, little is known at the molecular level for these processes in monocarpic perennials, and few studies have been carried out on bulbils. Histological samples revealed the early induction of umbel meristems soon after the initiation of the vegetative to inflorescence transition in A. tequilana. To identify candidate genes involved in the regulation of floral induction, a search for MADS-box transcription factor ESTs was conducted using an A. tequilana transcriptome database. Seven different MIKC MADS genes classified into 6 different types were identified based on previously characterized A. thaliana and O. sativa MADS genes and sequences from non-grass monocotyledons. Quantitative real-time PCR analysis of the seven candidate MADS genes in vegetative, inflorescence, bulbil and floral tissues uncovered novel patterns of expression for some of the genes in comparison with orthologous genes characterized in other species. In situ hybridization studies using two different genes showed expression in specific tissues of vegetative meristems and floral buds. Distinct MADS gene regulatory patterns in A. tequilana may be related to the specific reproductive strategies employed by this species.

Alteration in expression of hormone-related genes in wild emmer wheat roots associated with drought adaptation mechanisms

Transcriptomic and metabolomic profiles were used to unravel drought adaptation mechanisms in wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of cultivated wheat, by comparing the response to drought stress in roots of genotypes contrasting in drought tolerance. The differences between the drought resistant (R) and drought susceptible (S) genotypes were characterized mainly by shifts in expression of hormone-related genes (e.g., gibberellins, abscisic acid (ABA) and auxin), including biosynthesis, signalling and response; RNA binding; calcium (calmodulin, caleosin and annexin) and phosphatidylinositol signalling, in the R genotype. ABA content in the roots of the R genotype was higher in the well-watered treatment and increased in response to drought, while in the S genotype ABA was invariant. The metabolomic profiling revealed in the R genotype a higher accumulation of tricarboxylic acid cycle intermediates and drought-related metabolites, including glucose, trehalose, proline and glycine. The integration of transcriptomics and metabolomics results indicated that adaptation to drought included efficient regulation and signalling pathways leading to effective bio-energetic processes, carbon metabolism and cell homeostasis. In conclusion, mechanisms of drought tolerance were identified in roots of wild emmer wheat, supporting our previous studies on the potential of this genepool as a valuable source for novel candidate genes to improve drought tolerance in cultivated wheat.

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance

Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.

Chestnut species and jasmonic acid treatment influence development and community interactions of galls produced by the Asian chestnut gall wasp, Dryocosmus kuriphilus

Jasmonic acid (JA) is a plant-signaling hormone involved in defenses against insects and pathogens as well as the regulation of nutrient partitioning. Gall wasps (Hymenoptera: Cynipidae) induce the formation of galls on their host plants, which house immature wasps and provide them with nutrition and protection. The goal of this study was to investigate the effects of JA application on gall development and defenses. Dryocosmus kuriphilus Yasumatsu (Hymenoptera: Cynipidae) galls on American chestnut, Castanea dentata (Marsh.) Borkhausen (Fagales: Fagaceae), and Chinese chestnut, C. mollissima Blume, were treated with JA or a JA- inhibitor, diethyldithiocarbamic acid (DIECA), to determine the effects of these treatments on gall characteristics and defenses. Chinese chestnut galls treated with JA had greater volume and dry weight, thicker sclerenchyma layers, and fewer external fungal lesions compared with controls. Galls from both chestnut species treated with JA contained a lower proportion of empty chambers, and elevated tannin levels compared with controls. The effects of DIECA on galls were generally opposite from those of JA. American chestnut galls treated with DIECA had lower dry weight and fewer feeding punctures caused by the lesser chestnut weevil compared with controls. Galls from both chestnut species that were treated with DIECA were smaller and had more external fungal lesions compared with controls. Compared to American chestnut galls, Chinese chestnut galls had increased parasitism rates and fewer gall wasps. This study is the first to investigate the effects of JA on an insect gall, and indicates that JA treatments benefit gall wasps by increasing gall size and defenses.

Three MADS-box genes of Hevea brasiliensis expressed during somatic embryogenesis and in the laticifer cells

Three MADS-box genes, designated HbMADS1, HbMADS2 and HbMADS3, were isolated from Hevea brasiliensis. HbMADS1, HbMADS2 and HbMADS3 encode polypetides consisting of 245, 217 and 239 amino acids, respectively, containing conserved MADS-box motifs at N-terminus. Transcription pattern analysis revealed that three MADS-box genes had highly transcription in the laticifer cells. The transcriptions of HbMADS1and HbMADS3 were induced in the laticifer cells by jamonic acid, while HbMADS2 was not induction by jamonic acid. Ethephone is not effective in inducing their expression. The three genes were differentially expressed during somatic embryogenesis of rubber tree. Characterization of HbMADSs will attribute to understand their possible function in rubber tree.

Identification of an Arabidopsis Nodulin-related protein in heat stress

We identified a Nodulin-related protein 1 (NRP1) encoded by At2g03440, which was previously reported to be RPS2 interacting protein in yeast-two-hybrid assay. Northern blotting showed that AtNRP1 expression was suppressed by heat stress (42 degrees C) and induced by low temperature (4 degrees C) treatment. Strong GUS staining was observed in the sites of meristematic tissues of pAtNRP1:: GUS transgenic plants, such as shoot apex and root tips, young leaf veins, stamens and stigmas of flowers, and abscission layers of young siliques. To study AtNRP1 biological functions, we have characterized both loss-of-function T-DNA insertion and transgenic overexpression plants for AtNRP1 in Arabidopsis. The T-DNA insertion mutants displayed no obvious difference as compared to wild-type Arabidopsis under heat stress, but the significant enhanced susceptibility to heat stress was revealed in two independent AtNRP1-overexpressing transgenic lines. Further study found that the decreased thermotolerance in AtNRP1-overexpressing lines accompanied significantly decreased accumulation of ABA after heat treatment, which was probably due to AtNRP1 playing a role in negative-feedback regulation of the ABA synthesis pathway. These results support the viewpoint that the application of ABA inhibits nodulation and nodulin-related gene expression and threaten adverse ambient temperature can impact the nodulin-related gene expression.