Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

Genome-wide identification and expression pattern analysis of the Aux/IAA (auxin/indole-3-acetic acid) gene family in alfalfa (Medicago sativa) and the potential functions under drought stress

BACKGROUND

Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown.

RESULT

A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1-4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein-protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa.

CONCLUSION

This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.

Genome-Wide Analysis of Aux/IAA Gene Family in Artemisia argyi: Identification, Phylogenetic Analysis, and Determination of Response to Various Phytohormones

Artemisia argyi is a traditional herbal medicine plant, and its folium artemisia argyi is widely in demand due to moxibustion applications globally. The Auxin/indole-3-acetic acid (Aux/IAA, or IAA) gene family has critical roles in the primary auxin-response process, with extensive involvement in plant development and stresses, controlling various essential traits of plants. However, the systematic investigation of the Aux/IAA gene family in A. argyi remains limited. In this study, a total of 61 Aux/IAA genes were comprehensively identified and characterized. Gene structural analysis indicated that 46 Aux/IAA proteins contain the four typical domains, and 15 Aux/IAA proteins belong to non-canonical IAA proteins. Collinear prediction and phylogenetic relationship analyses suggested that Aux/IAA proteins were grouped into 13 distinct categories, and most Aux/IAA genes might experience gene loss during the tandem duplication process. Promoter cis-element investigation indicated that Aux/IAA promoters contain a variety of plant hormone response and stress response cis-elements. Protein interaction prediction analysis demonstrated that AaIAA26/29/7/34 proteins are possibly core members of the Aux/IAA family interaction. Expression analysis in roots and leaves via RNA-seq data indicated that the expression of some AaIAAs exhibited tissue-specific expression patterns, and some AaIAAs were involved in the regulation of salt and saline-alkali stresses. In addition, RT-qPCR results indicated that AaIAA genes have differential responses to auxin, with complex response patterns in response to other hormones, indicating that Aux/IAA may play a role in connecting auxin and other hormone signaling pathways. Overall, these findings shed more light on AaIAA genes and offer critical foundational knowledge toward the elucidation of their function during plant growth, stress response, and hormone networking of Aux/IAA family genes in A. argyi.

Genome-Wide Identification of the Paulownia fortunei Aux/IAA Gene Family and Its Response to Witches' Broom Caused by Phytoplasma

The typical symptom of Paulownia witches' broom (PaWB), caused by phytoplasma infection, is excessive branching, which is mainly triggered by auxin metabolism disorder. Aux/IAA is the early auxin-responsive gene that participates in regulating plant morphogenesis such as apical dominance, stem elongation, lateral branch development, and lateral root formation. However, no studies have investigated the response of the Aux/IAA gene family to phytoplasma infection in Paulownia fortunei. In this study, a total of 62 Aux/IAA genes were found in the genome. Phylogenetic analysis showed that PfAux/IAA genes could be divided into eight subgroups, which were formed by tandem duplication and fragment replication. Most of them had a simple gene structure, and several members lacked one or two conserved domains. By combining the expression of PfAux/IAA genes under phytoplasma stress and SA-treated phytoplasma-infected seedlings, we found that PfAux/IAA13/33/45 may play a vital role in the occurrence of PaWB. Functional analysis based on homologous relationships showed a strong correlation between PfAux/IAA45 and branching. Protein-protein interaction prediction showed that PfARF might be the binding partner of PfAux/IAA, and the yeast two-hybrid assay and bimolecular fluorescent complementary assay confirmed the interaction of PfAux/IAA45 and PfARF13. This study provides a theoretical basis for further understanding the function of the PfAux/IAA gene family and exploring the regulatory mechanism of branching symptoms caused by PaWB.

Analysis of Auxin-Encoding Gene Family in Vigna radiata and It's Cross-Species Expression Modulating Waterlogging Tolerance in Wild Vigna umbellata

Mungbean is known to be susceptible to waterlogging (WL) stress. Some of the wild species have the potential to tolerate this through various physiological and molecular mechanisms. Auxin Response Factor (ARF) and Auxin/Indole Acetic Acid (AUX/IAA), an early responsive gene family, has multiple functions in growth, development, and stress tolerance. Here, we report the first comprehensive analysis of the ARF and AUX/IAA gene family in mungbean. A total of 26 ARF and 19 AUX/IAA genes were identified from the mungbean genome. The ARF and AUX/IAA candidates were clearly grouped into two major clades. Further, the subgrouping within the major clades indicated the presence of significant diversity. The gene structure, motif analysis, and protein characterization provided the clue for further fundamental research. Out of the10 selected candidate genes, VrARF-5, VrARF-11, VrARF-25, and VrAUX/IAA-9 were found to significantly multiple-fold gene expression in the hypocotyl region of WL-tolerant wild relatives (PRR 2008-2) provides new insight into a role in the induction of lateral root formation under WL stress. The analysis provides an insight into the structural diversity of ARF and AUX/IAA genes in mungbean. These results increase our understanding of ARF and AUX/IAA genes and therefore offer robust information for functional investigations, which can be taken up in the future and will form a foundation for improving tolerance against waterlogging stress.

Genome-Wide Characterization of the Aux/IAA Gene Family in Orchardgrass and a Functional Analysis of DgIAA21 in Responding to Drought Stress

Drought stress is an important factor that reduces plant biomass production and quality. As one of the most important economic forage grasses, orchardgrass (Dactylis glomerata) has high drought tolerance. Auxin/indole-3-acetic acid (Aux/IAA) is one of the early responsive gene families of auxin and plays a key role in the response to drought stress. However, the characteristics of the Aux/IAA gene family in orchardgrass and their potential function in responding to drought stress remain unclear. Here, 30 Aux/IAA members were identified in orchardgrass. Segmental duplication may be an important driving force in the evolution of the Aux/IAA gene family in orchardgrass. Some Aux/IAA genes were induced by IAA, drought, salt, and temperature stresses, implying that these genes may play important roles in responding to abiotic stresses. Heterologous expression in yeast revealed that DgIAA21 can reduce drought tolerance. Similarly, the overexpression of DgIAA21 also reduced drought tolerance in transgenic Arabidopsis, which was supported by lower total chlorophyll content and relative water content as well as higher relative electrolyte leakage and malondialdehyde content (MDA) than Col-0 plants under drought conditions. The results of this study provided valuable insight into the function of DgIAAs in response to drought stress, which can be further used to improve forage grass breeding programs.

Regulatory Mechanisms of ArAux/IAA13 and ArAux/IAA16 in the Rooting Process of Acer rubrum

Acer rubrum is difficult to root during cutting propagation. Auxin/indole-acetic acids (Aux/IAA) proteins, which are encoded by the early response genes of auxin, are transcriptional repressors that play important roles in auxin-mediated root growth and development. In this study, ArAux/IAA13 and ArAux/IAA16, which were significantly differentially expressed after 300 mg/L indole butyric acid treatment, were cloned. Heatmap analysis revealed that they might be associated with the process of adventitious root (AR) growth and development mediated by auxin. Subcellular localization analysis showed that they performed their function in the nucleus. Bimolecular fluorescence complementation assays revealed the interactions between them and two auxin response factor (ARF) proteins, ArARF10 and ArARF18, confirming their relevance to AR growth and development. Overexpression of transgenic plants confirmed that the overexpression of ArAux/IAA13 and ArAux/IAA16 inhibited AR development. These results help elucidate the mechanisms of auxin-mediated AR growth and development during the propagation of A. rubrum and provide a molecular basis for the rooting of cuttings.

Genome-Wide Characterization of the Mitogen-Activated Protein Kinase Gene Family and Their Expression Patterns in Response to Drought and Colletotrichum Gloeosporioides in Walnut (Juglans regia)

Mitogen-activated protein kinases (MAPKs) are a family of Ser/Thr (serine/threonine) protein kinases that play very important roles in plant responses to biotic and abiotic stressors. However, the MAPK gene family in the important crop walnut (Juglans regia L.) has been less well studied compared with other species. We discovered 25 JrMAPK members in the Juglans genome in this study. The JrMAPK gene family was separated into four subfamilies based on phylogenetic analysis, and members of the same subgroup had similar motifs and exons/introns. A variety of cis-acting elements, mainly related to the light response, growth and development, stress response, and hormone responses, were detected in the JrMAPK gene promoters. Collinearity analysis showed that purification selection was the main driving force in JrMAPK gene evolution, and segmental and tandem duplications played key roles in the expansion of the JrMAPK gene family. The RNA-Seq (RNA Sequencing) results indicated that many of the JrMAPK genes were expressed in response to different levels of Colletotrichum gloeosporioides infection. JrMAPK1, JrMAPK3, JrMAPK4, JrMAPK5, JrMAPK6, JrMAPK7, JrMAPK9, JrMAPK11, JrMAPK12, JrMAPK13, JrMAPK17, JrMAPK19, JrMAPK20, and JrMAPK21 were upregulated at the transcriptional level in response to the drought stress treatment. The results of this study will help in further investigations of the evolutionary history and biological functions of the MAPK gene family in walnut.

Genome-wide identification and co-expression network analysis of Aux/IAA gene family in Salvia miltiorrhiza

The auxin/indole-3-acetic acid (Aux/IAA) gene family serves as a principal group of genes responsible for modulating plant growth and development through the auxin signaling pathway. Despite the significance of this gene family, the identification and characterization of members within the well-known Chinese medicinal herb Salvia miltiorrhiza (S. miltiorrhiza) have not been thoroughly investigated. In this study, we employed bioinformatics methods to identify 23 Aux/IAA genes within the genome of S. miltiorrhiza. These genes were classified into typical IAA and atypical IAA based on their domain structure. Our analysis of the promoter regions revealed that the expression of these genes is regulated not only by auxins, but also by other hormones and environmental factors. Furthermore, we found that the expression patterns of these genes varied across various tissues of S. miltiorrhiza. While our initial hypothesis suggested that the primary function of these genes was the interaction between SmIAA and ARF, gene co-expression network analysis revealed that they are also influenced by various other transcription factors, such as WRKY and ERF. The findings establish a sturdy basis for future investigations into the function of the Aux/IAA gene family and exhibit promising prospects for enhancing the genetics of this medicinal flora and its associated species.

Identification of the OsCML4 Gene in Rice Related to Salt Stress Using QTL Analysis

Soil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (Oryza sativa L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the Indica variety Cheongcheong and the Japonica variety Nagdong were used. A total of 23 QTLs for 8 different traits related to salinity resistance on chromosomes 1–3 and 5–12 were identified at the seedling stage. A QTL related to the salt injury score (SIS), qSIS-3b, had an LOD score of six within the interval RM3525–RM15904 on chromosome 3, and a phenotypic variation of 31% was further examined for the candidate genes. Among all the CNDH populations, five resistant lines (CNDH 27, CNDH 34-1, CNDH 64, CNDH 78, and CNDH 112), five susceptible lines (CNDH 52-1, CNDH 67, CNDH 69, CNDH 109, and CNDH 110), and the parent lines Cheongcheong and Nagdong were selected for relative gene expression analysis. Among all the genes, two candidate genes were highly upregulated in resistant lines, including the auxin-responsive protein IAA13 (Os03g0742900) and the calmodulin-like protein 4 (Os03g0743500-1). The calmodulin-like protein 4 (Os03g0743500-1) showed a higher expression in all the resistant lines than in the susceptible lines and a high similarity with other species in sequence alignment and phylogenetic tree, and it also showed a protein–protein interaction with other important proteins. The genes identified in our study will provide new genetic resources for improving salt resistance in rice using molecular breeding strategies in the future.

Identification and expression analysis of the lipid phosphate phosphatases gene family reveal their involvement in abiotic stress response in kiwifruit

Lipid phosphate phosphatases (LPPs) are a key enzyme in the production and degradation of phosphatidic acid (PA), which plays an important role in plant growth, development, stress resistance and plant hormone response. Thus far, little is known about the LPP family genes in kiwifruit (Actinidia spp.). According to this study, 7 members in the AcLPP family were identified from the whole genome of kiwifruit, the subcellular localization predictions were mainly on the plasma membrane. Chromosomal localization analysis showed that the AcLPP genes were unevenly distributed on 5 chromosomes, it was determined to have undergone strong purifying selection pressure. There were 5 duplicate gene pairs and all underwent segmental duplication events. The LPP genes of kiwifruit were conserved when compared with other plants, especially in terms of evolutionary relationships, conserved motifs, protein sequences, and gene structures. Cis-regulatory elements mainly included hormone response elements and abiotic response elements. Functional annotation of GO revealed that AcLPP genes were closely related to phosphatase/hydrolase activity, phosphorus metabolism and dephosphorylation. AcLPP genes family were predicted to be targets of miRNA. Transcript level analysis revealed that the AcLPP family played diverse functions in different tissues and during growth, development, and postharvest storage stages. qPCR analysis showed that the members of AcLPP gene family might be regulated by ETH, ABA, GA3, and IAA hormone signals. The family members were regulated by the stress of salt stress, osmotic stress, cold stress, and heat stress. These results would provide a basis and reference for studying the agricultural characteristics of kiwifruit and improving its stress resistance.

Comparative Transcriptomic Analysis of Root and Leaf Transcript Profiles Reveals the Coordinated Mechanisms in Response to Salinity Stress in Common Vetch

Owing to its strong environmental suitability to adverse abiotic stress conditions, common vetch (Vicia sativa) is grown worldwide for both forage and green manure purposes and is an important protein source for human consumption and livestock feed. The germination of common vetch seeds and growth of seedlings are severely affected by salinity stress, and the response of common vetch to salinity stress at the molecular level is still poorly understood. In this study, we report the first comparative transcriptomic analysis of the leaves and roots of common vetch under salinity stress. A total of 6361 differentially expressed genes were identified in leaves and roots. In the roots, the stress response was dominated by genes involved in peroxidase activity. However, the genes in leaves focused mainly on Ca²⁺ transport. Overexpression of six salinity-inducible transcription factors in yeast further confirmed their biological functions in the salinity stress response. Our study provides the most comprehensive transcriptomic analysis of common vetch leaf and root responses to salinity stress. Our findings broaden the knowledge of the common and distinct intrinsic molecular mechanisms within the leaves and roots of common vetch and could help to develop common vetch cultivars with high salinity tolerance.

Bioinformatics Study of Aux/IAA Family Genes and Their Expression in Response to Different Hormones Treatments during Japanese Apricot Fruit Development and Ripening

Auxin/indole-3-acetic acid (Aux/IAA) is a transcriptional repressor in the auxin signaling pathway that plays a role in several plant growth and development as well as fruit and embryo development. However, it is unclear what role they play in Japanese apricot (Prunus mume) fruit development and maturity. To investigate the role of Aux/IAA genes in fruit texture, development, and maturity, we comprehensively identified and expressed 19 PmIAA genes, and demonstrated their conserved domains and homology across species. The majority of PmIAA genes are highly responsive and expressed in different hormone treatments. PmIAA2, PmIAA5, PmIAA7, PmIAA10, PmIAA13, PmIAA18, and PmIAA19 showed a substantial increase in expression, suggesting that these genes are involved in fruit growth and maturity. During fruit maturation, alteration in the expression of PmIAA genes in response to 1-Methylcyclopropene (1-MCP) treatment revealed an interaction between auxin and ethylene. The current study investigated the response of Aux/IAA development regulators to auxin during fruit ripening, with the goal of better understanding their potential application in functional genomics.

Toward synthetic plant development

The ability to engineer plant form will enable the production of novel agricultural products designed to tolerate extreme stresses, boost yield, reduce waste, and improve manufacturing practices. While historically, plants were altered through breeding to change their size or shape, advances in our understanding of plant development and our ability to genetically engineer complex eukaryotes are leading to the direct engineering of plant structure. In this review, I highlight the central role of auxin in plant development and the synthetic biology approaches that could be used to turn auxin-response regulators into powerful tools for modifying plant form. I hypothesize that recoded, gain-of-function auxin response proteins combined with synthetic regulation could be used to override endogenous auxin signaling and control plant structure. I also argue that auxin-response regulators are key to engineering development in nonmodel plants and that single-cell -omics techniques will be essential for characterizing and modifying auxin response in these plants. Collectively, advances in synthetic biology, single-cell -omics, and our understanding of the molecular mechanisms underpinning development have set the stage for a new era in the engineering of plant structure.

Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Class III peroxidases (PODs) are plant-specific glycoproteins, that play essential roles in various plant physiological processes and defence responses. To date, scarce information is available about the POD gene family in soybean. Hence, the present study is the first comprehensive report about the genome-wide characterization of GmPOD gene family in soybean (Glycine max L.). Here, we identified a total of 124 GmPOD genes in soybean, that are unevenly distributed across the genome. Phylogenetic analysis classified them into six distinct sub-groups (A-F), with one soybean specific subgroup. Exon-intron and motif analysis suggested the existence of structural and functional diversity among the sub-groups. Duplication analysis identified 58 paralogous gene pairs; segmental duplication and positive/Darwinian selection were observed as the major factors involved in the evolution of GmPODs. Furthermore, RNA-seq analysis revealed that 23 out of a total 124 GmPODs showed differential expression between drought-tolerant and drought-sensitive genotypes under stress conditions; however, two of them (GmPOD40 and GmPOD42) revealed the maximum deregulation in all contrasting genotypes. Overexpression (OE) lines of GsPOD40 showed considerably higher drought tolerance compared to wild type (WT) plants under stress treatment. Moreover, the OE lines showed enhanced photosynthesis and enzymatic antioxidant activities under drought stress, resulting in alleviation of ROS induced oxidative damage. Hence, the GsPOD40 enhanced drought tolerance in soybean by regulating the key physiological and biochemical pathways involved in the defence response. Lastly, the results of our study will greatly assist in further functional characterization of GsPODs in plant growth and stress tolerance in soybean.

Genome-Wide Analysis of the Auxin/Indoleacetic Acid Gene Family and Response to Indole-3-Acetic Acid Stress in Tartary Buckwheat (Fagopyrum tataricum)

Auxin/indoleacetic acid (Aux/IAA) family genes respond to the hormone auxin, which have been implicated in the regulation of multiple biological processes. In this study, all 25 Aux/IAA family genes were identified in Tartary buckwheat (Fagopyrum tataricum) by a reiterative database search and manual annotation. Our study provided comprehensive information of Aux/IAA family genes in buckwheat, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. Aux/IAA family genes were nonuniformly distributed in the buckwheat chromosomes and divided into seven groups by phylogenetic analysis. Aux/IAA family genes maintained a certain correlation and a certain species-specificity through evolutionary analysis with Arabidopsis and other grain crops. In addition, all Aux/IAA genes showed a complex response pattern under treatment of indole-3-acetic acid (IAA). These results provide valuable reference information for dissecting function and molecular mechanism of Aux/IAA family genes in buckwheat.

Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L

Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.

Genome-Wide Identification and Expression Analysis of the Aux/IAA and Auxin Response Factor Gene Family in Medicago truncatula

Aux/IAA and auxin response transcription factor (ARF) genes are key regulators of auxin responses in plants. A total of 25 MtIAA and 40 MtARF genes were identified based on the latest updated Medicago truncatula reference genome sequence. They were clustered into 10 and 8 major groups, respectively. The homologs among M. truncatula, soybean, and Arabidopsis thaliana shared close relationships based on phylogenetic analysis. Gene structure analysis revealed that MtIAA and MtARF genes contained one to four concern motifs and they are localized to eight chromosomes, except chromosome 6 without MtARFs. In addition, some MtIAA and MtARF genes were expressed in all tissues, while others were specifically expressed in specific tissues. Analysis of cis-acting elements in promoter region and expression profiles revealed the potential response of MtIAA and MtARF genes to hormones and abiotic stresses. The prediction protein–protein interaction network showed that some ARF proteins could interact with multiple Aux/IAA proteins, and the reverse is also true. The investigation provides valuable, basic information for further studies on the biological functions of MtIAA and MtARF genes in the regulation of auxin-related pathways in M. truncatula.

OsIAA20, an Aux/IAA protein, mediates abiotic stress tolerance in rice through an ABA pathway

In plants, auxin and ABA play significant roles in conferring tolerance to environmental abiotic stresses. Earlier studies have been shown that some Aux/IAA genes, with important signaling factors in the auxin pathway, were induced in response to drought and other abiotic stresses. However, the mechanistic links between Aux/IAA expression and general drought response remain largely unknown. In this study, OsIAA20, a rice Aux/IAA protein, shown with important roles in abiotic stress. Phenotypic analyses revealed that OsIAA20 RNAi transgenic rice reduced drought and salt tolerance; whereas, OsIAA20 overexpression plants displayed the opposite phenotype. Physiological analyses of OsIAA20 RNAi rice grown under drought or salt stress showed that proline and chlorophyll content significantly decreased, while malondialdehyde content and the ratio of Na⁺/ K⁺ significantly increased. In addition, OsIAA20down-regulation reduced stomatal closure and increased the rate of water loss, while transgenic plants overexpressing OsIAA20 exhibited the opposite physiological responses. Furthermore, an ABA-responsive gene, OsRab21, was down-regulated in OsIAA20 RNAi rice lines and upregulated in OsIAA20 overexpression plants. Those results means OsIAA20 played an important role in plant drought and salt stress responses, by an ABA dependent mechanism, and it will be a candidate target gene used to breed abiotic stress tolerance.

Genome-wide identification of AUX/IAA in radish and functional characterization of RsIAA33 gene during taproot thickening

Auxin/indole-3-acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root-specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT-qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA-mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish.

Identification and Expression Analysis of miR160 and Their Target Genes in Cucumber

miR160 plays a crucial role in various biological processes by regulating their target gene auxin response factor (ARF) in plants. However, little is known about miR160 and ARF in cucumber fruit expansion. Here, 4 Csa-MIR160 family members and 17 CsARFs were identified through a genome-wide search. Csa-miR160 showed a closer relationship with those in melon. Phylogenetic analysis revealed that CsARFs were divided into four classes and most of CsARFs presented a closer evolutionary relationship with those from tomato. Putative cis-elements analysis predicted that Csa-MIR160 and CsARFs were involved in light, phytohormone and stress response, which proved that they might take part in light, phytohormone and stress signaling pathway by the miR160-ARF module. In addition, CsARF5, CsARF11, CsARF13 and CsARF14 were predicted as the target genes of Csa-miR160. qRT-PCR revealed that Csa-miR160 and their target gene CsARFs were differentially expressed in differential cucumber tissues and developmental stages. Csa-miR160d was only expressed in the expanded cucumber fruit. CsARF5, CsARF11 and CsARF13 exhibited the lower expression in the expanded fruit than those in the ovary, while, CsARF14 showed the reverse trend. Our results suggested that Csa-miR160d might play a crucial role in cucumber fruit expansion by negatively targeting CsARF5, CsARF11 and CsARF13. This is the first genome-wide analysis of miR160 in cucumber. These findings provide useful information and resources for further studying the role of miR160 and ARF in cucumber fruit expansion.

De novo transcriptome assembly and comparative transcriptomic analysis provide molecular insights into low temperature stress response of Canarium album

A de novo transcriptome analysis was performed in C. album, a temperature sensitive fruit tree in China, after treatment with varied temperatures. A total number of 168,385 transcripts were assembled, comprising of 109,439 unigenes, of which 70,530 were successfully annotated. Compared with control check group (CK), which was treated under 25 °C, the chilling stress (4 °C) treated group (CT), showed about 2810 up-regulated and 2567 down-regulated genes. Whereas, group treated under freezing (- 3 °C) stress (FT) showed an up-regulation and a down-regulation of 1748 and 1459 genes, respectively. GO classification analysis revealed that DEGs related to metabolic processes, single-organism metabolic process, and catalytic activity are significantly enriched in both CT and FT conditions. KEGG pathway enrichment analysis for both CT and FT treatments showed an enrichment of genes encoding or related to glycine/serine and threonine metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis, photosynthesis-antenna proteins, and circadian rhythm. However, genes related to photosynthesis, carbon fixation in photosynthetic organisms, glutathione metabolism, pyruvate metabolism, nicotinate and nicotinamide metabolism were specifically enriched in CT condition. Nevertheless, FT treatment induced genes related to plant-pathogen interaction, linoleic acid metabolism, plant hormone signal transduction and pentose phosphate pathway. Many of the genes involved in plant hormone signal transduction showed significantly different expression in both FT and CT conditions. However, the change was more evident in FT. Here we present the first of the reports for a de novo transcriptomic analysis in C. album, suggesting that the plant shows differential responses in chilling and freezing temperatures, where the hormone signaling and transduction contribute greatly to FT responses. Our study thus paves way for future research regarding functions of these potentially identified genes.

Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules

Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.

Aux/IAA14 Regulates microRNA-Mediated Cold Stress Response in Arabidopsis Roots

The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators of plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA (miR) in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4 °C revealed that the auxin signaling mutant, solitary root 1 (slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRs in the wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26–31 nt small RNA population in slr1 compared with wild type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRs in slr1 at 4 °C compared with wild type. Target gene expression analysis of the members from one potential candidate miR, miR169, revealed the possible involvement of miR169/NF-YA module in the Aux/IAA14-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRs in auxin and cold responses.

Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in apple (Malus domestica)

Auxin is a necessary phytohormone for fruit development, accompanying the whole process of fruit growth and development. The Aux/IAA gene family is one of the early auxin-responsive gene families. At present, there were few reports involved in Aux/IAA genes in the fruit, especially in apple. In our study, we identified 42 MdAux/IAAs, phylogenetic analysis showed that Aux/IAA proteins from apple, tomato, and strawberry were clustered into 5 groups, 42 MdAux/IAAs randomly distributed on 13 chromosomes. Additionally, a comprehensive analysis of Aux/IAA gene family was completed, including gene structures, conserved motifs, phylogenetic analysis, chromosome mapping, orthologous identification, selection pressure analyses, synteny analysis, and protein interaction. We also tested the expression of MdAux/IAAs in different tissues and fruit development stages using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), we found that the most members of Aux/IAA showed higher expression in seeds compared within stem and leaves, indicating they may play a role in regulating fruit development. We also declared that the expression of Aux/IAA gene was not consistent in the pericarp and seeds at the same developmental stage, 3 MdAux/IAAs of the pericarp were upregulated over 20-fold at 90 d and 5 MdAux/IAAs of the seeds were upregulated over 40-fold at 90 d. It was MdAux/IAA23 that showed extreme up-regulated expression in both pericarp and seeds. This study proved that the Aux/IAA gene families may perform a different function in apple fruit development and ripening, more importantly, it provided a foundation for further exploring the biological function of these MdAux/IAAs.

Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean (Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach

Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.

Identification of Candidate Auxin Response Factors Involved in Pomegranate Seed Coat Development

Auxin response factors (ARFs) are transcription factors, regulating the auxin signaling pathways involved in plant development and related processes. In this study, we performed the genome-wide identification and characterization of ARFs in pomegranate and compared them with ARFs from three other species. Seventeen PgrARFs were identified and clustered into four groups, according to their phylogenetic relationship with the remaining 59 ARFs. A recent whole-genome duplication event in pomegranate may have contributed to the expansion and diversification of PgrARFs. Genomic truncation and variant splicing mechanisms contributed to the divergence of PgrARFs, a conclusion that was supported by different exon-intron structures of genes and incomplete conserved domains of PgrARFs in a specific phylogenetic group (group III). Interestingly, the absence of motifs from certain PgrARF genes corresponded to their low transcription levels, which contrasted to the highly expressed PgrARFs with intact motifs. Specifically, PgrARF1 and PgrARF2 highly expressed in both inner and outer seed coat, and phylogenetically related to Arabidopsis orthologs which mediates cell divisions in seed coat. We infer these two PgrARFs might involve in seed coat development through cell divisions in response to auxin regulation. These findings provided information on the characteristics and evolutionary relationships of PgrARFs, but also shed lights on their potential roles during seed coat development in pomegranate.

Identification and Bioinformatic Analysis of the GmDOG1-Like Family in Soybean and Investigation of Their Expression in Response to Gibberellic Acid and Abscisic Acid

Seed germination is one of the most important stages during plant life cycle, and DOG1 (Delay of germination1) plays a pivotal regulatory role in seed dormancy and germination. In this study, we have identified the DOG1-Like (DOG1L) family in soybean (Glycine max), a staple oil crop worldwide, and investigated their chromosomal distribution, structure and expression patterns. The results showed that the GmDOG1L family is composed of 40 members, which can be divided into six subgroups, according to their evolutionary relationship with other known DOG1-Like genes. These GmDOG1Ls are distributed on 18 of 20 chromosomes in the soybean genome and the number of exons for all the 40 GmDOG1Ls varied greatly. Members of the different subgroups possess a similar motif structure composition. qRT-PCR assay showed that the expression patterns of different GmDOG1Ls were significantly altered in various tissues, and some GmDOG1Ls expressed primarily in soybean seeds. Gibberellic acid (GA) remarkably inhibited the expression of most of GmDOG1Ls, whereas Abscisic acid (ABA) inhibited some of the GmDOG1Ls expression while promoting others. It is speculated that some GmDOG1Ls regulate seed dormancy and germination by directly or indirectly relating to ABA and GA pathways, with complex interaction networks. This study provides an important theoretical basis for further investigation about the regulatory roles of GmDOG1L family on soybean seed germination.

Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.)

Aux/IAA genes are early auxin-responsive genes and essential for auxin signaling transduction. There is little information about Aux/IAAs in the agriculturally important cereal, barley. Using in silico method, we identified and subsequently characterized 36 Aux/IAAs from the barley genome. Based on their genomic sequences and the phylogenic relationship with Arabidopsis and rice Aux/IAA, the 36 HvIAAs were categorized into two major groups and 14 subgroups. The indication of the presence or absence of these domains for the biological functions and acting mechanisms was discussed. The cis-element distributions in HvIAA promoters suggests that the HvIAAs expressions may not only regulated by auxin (the presence of AuxREs and TGA-element) but also by other hormones and developmental and environmental cues. We then studied the HvIAAs expression in response to NAA (1-Naphthaleneacetic acid) using quantitative real-time PCR (qRT-PCR). Like the promoter analysis, only 14 HvIAAs were upregulated by NAA over two-fold at 4 h. HvIAAs were clustered into three groups based on the spatiotemporal expression data. We confirmed by qRT-PCR that most HvIAAs, especially HvIAA3, HvIAA7, HvIAA8, HvIAA18, HvIAA24 and HvIAA34, are expressed in the developing barley spike compared within seedling, suggesting their roles in regulating spike development. Taken together, our data provide a foundation for further revealing the biological function of these HvIAAs.

Molecular functional analysis of auxin/indole-3-acetic acid proteins (Aux/IAAs) in plant disease resistance in cassava

Auxin/indole-3-acetic acid proteins (Aux/IAAs) play important roles in auxin signaling pathways, with extensive involvement in plant development and plant response to abiotic and biotic stresses. Manihot esculenta (Cassava) is one of the most important biomass energy crops in tropical regions; however, the information about Aux/IAA proteins remain limited in cassava. In this study, 37 MeAux/IAA gene family members were identified in cassava and a phylogenetic analysis was performed. The transcript levels of MeAux/IAAs were commonly regulated by the pathogen Xanthomonas axonopodis pv manihotis (Xam), and some of them were specifically localized to the nucleus. Moreover, the overexpression of MeAux/IAAs confers an improved disease resistance against Xam in Nicotiana benthamiana, while MeAux/IAAs-silenced plants show disease sensitivity against Xam in cassava, as evidenced by the leaf phenotype and leaf bacterial population. Consistent with the disease resistance, MeAux/IAAs regulated the transcript levels of PATHOGENESIS-RELATED GENES (MePRs), reactive oxygen species accumulation and callose development in the plants' defense response. Taken together, gene profile and functional analysis identified several MeAux/IAAs as novel members in plant disease resistance, providing important information for further utilization of MeAux/IAAs.

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Auxin/Indole-3-Acetic Acid (Aux/IAA) genes are involved in auxin signaling pathway and play an important role in plant growth and development. However, many studies focus on Aux/IAA gene families and much less known in Bletilla striata. In this study, a total of 27 Aux/IAA genes (BsIAA1-27) were cloned from the transcriptome of Bletilla striata. Based on a phylogenetic analysis of the Aux/IAA protein sequences from B. striata, Arabidopsis thaliana and Dendrobium officinale, the Aux/IAA genes of B. striata (BsIAAs) were categorized into 2 subfamilies and 9 groups. While BsIAAs were more closer to those of D. officinale compared to A. thaliana. EST-SSR marker mining test showed that 4 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our results suggested that BsIAAs were involved in the process of tuber development and provided insights into functional roles of Aux/IAA genes in B. striata and other plants.

A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea (Cicer arietinum L.)

The aim of this study was to provide a comprehensive analysis of the plant-specific B3 domain-containing transcription factors (TFs) in chickpea. Scanning of the chickpea genome resulted in the identification of 51 B3 domain-containing TFs that were located on seven out of eight chickpea chromosomes. Based on the presence of additional domains other than the B3 domain, the candidates were classified into four subfamilies, i.e., ARF (24), REM (19), LAV (6) and RAV (2). Phylogenetic analysis classified them into four groups in which members of the same group had similar intron-exon organization and motif composition. Genome duplication analysis of the candidate B3 genes revealed an event of segmental duplication that was instrumental in the expansion of the B3 gene family. Ka/Ks analysis showed that the B3 gene family was under purifying selection. Further, chickpea B3 genes showed maximum orthology with Medicago followed by soybean and Arabidopsis. Promoter analyses of the B3 genes led to the identification of several tissue-specific and stress-responsive cis-regulatory elements. Expression profiling of the candidate B3 genes using publicly available RNA-seq data of several chickpea tissues indicated their putative role in plant development and abiotic stress response. These findings were further validated by real-time expression analysis. Overall, this study provides a comprehensive analysis of the B3 domain-containing proteins in chickpea that would aid in devising strategies for crop manipulation in chickpea.

Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes

We have isolated several Osiaa23 rice mutants with different knockout genotypes, resulting in different phenotypes, which suggested that different genetic backgrounds or mutation types influence gene function. The Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family performs critical roles in auxin signal transduction in plants. In rice, the gene OsIAA23 (Os06t0597000) is known to affect development of roots and shoots, but previous knockouts in OsIAA23 have been sterile and difficult for research continuously. Here, we isolate new Osiaa23 mutants using the CRISPR/Cas9 system in japonica (Wuyunjing24) and indica (Kasalath) rice, with extensive genome re-sequencing to confirm the absence of off-target effects. In Kasalath, mutants with a 13-amino acid deletion showed profoundly greater dwarfing, lateral root developmental disorder, and fertility deficiency, relative to mutants with a single amino acid deletion, demonstrating that those 13 amino acids in Kasalath are essential to gene function. In Wuyunjing24, we predicted that mutants with a single base-pair frameshift insertion would experience premature termination and strong phenotypic defects, but instead these lines exhibited negligible phenotypic difference and normal fertility. Through RNA-seq, we show here that new mosaic transcripts of OsIAA23 were produced de novo, which circumvented the premature termination and thereby preserved the wild-type phenotype. This finding is a notable demonstration in plants that mutants can mask loss of function CRISPR/Cas9 editing of the target gene through de novo changes in alternative splicing.

Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

Genome-Wide Identification of the Aux/IAA Family Genes (MdIAA) and Functional Analysis of MdIAA18 for Apple Tree Ideotype

The Aux/IAA (auxin/indole-3-acetic acid) gene family is one of the early auxin-responsive gene families, which play a central role in auxin response. Few reports are involved in Aux/IAA genes in fruit trees, especially in apple (Malus × domestica Borkh.). A total of 33 MdIAA members were identified, of which 27 members contained four conserved domains, whereas the others lost one or two conserved domains. Several cis-elements in promoters of MdIAAs were predicted responsive to hormones and abiotic stress. Tissue-specific expression patterns of MdIAAs in different apple tree ideotypes were investigated by quantitative real-time PCR. A large number of MdIAAs were highly expressed in leaf buds and reproductive organs, and MdIAAs clustered in same group showed similar expression profiles. Overexpression of MdIAA18 in Arabidopsis resulted in compact phenotype. These results indicated that MdIAA genes may be involved in vegetative and reproductive growth of apple. Taken together, the results provide useful clues to reveal the function of MdIAAs in apple and control apple tree architecture by manipulation of MdIAAs.

Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles

Acetylserotonin methyltransferase (ASMT) in plant species, one of the most important enzymes in melatonin biosynthesis, plays a rate-limiting role in the melatonin production. In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. The results showed that at least 16 CaASMT genes were identified in the pepper genome. Phylogenetic analyses of all the CaASMTs were divided into three groups (group I, group II, and group III) with a high bootstrap value. Through the online MEME tool, six distinct motifs (motif 1 to motif 6) were identified. Chromosome location found that most CaASMT genes were mapped in the distal ends of the pepper chromosomes. In addition, RNA-seq analysis revealed that, during the vegetative and reproductive development, the difference in abundance and distinct expression patterns of these CaASMT genes suggests different functions. The qRT-PCR analysis showed that high abundance of CaASMT03, CaASMT04, and CaASMT06 occurred in mature green fruit and mature red fruit. Finally, using RNA-seq and qRT-PCR technology, we also found that several CaASMT genes were induced under abiotic stress conditions. The results will not only contribute to elucidate the evolutionary relationship of ASMT genes but also ascertain the biological function in pepper plant response to abiotic stresses.

TIR1 auxin receptors are implicated in the differential response to 4-Cl-IAA and IAA in developing pea fruit

The auxins indole-3-acetic acid (IAA) and 4-chloroindole-3-acetic acid (4-Cl-IAA) occur naturally in pea (Pisum sativum); however, only 4-Cl-IAA mimics the presence of seeds in stimulating pericarp growth. To examine if this differential auxin effect is mediated through TIR1/AFB auxin receptors, pea TIR1 and AFB2 homologs were functionally characterized in Arabidopsis, and receptor expression, and auxin distribution and action were profiled in developing pea fruits. PsTIR1a, PsTIR1b, and PsAFB2 restored the auxin-sensitive root growth response to the mutant Arabidopsis seedlings Attir1-10 and/or Attir1-10 afb2-3. Expression of PsTIR1 or AtTIR1 in Attir1-10 afb2-3 mutants also restored the greater root inhibitory response of 4-Cl-IAA compared to that of IAA, implicating TIR1 receptors in this response. The ability of 4-Cl-IAA to stimulate a stronger DR5::GUS auxin response than IAA at the same concentration in pea pericarps was associated with its ability to enrich the auxin-receptor transcript pool with PsTIR1a and PsAFB2 by decreasing the transcript abundance of PsTIR1b (mimicking results in pericarps with developing seeds). Therefore, the markedly different effect of IAA and 4-Cl-IAA on pea fruit growth may at least partially involve TIR1/AFB receptors and the differential modulation of their population, resulting in specific Aux/IAA protein degradation that leads to an auxin-specific tissue response.

Genome reorganization of the GmSHMT gene family in soybean showed a lack of functional redundancy in resistance to soybean cyst nematode

In soybeans, eighteen members constitute the serine hydroxymethyltransferase (GmSHMT) gene family, of which the cytosolic-targeted GmSHMT08c member has been reported to mediate resistance to soybean cyst nematode (SCN). This work presents a comprehensive study of the SHMT gene family members, including synteny, phylogeny, subcellular localizations, haplotypes, protein homology modeling, mutational, and expression analyses. Phylogenetic analysis showed that SHMT genes are divided into four classes reflecting their subcellular distribution (cytosol, nucleus, mitochondrion, and chloroplast). Subcellular localization of selected GmSHMT members supports their in-silico predictions and phylogenetic distribution. Expression and functional analyses showed that GmSHMT genes display many overlapping, but some divergent responses during SCN infection. Furthermore, mutational analysis reveals that all isolated EMS mutants that lose their resistance to SCN carry missense and nonsense mutations at the GmSHMT08c, but none of the Gmshmt08c mutants carried mutations in the other GmSHMT genes. Haplotype clustering analysis using the whole genome resequencing data from a collection of 106 diverse soybean germplams (15X) was performed to identify allelic variants and haplotypes within the GmSHMT gene family. Interestingly, only the cytosolic-localized GmSHMT08c presented SNP clusters that were associated with SCN resistance, supporting our mutational analysis. Although eight GmSHMT members respond to the nematode infestation, functional and mutational analysis has shown the absence of functional redundancy in resistance to SCN. Structural analysis and protein homology modeling showed the presence of spontaneous mutations at important residues within the GmSHMT proteins, suggesting the presence of altered enzyme activities based on substrate affinities. Due to the accumulation of mutations during the evolution of the soybean genome, the other GmSHMT members have undergone neofunctionalization and subfunctionalization events.

Systematic identification and expression pattern analysis of the Aux/IAA and ARF gene families in moso bamboo (Phyllostachys edulis)

Auxin plays a central role in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. However, little is known about the Aux/IAA and ARF gene families in moso bamboo (Phyllostachys edulis). In this paper, we first identified 35 putative PeIAAs and 24 PeARFs in the moso bamboo genome. These genes were clustered into two major groups (A and B) and four groups (I-IV), respectively, based on phylogenetic analysis. Next, analyses of evolutionary patterns and divergence demonstrated that both the PeIAAs and PeARFs experienced a large-scale duplication event around 15 million years ago (MYA). The divergence times of the two gene families were 31 MYA between moso bamboo and rice, and 46 MYA between moso bamboo and maize. Furthermore, the expression profiling of PeIAA and PeARF genes in various tissues and developmental stages revealed tissue-specific expression. qRT-PCR analysis confirmed the differential expression patterns of selected PeIAA and PeARF genes. And then a comprehensive expression analysis of these genes was also performed under exogenous hormone treatment by qRT-PCR. Many PeIAAs and PeARFs showed differential expression in response to IAA treatment. Subcellular localization results show that PeIAA8 is a nuclear localization protein. Most importantly, we demonstrate that single moso bamboo ARF can interact with multiple Aux/IAA proteins and vice versa. Collectively, the detailed analyses presented here will help in understanding the roles of the PeIAA and PeARF gene families and contribute to further research on their biological functions during development in moso bamboo.

Genome-wide identification of the auxin/indole-3-acetic acid (Aux/IAA) gene family in pepper, its characterisation, and comprehensive expression profiling under environmental and phytohormones stress

Auxin is an essential phytohormone that plays a crucial role in the growth and development of plants in stressful environments. Here, we analysed the auxin/indole-3-acetic acid (Aux/IAA) gene family, which produces auxin in pepper, and succeeded in identifying 27 putative members containing four conserved domains (I. II. III and IV) in their protein sequences. Sequence analysis, chromosomal mapping and motif prediction of all identified CaAux/IAA genes were performed. It was observed that these genes contained four conserved motifs divided into nine different groups and distributed across nine chromosomes in pepper plants. RNA-seq analysis revealed the organ specific expression of many CaAux/IAA genes. However, the majority of genes were expressed with high expression levels in the early stages of fruit development. However, the maximum expression level of the CA03g34540 gene was observed in the breaker stage. Moreover, thirteen CaAux/IAA genes were labelled as early responsive genes to various phytohormone and abiotic stresses. Furthermore, RNA-seq analysis in response to pathogen inoculation (PepMoV, TMV strains P0/P1, and Phytophthora capsici) showed distinct expression profiles of all identified genes, suggesting the diverse expression nature of genes under these stress conditions. Overall, this study provides insight into the dynamic response of CaAux/IAA genes under environmental and phytohormones stress conditions, providing bases to further explore the importance of these genes through mutant/transgenic analysis in pepper.

Current advances in chickpea genomics: applications and future perspectives

Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.

Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function

Auxin plays a crucial role in the diverse cellular and developmental responses of plants across their lifespan. Plants can quickly sense and respond to changes in auxin levels, and these responses involve several major classes of auxin-responsive genes, including the Auxin/Indole-3-Acetic Acid (Aux/IAA) family, the auxin response factor (ARF) family, small auxin upregulated RNA (SAUR), and the auxin-responsive Gretchen Hagen3 (GH3) family. Aux/IAA proteins are short-lived nuclear proteins comprising several highly conserved domains that are encoded by the auxin early response gene family. These proteins have specific domains that interact with ARFs and inhibit the transcription of genes activated by ARFs. Molecular studies have revealed that Aux/IAA family members can form diverse dimers with ARFs to regulate genes in various ways. Functional analyses of Aux/IAA family members have indicated that they have various roles in plant development, such as root development, shoot growth, and fruit ripening. In this review, recently discovered details regarding the molecular characteristics, regulation, and protein-protein interactions of the Aux/IAA proteins are discussed. These details provide new insights into the molecular basis of the Aux/IAA protein functions in plant developmental processes.

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

BACKGROUND

Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known.

RESULTS

In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation.

CONCLUSIONS

Members of the Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of the Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

Genome-wide analysis and transcriptomic profiling of the auxin biosynthesis, transport and signaling family genes in moso bamboo (Phyllostachys heterocycla)

Background

Auxin is essential for plant growth and development. Although substantial progress has been made in understanding auxin pathways in model plants such as Arabidopsis and rice, little is known in moso bamboo which is famous for its fast growth resulting from the rapid cell elongation and division.

Results

Here we showed that exogenous auxin has strong effects on crown and primary roots. Genes involved in auxin action, including 13 YUCCA (YUC) genes involved in auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) and 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) members involved in auxin transport, 10 auxin receptors (AFB) involved in auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) genes, and 41 auxin response factors (ARF) involved in auxin signaling were identified through genome-wide analysis. Phylogenetic analysis of these genes from Arabidopsis, Oryza sativa and bamboo revealed that auxin biosynthesis, transport, and signaling pathways are conserved in these species. A comprehensive study of auxin-responsive genes using RNA sequencing technology was performed, and the results also supported that moso bamboo shared a conserved regulatory mechanism for the expression of auxin pathway genes; meanwhile it harbors its own specific properties.

Conclusions

In summary, we generated an overview of the auxin pathway in bamboo, which provides information for uncovering the precise roles of auxin pathway in this important species in the future.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4250-0) contains supplementary material, which is available to authorized users.

Evolution Analysis of the Aux/IAA Gene Family in Plants Shows Dual Origins and Variable Nuclear Localization Signals

The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea

Auxin response factors (ARFs) are the transcription factors that regulate auxin responses in various aspects of plant growth and development. Although genome-wide analysis of ARF gene family has been done in some species, no information is available regarding ARF genes in chickpea. In this study, we identified 28 ARF genes (CaARF) in the chickpea genome. Phylogenetic analysis revealed that CaARFs can be divided into four different groups. Duplication analysis revealed that 50% of CaARF genes arose from duplication events. We analyzed expression pattern of CaARFs in various developmental stages. CaARF16.3, CaARF17.1 and CaARF17.2 showed highest expression at initial stages of flower bud development, while CaARF6.2 had higher expression at later stages of flower development. Further, CaARF4.2, CaARF9.2, CaARF16.2 and CaARF7.1 exhibited differential expression under different abiotic stress conditions, suggesting their role in abiotic stress responses. Co-expression network analysis among CaARF, CaIAA and CaGH3 genes enabled us to recognize components involved in the regulatory network associated with CaARFs. Further, we identified microRNAs that target CaARFs and TAS3 locus that trigger production of trans-acting siRNAs targeting CaARFs. The analyses presented here provide comprehensive information on ARF family members and will help in elucidating their exact function in chickpea.

Genome-wide identification and evolution of the PIN-FORMED (PIN) gene family in Glycine max

Soybean (Glycine max) is one of the most important crop plants. Wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, and seed coat development; these characters may be related to auxin biology. The PIN gene family encodes essential transport proteins in cell-to-cell auxin transport, but little research on soybean PIN genes (GmPIN genes) has been done, especially with respect to the evolution and differences between wild and cultivated soybean. In this study, we retrieved 23 GmPIN genes from the latest updated G. max genome database; six GmPIN protein sequences were changed compared with the previous database. Based on the Plant Genome Duplication Database, 18 GmPIN genes have been involved in segment duplication. Three pairs of GmPIN genes arose after the second soybean genome duplication, and six occurred after the first genome duplication. The duplicated GmPIN genes retained similar expression patterns. All the duplicated GmPIN genes experienced purifying selection (Ka/Ks < 1) to prevent accumulation of non-synonymous mutations and thus remained more similar. In addition, we also focused on the artificial selection of the soybean PIN genes. Five artificially selected GmPIN genes were identified by comparing the genome sequence of 17 wild and 14 cultivated soybean varieties. Our research provides useful and comprehensive basic information for understanding GmPIN genes.

Genome-wide identification of membrane-bound fatty acid desaturase genes in Gossypium hirsutum and their expressions during abiotic stress

Membrane-bound fatty acid desaturases (FADs) are of great importance and play multiple roles in plant growth and development. In the present study, 39 full-length FAD genes, based on database searches, were identified in tetraploid upland cotton (Gossypium hirsutum L.) and were phylogenetically clustered into four subfamilies. Genomic localization revealed that 34 genes were mapped on 22 chromosomes, and five genes were positioned on the scaffold sequences. The FAD genes of G. hirsutum in the same subfamily had similar gene structures. The structures of paralogous genes were considerably conserved in exons number and introns length. It was suggested that the FAD gene families in G. hirsutum might be duplicated mainly by segmental duplication. Moreover, the FAD genes were differentially expressed in different G. hirsutum tissues in response to different levels of salt and cold stresses, as determined by qRT-PCR analysis. The identification and functional analysis of FAD genes in G. hirsutum may provide more candidate genes for genetic modification.

Characterization of the Soluble NSF Attachment Protein gene family identifies two members involved in additive resistance to a plant pathogen

Proteins with Tetratricopeptide-repeat (TPR) domains are encoded by large gene families and distributed in all plant lineages. In this study, the Soluble NSF-Attachment Protein (SNAP) subfamily of TPR containing proteins is characterized. In soybean, five members constitute the SNAP gene family: GmSNAP18, GmSNAP11, GmSNAP14, GmSNAP02, and GmSNAP09. Recently, GmSNAP18 has been reported to mediate resistance to soybean cyst nematode (SCN). Using a population of recombinant inbred lines from resistant and susceptible parents, the divergence of the SNAP gene family is analysed over time. Phylogenetic analysis of SNAP genes from 22 diverse plant species showed that SNAPs were distributed in six monophyletic clades corresponding to the major plant lineages. Conservation of the four TPR motifs in all species, including ancestral lineages, supports the hypothesis that SNAPs were duplicated and derived from a common ancestor and unique gene still present in chlorophytic algae. Syntenic analysis of regions harbouring GmSNAP genes in soybean reveals that this family expanded from segmental and tandem duplications following a tetraploidization event. qRT-PCR analysis of GmSNAPs indicates a co-regulation following SCN infection. Finally, genetic analysis demonstrates that GmSNAP11 contributes to an additive resistance to SCN. Thus, GmSNAP11 is identified as a novel minor gene conferring resistance to SCN.