Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1

Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata

Fritillaria unibracteata is an endangered medicinal plant whose bulb has been used as a Chinese herb to suppress cough, asthma and excessive phlegm for centuries. Steroidal alkaloids, which are synthesized via the steroid synthesis pathways, are their significant bioactive constituents. However, few studies on genes involved in steroidal alkaloid biosynthesis in F. unibracteata have been reported, mainly due to the lack of the F. unibracteata genome. In this paper, comparative transcriptomic and metabolomic analyses of four different tissues of F. unibracteata (leaves, flowers, stems, and bulbs) were performed. Imperialine, peiminine, and peimisine were among the significant bioactive compounds that were considerably abundant in bulb tissue, according to the metabolomic findings. Then, 83.60 Gb transcriptome sequencing of four different tissues was performed, of which one gene encoding phosphomevalonate kinase was directly functionally characterized to verify the accuracy of sequences obtained from the transcriptome. A total of 9217 differentially expressed unigenes (DEGs) were identified in four different tissues of F. unibracteata. GO and KEGG enrichments revealed that phenylpropanoid biosynthesis, MVA-mediated terpenoid backbone biosynthesis, and steroid biosynthesis were enriched in bulb tissue, whereas enrichment of MEP-mediated terpenoid backbone biosynthesis, photosynthesis, photosynthesis-antenna protein and carotenoid biosynthesis was observed in aerial tissues. Moreover, clustering analysis indicated that the downstream steroid biosynthesis pathway was more important in steroidal alkaloid biosynthesis compared to the upstream terpenoid backbone biosynthesis pathway. Hence, MVA-mediated biosynthesis of steroidal alkaloids was proposed, in which 15 bulb-clustered DEGs were positively correlated with a high accumulation of bioactive steroid alkaloids, further validating our proposal. In addition, 36 CYP450s showing a positive correlation with bioactive steroidal alkaloids provided candidate enzymes to catalyze the subsequent steps of steroidal alkaloid biosynthesis. In addition, the transcription factors and ABC transporters clustered in bulb tissue might be responsible for the regulation and transportation of steroidal alkaloid biosynthesis. Protein-protein interaction analysis implied a highly complex steroid alkaloid biosynthesis network in which delta (24)-sterol reductase might be one of the central catalysts. Based on the integrated transcriptome and metabolome, this current study is a first step in understanding the tissue-specific biosynthesis of steroidal alkaloids in F. unibracteata. Furthermore, key genes and regulators identified herein could facilitate metabolic engineering to improve steroidal alkaloids in F. unibracteata.

Identification of genomic regions governing moisture and heat stress tolerance employing association mapping in rice (Oryza sativa L.)

BACKGROUND

Rice crop is damaged extremely by abiotic stress world-wide. The best approach to enhance drought tolerance in rice varieties is to identify and introgress yield QTLs with major effects. The Association mapping approach helps in the identification of genomic regions governing physiological, yield and yield attributes under moisture and heat stress conditions in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome.

METHODS AND RESULTS

The association mapping panel of 110 rice germplasm lines exhibited significant variation for all the traits in both irrigated and moisture stress conditions. The extent of yield reduction ranged to 83% during rabi, 2018-19, 53% in rabi, 2019-20 and 68% in pooled analysis. The genotypes Badami, Badshabhog, Pankaj, Varalu, Vasundhara, Vivekdhan, Krishna and Minghui63 exhibited drought tolerance with least yield penalty under moisture stress conditions. The genotypes Konark, MTU3626, NLR33671, PR118 and Triguna exhibited minimal reduction in heat stress tolerance traits. Association mapping of germplasm using 37808 SNP markers detected a total of 10 major MTA (Marker-trait association) clusters distributed on chromosomes 1, 3, 4 and 11 through mixed linear model (MLM) governing multiple traits from individual data analysis which are consistent across the years and situations. The pooled data generated a total of five MTA clusters located on chromosome 6. In addition, several novel unique MTAs were also identified. Heat stress analysis generated a total of 23 MTAs distributed on chromosomes 1, 5, 6 and 11. Candidate gene analysis detected a total of 53 and 38 genes under individual and pooled data analysis for various yield and yield attributes under control and moisture stress conditions, respectively and a total of 11 candidate genes in heat stress Conditions.

CONCLUSION

The major and novel MTAs identified in the present investigation for various drought and heat tolerant traits can be utilized for breeding climate-resilient rice varieties. The candidate genes predicted for key MTAs are of great value to deploy into the rice breeding after functional characterization.

Conuping BSA-Seq and RNA-Seq Reveal the Molecular Pathway and Genes Associated with the Plant Height of Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica) plays an important role in C4 crop research and agricultural development in arid areas due to its short growth period, drought tolerance, and barren tolerance. Exploration of the dwarfing mechanism and the dwarf genes of foxtail millet can provide a reference for dwarf breeding and dwarf research of other C4 crops. In this study, genetic analysis was performed using phenotypic data, candidate genes were screened by bulk segregant analysis sequencing (BSA-Seq); differentially expressed genes and metabolic pathways in different strains of high samples were analyzed by RNA sequencing (RNA-Seq). The association analysis of BSA-Seq and RNA-Seq further narrowed the candidate range. As a result, a total of three quantitative trait loci (QTLs) and nine candidate genes related to plant height were obtained on chromosomes I and IX. Based on the functional prediction of the candidate genes, we propose a hypothetical mechanism for the formation of millet dwarfing, in which, metabolism and MAPK signaling play important roles in the formation of foxtail millet plant height.

Integrated Analysis of Single-Molecule Real-Time Sequencing and Next-Generation Sequencing Eveals Insights into Drought Tolerance Mechanism of Lolium multiflorum

Lolium multiflorum is widely planted in temperate and subtropical regions globally, and it has high economic value owing to its use as forage grass for a wide variety of livestock and poultry. However, drought seriously restricts its yield and quality. At present, owing to the lack of available genomic resources, many types of basic research cannot be conducted, which severely limits the in-depth functional analysis of genes in L. multiflorum. Therefore, we used single-molecule real-time (SMRT) and next-generation sequencing (NGS) to sequence the complex transcriptome of L. multiflorum under drought. We identified 41,141 DEGs in leaves, 35,559 DEGs in roots, respectively. Moreover, we identified 1243 alternative splicing events under drought. LmPIP5K9 produced two different transcripts with opposite expression patterns, possibly through the phospholipid signaling pathway or the negatively regulated sugar-mediated root growth response to drought stress, respectively. Additionally, 13,079 transcription factors in 90 families were obtained. An in-depth analysis of R2R3-MYB gene family members was performed to preliminarily demonstrate their functions by utilizing subcellular localization and overexpression in yeast. Our data make a significant contribution to the genetics of L. multiflorum, offering a current understanding of plant adaptation to drought stress.

Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses

BACKGROUND

The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.

RESULTS

We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper.

CONCLUSIONS

Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)

Alfalfa is an important legume forage grown worldwide and its productivity is affected by environmental stresses such as drought and high salinity. In this work, three alfalfa germplasms with contrasting tolerances to drought and high salinity were used for unraveling the transcriptomic responses to drought and salt stresses. Twenty-one different RNA samples from different germplasm, stress conditions or tissue sources (leaf, stem and root) were extracted and sequenced using the PacBio (Iso-Seq) and the Illumina platforms to obtain full-length transcriptomic profiles. A total of 1,124,275 and 91,378 unique isoforms and genes were obtained, respectively. Comparative analysis of transcriptomes identified differentially expressed genes and isoforms as well as transcriptional and post-transcriptional modifications such as alternative splicing events, fusion genes and nonsense-mediated mRNA decay events and non-coding RNA such as circRNA and lncRNA. This is the first time to identify the diversity of circRNA and lncRNA in response to drought and high salinity in alfalfa. The analysis of weighted gene co-expression network allowed to identify master genes and isoforms that may play important roles on drought and salt stress tolerance in alfalfa. This work provides insight for understanding the mechanisms by which drought and salt stresses affect alfalfa growth at the whole genome level.

SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces

BACKGROUND

As rice is the staple food for more than half of the world's population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement.

METHODS AND RESULTS

The present study revealed a high level of genetic diversity among the unexploited rice landraces cultivated by the farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. Polymorphic Information Content (PIC) value ranged from 0.459 to 0.809, and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with a high value of 0.809. The current study indicated that the rice landraces are highly diverse with higher values of the adequate number of alleles, PIC, and Shannon information index. Utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome inherited together, and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study.

CONCLUSIONS

The present investigation revealed the genetic diversity of rice landraces and the haplotype analysis will open the way for genome-wide association studies, QTL identification, and marker-assisted selection in the unexplored rice landraces collected from Kerala.

Proteomics Revealed Distinct Responses to Salinity between the Halophytes Suaeda maritima (L.) Dumort and Salicornia brachiata (Roxb)

Plant resistance to salinity stress is one of the main challenges of agriculture. The comprehension of the molecular and cellular mechanisms involved in plant tolerance to salinity can help to contrast crop losses due to high salt conditions in soil. In this study, Salicornia brachiata and Suaeda maritima, two plants with capacity to adapt to high salinity levels, were investigated at proteome level to highlight the key processes involved in their tolerance to NaCl. With this purpose, plants were treated with 200 mM NaCl as optimal concentration and 500 mM NaCl as a moderate stressing concentration for 14 days. Indeed, 200 mM NaCl did not result in an evident stress condition for both species, although photosynthesis was affected (with a general up accumulation of photosynthesis-related proteins in S. brachiata under salinity). Our findings indicate a coordinated response to salinity in both the halophytes considered, under NaCl conditions. In addition to photosynthesis, heat shock proteins and peroxidase, expansins, signaling processes, and modulation of transcription/translation were affected by salinity. Interestingly, our results suggested distinct mechanisms of tolerance to salinity between the two species considered, with S. brachiata likely having a more efficient mechanism of response to NaCl.

Unveiling gibberellin-responsive coding and long noncoding RNAs in maize

We report coding and long noncoding RNAs in maize upon phytohormone gibberellin stimulation. Plant hormone gibberellin (GA) orchestrates various facets of biological processes. Dissection the transcriptomic dynamics upon GA stimulation has biological significance. Feature of maize transcriptome in response to GA application remains largely elusive. Herein, two types of plants, one was with normal height, the other was GA-sensitive dwarfism, were selected from advanced backcross population for GA₃ treatment with different concentrations. In control and GA₃-treated plants, we identified a large number of coding and long noncoding RNAs (lncRNAs) through sequencing eight ribosomal-depleted RNA libraries. Transcripts encoding GA biosynthetic and metabolic enzymes KS, GA20ox, GA3ox, and GA2ox were significantly differentially expressed in GA₃-treated samples. A total of 78 protein-coding transcripts were shared between GA₃-treated normal height and dwarf plants. Shared transcripts encoding terpene synthase, MYB transcription factor, and receptor-like protein kinase were co-regulated with their corresponding partners. Out of identified lncRNAs, 22 and 34 significantly differentially expressed lncRNAs were responsive to GA application in normal height and dwarf plants, respectively. Shared GA-responsive lncRNAs were found in GA₃-treated normal height and dwarf plants. Some lncRNAs corresponded to precursors of known miRNA, such as zma-miR528a and zma-miR528b. Multiple promising targets of significantly differentially expressed lncRNAs were discovered, including Lazy plant1 for auxin- and GA-mediated shoot gravitropism, bZIP transcription factor member for GA-controlled cell elongation. This study will improve our knowledge of GA-triggered transcriptome change and facilitate a comprehensive understanding of regulatory cascade centering on GA.

A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight

BACKGROUND

Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection.

RESULTS

We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway.

CONCLUSIONS

The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.

Genome-wide identification and functional analysis of genes expressed ubiquitously in rice

Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.

Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments

BACKGROUND

Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported.

METHODS AND FINDINGS

An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns.

CONCLUSIONS

This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.

SALT-RESPONSIVE ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice

Grain quality is an important agricultural trait that is mainly determined by grain size and composition. Here, we characterize the role of the rice transcription factor (TF) SALT-RESPONSIVE ERF1 (SERF1) during grain development. Through genome-wide expression profiling and chromatin immunoprecipitation, we found that SERF1 directly regulates RICE PROLAMIN-BOX BINDING FACTOR (RPBF), a TF that functions as a positive regulator of grain filling. Loss of SERF1 enhances RPBF expression resulting in larger grains with increased starch content, while SERF1 overexpression represses RPBF resulting in smaller grains. Consistently, during grain filling, starch biosynthesis genes such as GRANULE-BOUND STARCH SYNTHASEI (GBSSI), STARCH SYNTHASEI (SSI), SSIIIa, and ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT2 (AGPL2) are up-regulated in SERF1 knockout grains. Moreover, SERF1 is a direct upstream regulator of GBSSI. In addition, SERF1 negatively regulates germination by controlling RPBF expression, which mediates the gibberellic acid (GA)-induced expression of RICE AMYLASE1A (RAmy1A). Loss of SERF1 results in more rapid seedling establishment, while SERF1 overexpression has the opposite effect. Our study reveals that SERF1 represents a negative regulator of grain filling and seedling establishment by timing the expression of RPBF.

Natural variation in Early flowering1 contributes to early flowering in japonica rice under long days

Natural variation in heading-date genes enables rice, a short-day (SD) plant, to flower early under long-day (LD) conditions at high latitudes. Through analysis of heading-date quantitative trait loci (QTL) with F7 recombinant inbred lines from the cross of early heading 'H143' and late heading 'Milyang23 (M23)', we found a minor-effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/CKI in H143 and Koshihikari are non-functional. In F7:9 heterogeneous inbred family-near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD-dependent flowering repressor, down-regulating Ehd1 expression. In the world rice collection, two types of non-functional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions.