Homeobox-leucine Zipper Protein Research Articles

Exploring Genomic Regions Associated with Fruit Traits in Pepper: Insights from Multiple GWAS Models.

This study utilized 303 pepper accessions from diverse Capsicum species to explore fruit traits, including length, width, wall thickness, and weight. Descriptive statistics revealed a mean fruit length of 66.19 mm, width of 23.48 mm, wall thickness of 1.89 mm, and weight of 15.29 g, with significant variability, particularly in fruit weight. Correlation analysis demonstrated strong positive relationships between fruit width, weight, and fruit wall thickness (r = 0.89 and r = 0.86, respectively), while fruit length showed weaker correlations with these traits. Analysis of fruit positions revealed that the majority of accessions had a pendent fruit position (156), followed by erect (85) and intermediate (8). In terms of fruit shape, triangular and narrow triangular shapes were the most common, observed in 102 and 98 accessions, respectively. Genome-wide association studies (GWAS) identified significant single nucleotide polymorphisms (SNPs) associated with fruit traits across four models (Blink, FarmCPU, MLM, MLMM). The number of significantly associated SNPs were as follows: fruit length (89), fruit width (55), fruit weight (63), fruit wall thickness (48), fruit shape (151), and fruit position (51). Several genes were also identified where the SNPs are located or adjacent to, providing candidate genes for further exploration of the genetic basis of fruit morphology. Notably, genes such as E3 ubiquitin-protein ligase RGLG1 (associated with fruit width), Homeobox-leucine zipper protein HDG11 (involved in fruit width), Auxin response factor 23 (linked to fruit shape), and ATP-dependent zinc metalloprotease FtsH (related to fruit weight) were identified. These findings enhance our understanding of the genetic basis of fruit morphology in Capsicum, offering valuable insights for breeding and agricultural practices.

Identification of Transcription Factors of Santalene Synthase Gene Promoters and SaSSY Cis-Elements through Yeast One-Hybrid Screening in Santalum album L.

The main components of sandalwood heartwood essential oil are terpenoids, approximately 80% of which are α-santalol and β-santalol. In the synthesis of the main secondary metabolites of sandalwood heartwood, the key gene, santalene synthase (SaSSY), can produce α-santalene and β-santalene by catalyzed (E, E)-FPP. Furthermore, santalene is catalyzed by the cytochrome monooxygenase SaCYP736A167 to form sandalwood essential oil, which then produces a fragrance. However, the upstream regulatory mechanism of the key gene santalene synthase remains unclear. In this study, SaSSY (Sal3G10690) promoter transcription factors and SaSSY cis-elements were screened. The results showed that the titer of the sandalwood cDNA library was 1.75 × 107 CFU/mL, 80% of the inserted fragments identified by PCR were over 750 bp in length, and the positivity rate of the library was greater than 90%. The promoter region of the SaSSY gene was shown to have the structural basis for potential regulatory factor binding. After sequencing and bioinformatics analysis, we successfully obtained 51 positive clones and identified four potential SaSSY transcriptional regulators. Sal6G03620 was annotated as the transcription factor MYB36-like, and Sal8G07920 was annotated as the small heat shock protein HSP20 in sandalwood. Sal1G00910 was annotated as a hypothetical protein of sandalwood. Sal4G10880 was annotated as a homeobox-leucine zipper protein (ATHB-15) in sandalwood. In this study, a cDNA library of sandalwood was successfully constructed using a yeast one-hybrid technique, and the transcription factors that might interact with SaSSY gene promoters were screened. This study provides a foundation for exploring the molecular regulatory mechanism involved in the formation of sandalwood heartwood.

Transcriptome-Based Weighted Gene Co-Expression Network Analysis Reveals the Photosynthesis Pathway and Hub Genes Involved in Promoting Tiller Growth under Repeated Drought–Rewatering Cycles in Perennial Ryegrass

Drought stress, which often occurs repeatedly across the world, can cause multiple and long-term effects on plant growth. However, the repeated drought–rewatering effects on plant growth remain uncertain. This study was conducted to determine the effects of drought–rewatering cycles on aboveground growth and explore the underlying mechanisms. Perennial ryegrass plants were subjected to three watering regimes: well-watered control (W), two cycles of drought–rewatering (D2R), and one cycle of drought–rewatering (D1R). The results indicated that the D2R treatment increased the tiller number by 40.9% and accumulated 28.3% more aboveground biomass compared with W; whereas the D1R treatment reduced the tiller number by 23.9% and biomass by 42.2% compared to the W treatment. A time-course transcriptome analysis was performed using crown tissues obtained from plants under D2R and W treatments at 14, 17, 30, and 33 days (d). A total number of 2272 differentially expressed genes (DEGs) were identified. In addition, an in-depth weighted gene co-expression network analysis (WGCNA) was carried out to investigate the relationship between RNA-seq data and tiller number. The results indicated that DEGs were enriched in photosynthesis-related pathways and were further supported by chlorophyll content measurements. Moreover, tiller-development-related hub genes were identified in the D2R treatment, including F-box/LRR-repeat MAX2 homolog (D3), homeobox-leucine zipper protein HOX12-like (HOX12), and putative laccase-17 (LAC17). The consistency of RNA-seq and qRT-PCR data were validated by high Pearson’s correlation coefficients ranging from 0.899 to 0.998. This study can provide a new irrigation management strategy that might increase plant biomass with less water consumption. In addition, candidate photosynthesis and hub genes in regulating tiller growth may provide new insights for drought-resistant breeding.

Transcriptome Analysis and Metabolic Profiling Reveal the Key Regulatory Pathways in Drought Stress Responses and Recovery in Tomatoes.

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis-antenna proteins, nitrogen metabolism, plant-pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5'-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, the biosynthesis of secondary metabolites, the biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomatoes to enhance drought tolerance.

Seasonal differences in softening of early-harvested ‘Royal Gala’ apple fruit are correlated with at-harvest biomarkers indicative of abiotic stress responses

Softening of apple fruit depends on maturity at harvest and a range of orchard and environmental factors. We investigated seasonal effects on ‘Royal Gala’ storage performance independent of maturity and separate from potential orchard effects. In two consecutive seasons, fruit were harvested at four times: very early (H1), early (H2), commercial (H3) and late (H4), and were cold-stored at 0.5 °C for 100 d followed by a shelf-life period. In Year 1, fruit from H1 and H2 softened much less during storage than did fruit from Year 2. Later-harvested fruit (H3 and H4) did not show this seasonal difference and softened similarly in storage. A combined at-harvest transcriptomic and metabolomic study was analysed using mixOmics. Retained firmness in storage was correlated with increased abundance of transcripts indicative of abiotic stress, including those encoding universal stress protein, a drought stress protein, and several heat shock proteins and aquaporins. Greater softening in storage was correlated with higher abundance of fewer and different stress genes, and genes involved in cell wall metabolism. The data suggest that preharvest stresses experienced by the fruit have a profound effect on subsequent softening, at least in early-harvested fruit before ripening-related ethylene becomes the main driver. Ten potential at-harvest biomarkers were identified, including titratable acidity, erythritol and eight transcripts (notably Universal stress protein PHOS32-like and Homeobox leucine zipper protein HAT5-like). These could be useful for predicting the subsequent storage performance of batches of fruit.

What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima.

Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to integrate with local cuisines, and their long shelf life. Competition for growing the showy type or mammoth-sized pumpkins that produce the largest fruit of the entire plant kingdom has drawn attention. In this study, we used genome-wide single nucleotide polymorphisms to resolve admixture among different pumpkin groups. Also, to resolve population differentiation, genome-wide divergence and evolutionary forces underlying the evolution of mammoth-sized pumpkin. The admixture analysis indicates that the mammoth group (also called Display or Giant) evolved from the hubbard group with genome-wide introgressions from the buttercup group. We archived a set of private alleles underlying fruit development in mammoth group, and resolved haplotype level divergence involved in the evolutionary mechanisms. Our genome-wide association study identified three major allelic effects underlying various fruit-size genes in this study. For fruit weight, a missense variant in the homeobox-leucine zipper protein ATHB-20-like (S04_18528409) was significantly associated (false discovery rate = 0.000004) with fruit weight, while high allelic effect was consistent across the 3 years of the study. A cofactor (S08_217549) on chromosome 8 is strongly associated with fruit length, having superior allelic effect across the 3 years of this study. A missense variant (S10_4639871) on translocation protein SEC62 is a cofactor for fruit diameter. Several known molecular mechanisms are likely controlling giant fruit size, including endoreduplication, hormonal regulation, CLV-WUS signaling pathway, MADS-box family, and ubiquitin-proteasome pathway. This study provides a general framework for the evolutionary relationship among horticulture groups of C. maxima and elucidates the origins of rare variants contributing to the giant pumpkin fruit size.

Overexpression of the homeobox-leucine zipper protein ATHB-6 improves the drought tolerance of maize (Zea mays L.)

Homeo-Leucine Zipper (HD-Zip) proteins are a class of transcription factors unique to higher plants and are involved in plant stress responses and regulation of growth and development. However, the function of maize HD-Zip genes in enhancing drought tolerance is unknown. Here, Sub-Cellular Localization results showed that ATHB-6 fusion proteins were only localized in the nucleus. The malondialdehyde content was lower than the wild type under drought tolerance, proving that the introduction of the ATHB-6 gene can improve the drought tolerance of plants. Follow-up analysis showed that ATHB-6 could promote root growth and activities of a series of ROS-scavenging enzymes in maize. Moreover, overexpression of ATHB-6 in maize activated the expression of critical genes in the ROS signals pathway and ABA-dependent pathway under drought tolerance.Our results provides a significant advancement in undestanding the functions of HD-Zip transcription factors in maize.

Comparison of Arabidopsis thaliana Strains Exposed to Heavy Metals: Applied to Agriculture

This study reports the resistance to chromium sulfate (Cr2(SO4)3), nickel sulfate (NiSO4) and copper sulfate (CuSO4) in the Col-0, Lov-1, Ws-2 and Santa Clara strains of Arabidopsis thaliana. Previous reports have shown illness-associated with consuming crops grown in environments contaminated with such heavy metals (Shams, et al., 2018). Plant growth and biomass are also affected by considerable amounts of heavy metals in soil. To investigate the effects of heavy metals on Arabidopsis thaliana, plants were exposed to the heavy metals every two days, after 14 days of growth under normal conditions. Plant height was tallied daily and spectrophotometry was performed. BLAST was conducted to locate characteric similarities/differences between the genome sequences of the strains. Based on phenotypic observations, copper, nickel and chromium sulfate were found to have no significant effect on the plants, in comparison with the control. Interestingly, WS-2 exhibited excessive growth when exposed to nickel sulfate, reaching 125mm on Day 25. Only after exposing the plants to the heavy metals for the fourth time, plants exhibited wilting and leaf browning. However, statistical analysis [p result = 0.048 (<0.05)] indicated that only Col-0 was resistant to nickel sulfate. Significant differences in nucleotide strings of Col-0 include F-Box protein, Homeobox Leucine Zipper protein family (HD Zip), YABBY protein family, radical fringe and SAT gene. The elucidation of a heavy metal-resistant gene in Arabidopsis thaliana could potentially lead to genetic engineering of genes to cultivate heavy metal resistant plants that are safe for human and animal ingestion.

Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation.

We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BackgroundFruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.ResultsTo accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively.ConclusionsShotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

Documentation of conserved and novel miRNAs participated in plant secondary metabolic pathways of sanctified Aegle marmelos

MicroRNAs are small sized endogenous non-coding RNA, of ~18‐25 (nt) that regulates the expression of their target genes in plants at post transcriptional level and play very significant roles in multiple biological processes. These ribosw itches may play the role of master regulator in important biological processes and plant metabolic pathways. In the present study, we performed small RNA profiling to identify miRNAs present in the holy tree Aegle marmelos and their involvement in different metabolic pathways. A total of 9,192,725 (88.52%) clean reads out of 10,384,409 (100%) reads were identified with size ranging from 15‐ to 24 nt. Using computational tools and bioinformatics approaches we revealed around 253 conserved miRNAs accounting into 20 miRNA families and a total of 395 annotated targets were found for 6 novel miRNAs within the plant. Functional annotation revealed Homeobox-leucine zipper protein and ERF like transcription factors as targets of conserved miRNAs. The present study provides a first report on elucidation of genome-wide miRNA profile of A. marmelos which can be further explored to manipulate their expression to scale-up biosynthesis of active metabolites using metabolic engineering approaches.

Development of SSR markers and association studies of markers with phenology and yield-related traits in grass pea (Lathyrus sativus)

Grass pea (Lathyrus sativus L.) is an important food crop cultivated in dryland agricultural ecosystem. It is an important source of dietary protein to millions of people living in low-income countries in South-east Asia and Africa. The present study emphasises the development of genomic resources and their application in marker–trait association for plant phenology and yield-related traits in lathyrus. In silico mining of nucleotide sequences identified 203 simple sequence repeat (SSR) motifs, of which trimer repeats (62%) were most abundant followed by tetramer (19%), hexamer (10%), pentamer (6%) and dimer (3%) nucleotide repeats. Of 150 SSR markers screened, 60 markers were amplified 75 alleles from 50 germplasm lines with 2–3 alleles per locus and the polymorphic information content of 0.45 was observed. We report 6 significant marker–trait associations using the developed SSR markers for plant phenology and yield-related traits following mixed linear model (Q+K) analysis. Gene ontology search of trait linked markers revealed marker regions encoding genes related to homeobox-leucine zipper protein ATHB-6-like, rubredoxin family protein, and cationic peroxidise. Understanding the association of novel alleles in trait expression will play a significant role in future lathyrus crop improvement programmes.

Combined GWAS and QTL analysis for dissecting the genetic architecture of kernel test weight in maize.

Kernel weight in a unit volume is referred to as kernel test weight (KTW) that directly reflects maize (Zea mays L.) grain quality. In this study, an inter-mated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population and an association panel were used to identify loci responsible for KTW of maize across multiple environments. A total of 18 significant KTW-related single-nucleotide polymorphisms (SNPs) were identified using genome-wide association study (GWAS); they were closely linked to 12 candidate genes. In the IBM Syn10 DH population, linkage analysis detected 19 common quantitative trait loci (QTL), five of which were repeatedly detected among multiple environments. Several verified genes that regulate maize seed development were found in the confidence intervals of the mapped QTL and the LD regions of GWAS, such as ZmYUC1, BAP2, ZmTCRR-1, dek36 and ZmSWEET4c. Combined QTL mapping and GWAS identified one significant SNP that was co-identified in the both populations. Based on the co-localized SNP across the both populations, 17 candidate genes were identified. Of them, Zm00001d044075, Zm00001d044086, and Zm00001d044081 were further identified by candidate gene association study for KTW. Zm00001d044081 encodes homeobox-leucine zipper protein ATHB-4, which has been demonstrated to control apical embryo development in Arabidopsis. Our findings provided insights into the mechanism underlying maize KTW and contributed to the application of molecular-assisted selection of high KTW breeding in maize.

EjHAT1 Participates in Heat Alleviation of Loquat Fruit Lignification by Suppressing the Promoter Activity of Key Lignin Monomer Synthesis Gene EjCAD5.

Texture attributes such as firmness and lignification are important for fruit quality. Lignification has been widely studied in model plants and energy crops, but fruit lignification has rarely been investigated, despite having an adverse effect on fruit quality and consumer preference. Chilling-induced loquat fruit lignification that occurs after harvest can be alleviated by heat treatment (HT) applied prior to low temperature storage. Enzyme activity assay showed that HT treatment could retard the low temperature-induced increase in cinnamyl alcohol dehydrogenase (CAD) activity. Transcript analysis and substrate activity assays of recombinant CAD proteins highlighted the key role of EjCAD5 in chilling-induced lignin biosynthesis. A novel homeobox-leucine zipper protein ( EjHAT1) was identified as a negative regulator of EjCAD5. Therefore, the effect of HT treatment on lignification may be partially due to the suppression of the EjCAD5 promoter activity by EjHAT1.

RNA-Seq and Bulked Segregant Analysis of Genes Related to High Growth in <i>Ginkgo biloba</i> Half-Sibling Families

The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA) to fine map significant agronomic trait genes by developing polymorphism molecular markers at the transcriptome level. In this study, transcriptome sequencing of high growth (GD) and low growth (BD) samples of G. biloba half-sib families was performed. After assembling the clean reads, 601 differential expression genes were detected and 513 of them were assigned functional annotations. Single nucleotide polymorphism (SNP) analysis identified SNPs associated with 119 genes in the GD and BD groups; 58 of these genes were annotated. Two Homeobox-leucine zipper protein genes were up-regulated in the GD group compared with the BD group; therefore, these are very likely related to high growth of G. biloba. This study provides molecular level data that could be used for seed selection of high growth G. biloba half-sib families for future breeding programs.

Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton (Gossypium hirsutum L.).

Cotton is an important industrial crop worldwide and upland cotton (Gossypium hirsutum L.) is most widely cultivated in the world. Due to ever-increasing water deficit, drought stress brings a major threat to cotton production. Thus, it is important to reveal the genetic basis under drought stress and develop drought tolerant cotton cultivars. To address this issue, in present study, 319 upland cotton accessions were genotyped by 55,060 single nucleotide polymorphisms (SNPs) from high-density CottonSNP80K array and phenotyped nine drought tolerance related traits. The two datasets were used to identify quantitative trait nucleotides (QTNs) for the above nine traits using multi-locus random-SNP-effect mixed linear model method. As a result, a total of 20 QTNs distributed on 16 chromosomes were found to be significantly associated with six drought tolerance related traits. Of the 1,326 genes around the 20 QTNs, 205 were induced after drought stress treatment, and 46 were further mapped to Gene ontology (GO) term “response to stress.” Taken genome-wide association study (GWAS) analysis, RNA-seq data and qRT-PCR verification, four genes, RD2 encoding a response to desiccation 2 protein, HAT22 encoding a homeobox-leucine zipper protein, PIP2 encoding a plasma membrane intrinsic protein 2, and PP2C encoding a protein phosphatase 2C, were proposed to be potentially important for drought tolerance in cotton. These results will deepen our understanding of the genetic basis of drought stress tolerance in cotton and provide candidate markers to accelerate the development of drought-tolerant cotton cultivars.

Identification of QTLs for branching in soybean (Glycine max (L.) Merrill)

In soybean, the number of branches directly affects total pod number per plant. In this study, we sought to identify QTLs and candidate genes associated with branching in 200 F6 recombinant inbred lines derived from a cross between Jiyu69 and SS0404-T5-76, which exhibit significant differences in branch number. Using a high-resolution genetic map constructed using the BARCSoySNP6K chip, we detected a novel QTL and confirmed three known QTLs related to branching, as well as two known QTLs for total pod number. Two of the QTLs conferring branching, including a major QTL on chromosome six with an R 2 value of 14.5%, were co-localized with QTLs associated with total pod number. Although several of the QTLs we identified for the two traits were located near identified QTLs, the high-resolution map enabled us to significantly narrow down the genomic regions for these QTLs (from 26 Mb to 460 kb at most), facilitating identification of promising candidate genes. From the QTL regions we identified, we selected six candidate genes, mostly encoding transcription factors regulating expression of gene networks involved in axillary branching via interactions with the auxin hormone network, including a TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factor (BRANCHED1: BRC1) and a homeobox-leucine zipper protein (REVOLUTA: REV). The results of this study will help breeders improve soybean yield by increasing the branch number using marker-assisted selection, and will facilitate identification of the causative genes for branching.

Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato.

In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co-expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid- and environmental stress-inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection.

Prospecting NGS-transcriptomes to assess regulation of miRNA-mediated secondary metabolites biosynthesis in Swertia chirayita, a medicinal herb of the North-Western Himalayas

Swertia chirayita is a high value medicinal herb that possesses diverse therapeutic traits. Molecular data related to the biosynthesis of major secondary metabolites exhibiting these pharmacological properties are limited. Growing demand and poor cultural procedures necessitate improved genetic intervention strategies, which can be implemented to positively influence the biosynthetic machinery and its regulatory network. miRNAs are indicated to play pivotal role in various biological processes, including growth and secondary metabolism. In an attempt to identify conserved miRNAs, computational methods were followed across two transciptomes of Swertia contrasting for metabolite levels and cultural conditions. A total of ten miRNAs were predicted followed by target prediction that resulted in the identification of eleven potential targets having roles in secondary metabolism. RT-qPCR analysis showed six miRNAs (miR-168, miR-11320, miR-166a, miR-11071, miR-156a and miR-166b), targeting Acetyl -CoA acetyltransferase (AACT), Aspar tate aminotransferase (PHAT), premnaspirodiene oxygenase (PSO), ribulose-phosphate 3-epimerase (RPE), phosphoglycerate mutase (PGM) and a gene encoding homeobox-leucine zipper protein (HD-ZIP) having negative correlations with their targets, thereby indicating their possible association in secondary metabolites biosynthesis. The study sheds light on miRNA mediated regulation of secondary metabolites biosynthesis in a lesser explored herbal plant Swertia chirayita. Besides, the putatively identified miRNAs can be targeted for genetic manipulation to enhance secondary metabolites biosynthesis in S. chirayita.

Comparative Physiological and Proteomic Analysis Reveals the Leaf Response to Cadmium-Induced Stress in Poplar (Populus yunnanensis).

Excess amounts of heavy metals are important environmental pollutants with significant ecological and nutritional effects. Cdmium (Cd) is of particular concern because of its widespread occurrence and high toxicity. We conducted physiological and proteomic analyses to improve our understanding of the responses of Populus yunnanensis to Cd stress. The plantlets experienced two apparent stages in their response to Cd stress. During the first stage, transiently induced defense-response molecules, photosynthesis- and energy-associated proteins, antioxidant enzymes and heat shock proteins (HSPs) accumulated to enhance protein stability and establish a new cellular homeostasis. This activity explains why plant photosynthetic capability during this period barely changed. During the second stage, a decline of ribulose-1, 5-bisphosphate carboxylase (RuBisCO) and HSP levels led to imbalance of the plant photosynthetic system. Additionally, the expression of Mitogen-activated protein kinase 3 (MPK3), Mitogen-activated protein kinase 6 (MPK6) and a homeobox-leucine zipper protein was higher in the second stage. Higher expression of caffeoyl-CoA O-methyltransferase (CCoAOMT) may regulate plant cell wall synthesis for greater Cd storage. These genes may be candidates for further research and use in genetic manipulation of poplar tolerance to Cd stress.