The Homeodomain leucine zipper (HD-Zip) transcription factor family is one of the most important transcription factor families in the plant kingdom and it plays pivotal roles in plant development, growth as well as response to all kinds of stresses. However, the HD-Zip gene family has not been characterized in pineapple yet. Pineapple is one of the most economically important tropical fruit in the

Fusarium wilt, caused by the fungus Fusarium oxysporum Schlecht. f. sp. vasinfectum (Fov) is a destructive soil-borne cotton disease. To profile the genes and pathways responding to Fov infection, we compared transcriptomic responses before and after F. oxysporum inoculation in a highly resistant cotton cultivar, Yumian21, and a highly susceptible cultivar, Jimian11. Although the overall gene expression

Fatty acid desaturase 2 (FAD2) is a crucial enzyme in the biosynthesis of polyunsaturated fatty acids in plants, which introduce a double bond into oleic acid to produce linoleic acid. FAD2 is imperative to the application and nutritional value of vegetable oil as both oleic acid and linoleic acid are the primary constituent fatty acids and their relative proportion determines the nutritional value

The purine alkaloid theacrine, synthesized in a high amount in Kucha (Camellia kucha (Chang et Wang) Chang), has shown multiple pharmacological effects such as anti-depression, dehydration and hypnotic activities. It is critical to better understand the theacrine metabolism at the molecular level for future breeding programs. To identify the putative genes involved in theacrine biosynthesis, we carried

The basic helix-loop-helix (bHLH) transcription factor family, which is widely prevalent in higher plants, plays an important role in regulating plant growth and development under various environmental factors. However, there is still no genome-wide analysis of the bHLH family conducted in mango (Mangifera indica L.). In this study, 212 MibHLH genes were identified in the mango genome by genome wide-analysis

The YABBY gene family encodes small plant-specific transcription factors. The first function described for these genes was their role in the establishment and equilibrium of the adaxial-abaxial axes in lateral organs of angiosperms, which includes leaves and leaf-derived organs, such as sepals, petals, stamens, and carpels, and specific floral organs such as ovule integuments and nectaries. From these

Oil palm (Elaeis guineensis Jacq.) is the key vegetable oil yielded crop and widely distributed in the southern region of China. The present study aimed at analyzing the genetic diversity and population structure of 223 oil palm accessions collected from four provinces of China by using the sequence-related amplified polymorphism (SRAP) markers. A set of 33 SRAP molecular markers were employed to analyze

Plants undergo distinct phase transitions during their post-embryonic development and progresses from the juvenile to the adult and reproductive phases. These transitions are characterized by morphological and molecular changes and are differently influenced by gibberellins (GAs) and cytokinins (CKs). GAs are notably known to either induce or repress phase transition and flowering in diverse plant

Several studies involving the TCP family have been carried out in the last two decades since the first members were discovered and the family was defined. The domain that names the family was well characterized and we know that the protein is a transcription factor that forms a non-canonical bHLH type structure capable of binding to the DNA molecule and promoting interactions between proteins. In recent

The major challenge of cassava cultivation is phytopathogen damage and lack of resistant cultivars. Investigating the defense mechanism in cassava should provide insights into the development of new disease control strategies. Colletotrichum gloeosporioides f. sp. manihotis (CAD) is a fungal pathogen that causes cassava anthracnose disease, which is a serious disease worldwide, affecting cassava production

Leaf angle (LA) and leaf orientation value (LOV) are two crucial traits constituting the plant architecture (PA) of maize. Screening of quantitative trait loci (QTLs) and candidate genes (CGs) related to leaf angle and leaf orientation value provides the molecular basis for the improvement of maize plant architecture. In this study, we utilized genotyping by sequencing (GBS) on 179 maize recombined

The multigene family WRKY is plant-specific transcription factors, which is involved in numerous aspects of plant growth and development. Here, we report a genome-wide search for the rubber tree WRKY (HbWRKY) genes and their expression profiles at various tissues including latexes. We also present a comprehensive overview of whole HbWRKY gene family, including gene structure, chromosomal locations

Quantitative real-time PCR (qRT-PCR) is a convenient tool for gene expression analysis. However, reliability of its result is influenced largely by the selection of reference genes. Pineapple molecular breeding is limited due to lack of understanding of sexual organs’ development. Similarly, only a few reference genes have identified for qRT-PCR analysis in pineapple stamen and ovule. In this study

Cacao is an economically important crop, since it provides the raw material for the multibillion dollar global chocolate industry. Yunnan Province is in the far southwestern region of China where tropical agriculture makes up a significant part of the provincial GDP. There is great potential for cacao production in Yunnan, given the rapid increase of chocolate consumption in China. Understanding the

Isolated sperm cells and egg cells provide useful materials for the study of fertilization in higher plants, under controlled conditions, in the absence of somatic tissue. Viable egg cells from Bauhinia blakeana were isolated using enzymatic digestion and mechanical dissection. Ovules were digested with enzymes for 40–50 min and then transferred to a solution without enzymes for dissection. The three

Soil salinization is a serious agricultural issue that is severely affecting crop production across the world. Salt induced stresses are mainly included osmotic and ionic stresses, which could lead to other stresses e.g., oxidative stress in plants. The evolved plant mechanisms in salt tolerance are categorized into osmotic tolerance and ionic homeostasis mediated by ion exclusion and ions sequestration

The negative correlation between grain yield and popping expansion is an issue to obtain popcorn varieties. Simultaneous selection applying trait index selection is an efficient method to reach a maximum of combined genetic gain, and it is an alternative to aggregate interesting market trait in new popcorn varieties. This study aimed to evaluate intercharacter genetic parameters and to identify improved

Powdery mildew (PM) is one of the most destructive diseases affecting rubber trees (Hevea brasiliensis), leading to severe yield losses. Sulfur dusting is used to control the propagation of the disease, and no specific fungicides have been developed yet. Therefore, identification of genetic level disease resistance in the rubber trees is very crucial. In this study, we describe the whole-genome sequencing

Atypical dual-specific phosphatases (PFA-DSP) is a kind of special phosphatase in plants, and play key roles in physiological processes. OsPFA-DSP2 is a member of PFA-DSP family, and negatively regulates Magnaporthe grisea responses in when overexpressed in rice. Whereas, their activity and function response to bacterial pathogen stress are still unknown. The results showed that OsPFA-DSP2 was a tyrosine-specific

Sugarcane generates the vast majority of sugar consumed worldwide. The large-scale development of EST-SSR markers are crucial for the analysis of genetic mechanisms important in agronomic traits of sugarcane. In this study, based on published 107,598 full-length expressed sequence tags (ESTs) from 22 sugarcane cultivars, we identified a total of 46,043 loci of simple repeat sequences. The SSRs with

Chloroplastic pyruvate phosphate dikinase (PPDK) (chlPPDK) is a key enzyme in the photosynthesis of C4 plants. PPDK is expressed in high abundance in C4 plants but only in trace amounts in C3 plants. The existing research reveals a higher expression of MechlPPDK in cultivated cassava varieties than that in wild cassava W14. However, knowledge about the transcriptional regulation of the MechlPPDK gene

Association mapping (AM) is an approach that accounts for thousands of polymorphisms to evaluate the effects of quantitative trait loci (QTL). It is an important instrument for identification of alleles and new genes as well as dissection of complex characters. AM is more advantageous than linkage analysis due to the comparatively high-resolution provided, which is based on the structure of linkage

Oversprouting is a poorly studied disease of guarana plant (Paullinia cupana var. sorbilis), a native species from Amazon Rainforest caused by Fusarium decemcellulare (FDC) that affects the plant growth and reproduction, severely compromising productivity. The sorbilis variety of guarana is anciently cultivated and is used today for the industry of soft drinks, cosmetic and pharmaceutical. Transcriptome

Both plant height (PH) and ear height (EH) are key agronomic traits in maize that are associated with plant lodging resistance and population density. To explore the genetic basis for PH and EH in maize, we conducted a genome-wide association study (GWAS) based upon 1.49 × 106 single nucleotide polymorphisms (SNPs) identified following the sequencing of 80 backbone inbred maize lines in Jilin Province

Drought is a main factor affecting plant growth and crop production. APETALA2/Ethylene Responsive Element Binding Protein (AP2/EREBP) transcription factors (TFs) are involved in the response to abiotic stress and their functions in ABA signaling and the regulation of drought response have been intensively studied. However, AP2/EREBP TFs have been limited in the maize. The objective of our study was

Climate change is expected to result in more frequent periods of both low rainfall and above normal temperatures for many coffee growing regions. To understand how coffee reacts to such change, we studied the physiological and gene expression responses of the clonal variety C. canephora FRT07 exposed to water deficits under two different temperature regimes. Variations in the time-dependent impact

Climate change and its impact on agriculture are one of the ongoing research areas, and the major task among agricultural managers is to meet the food demand in the future in the context of the production gap of major food grain crops. Literature analysis is carried out to understand the climate resilience of cassava, one of the major tuber crops and is considered to bridge the food demand gap in the

The quality concept for cooked rice (Oryza sativa L.) varies according to customers culture and habits, varying from stickier, in Asia, to looser grains, more appreciated in South America. This parameter, no matter the taste, is an important factor in the evaluation of what constitutes a good rice grain. Higher grain stickiness is associated not only with lower amylose content, but also with amylopectin

Plant Cryptochromes (CRYs) are photolyase-like flavoproteins that have been reported in all evolutionary lineages. As UV-A/blue light photoreceptors, CRYs play a vital role in plant growth and development. In the present study, a total of 94 CRY1 and 68 CRY2 candidate genes were retrieved from 58 and 50 plant genomes, respectively. Phylogenetic analysis indicates that CRY genes could be divided into

A genome-wide association study (GWAS) and quantitative trait loci (QTL) analysis using two bi-parental (parental cultivars Smooth Cayenne and MD-2) pineapple seedling populations segregating for spiny and spiny-tip leaf margin and 12 wild and pre-Columbian domesticated genotypes were used to identify single nucleotide polymorphism (SNP) and silicoDArT markers associated with the spiny-tip leaf margin

As a native in Southeast Asia, Sagittaria trifolia L. var. sinensis (arrowhead) is an aquatic perennial herb of Alismataceae family. For the aim of discovering genes and development molecular markers, high-throughput transcriptome sequencing is applied to generate enormous transcript sequences from arrowhead leaf generate. Through trimmed and assembled, 51, 836 contigs were obtained with mean length

The Chinese narcissus is a well-known monocotyledon plant with a beautiful color, and fresh with a sweet floral scent. Lack of transcriptomic and genomic information hinders understanding of the molecular mechanisms underlying the biosynthesis of narcissus floral scent volatiles. Here we predicted the functions of identified significantly differentially expressed genes (DEGs), according to public protein

NRT2 family of nitrate transporters normally require a partner protein, NAR2 (nitrate assimilation related protein), to transport nitrate to a high-affinity (high affinity nitrate transport system, HATS), although its role is still not well understood. In this study, the CcNRT2.1 and CcNAR2 cDNAs from of Capsicum chinense were cloned and characterized in terms of their structure, phylogeny, and their

In order to study the genetic diversity and population structure of broomcorn, a special type of sorghum for broom making, a total of 140 accessions of sorghum varieties including broomcorn (72), half-broomcorn (4), non-broomcorn (64) accessions were genotyped by using 45 simple sequence repeat (SSR) markers that are evenly distributed throughout the sorghum genome. These genotyping analyses demonstrated

Late leaf spot (LLS) is the major foliar disease, which often occur with rust and cause severe yield losses worldwide in peanut (Arachis hypogaea L.). In order to map and introgress the resistance alleles for LLS into an elite cultivar ICGS 76, the advanced backcross approach was used for identification of quantitative trait locus (QTL). The synthetic amphidiploid ISATGR 278–18 (A. duranensis ICG 8138 × A

MADS-box transcription factors are essential mediators of the vegetative and reproductive development of seed plants. Although MADS-box genes have been extensively characterized in angiosperms, their functions are not well-understood in gymnosperms, especially the Gnetales, due to an ambiguous phylogeny of seed plants. Here, we performed a genome-wide search for MADS-box genes in Gnetum luofuense and

LATE ELONGATED HYPOCOTYL (LHY) gene is well known to be the core circadian function in Arabidopsis. In this study, DhLHY was obtained from Doritaenopsis ‘Tinny Tender’ (Doritaenopsis Happy smile × Happy valentine), and the sequence contained 2594 base pair (bp) in whole with an open reading frame (ORF) of 1962 bp encoding 653 amino acids. The putative protein of DhLHY included a HTH myb domain and

Diospyros lasiocalyx (Mart.) B. Wall. is a dioecious tree species found in the threatened and fragmented Brazilian Cerrado. Its fleshy fruits, which are consumed extensively by wildlife, make the species ideal for use in restoration. This study includes a ten-year phenological observation, germination tests, and analysis of molecular markers to understand the reproductive strategy of D. lasiocalyx

Lead (Pb) is a rapidly increasing heavy metal due to different human activities. It is highly toxic to plants, and its toxicity can impair various morphological, physiological and biochemical functions in plants. In the present study, an experiment was designed to investigate the response mechanisms to counteract Pb in the seedlings of Jatropha curcas. For this purpose, Pb accumulation, metabolite

Laccases play crucial roles in catalyzing lignin and flavonoid biosynthesis in plants, and are predominantly involved in lignin breakdown of bacteria and fungi. Lignin distributes in all parts of plant and is a key component in plant morphogenesis. The complex sugarcane genome limited the study of laccase genes, but our completed reference genome of tetraploid S. spontaneum AP85–441 makes it possible

The TCP family genes have been under selection during domestication in maize and related andropogoneae crops. They encode plant-specific transcription factors involved in growth and development, especially in shaping the plant morphology and architecture. Sugarcane (Saccharum spp.) is the most productive in harvesting tonnage and 5th economically valuable crops worldwide for supporting world’s sugar

RNA-dependent RNA polymerases (RDRs), involved in the production of various small interfering RNA (siRNA), play critical roles in plant growth, development process, and abiotic/biotic stresses. In this study, 5 RDR genes (AcRDRs) were identified from the pineapple genome. Phylogenetic analysis showed that AcRDRs could be divided into 4 subgroups. Gene structure analysis showed that the number of introns

Genetically modified (GM) sugarcane is being developed for use in commercial production in several countries. Regulatory approval is required before these cultivars can be released and grown. Part of the approval process is to understand and assess the potential for environmental harm that might result from introduction of a GM organism. A key piece of biological information to assist in this analysis

Sugarcane stalks sequentially produce internodes, with the most immature and mature internodes at the top and base of the stalk, respectively. Resulting in a range of internodes at different developmental stages in each stalk. When sampling similar developmental internodes, replicate plants may differ in chronological age due to various reasons, including different germination rates, regeneration from

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important legume crop for South East Asia. Smallholder farmers rely on this crop to diversify income streams and enrich soils through N-fixation. To produce new varieties that stabilize mungbean productivity under biotic and abiotic stresses, breeders need to take advantage of genomic tools. Genome-Wide Association Studies (GWAS) are an effective

MicroRNAs as regulators of gene expression have been known for over a decade and have been correlated with various types of abiotic and biotic stresses. IsomiRs are modified forms of typical miRNAs altered by one or few nucleotides as a result of post transcriptional modifications of miRNAs at terminals or SNPs containing miRNA sequences producing 5′/3′ isomiRs or SNP_isomiRs. These isoforms function

TALE (Three Amino-acid Loop Extension) transcription factors belong to a large gene family in plants and are also widespread in other Eukaryotes, including animals. We have in detail studied TALE genes in the economically important crop plant pineapple (Ananas comosus) but also compared these gene sequences with other plant TALE-genes. Using the webtool HMMER we found 18 TALE gene sequences in the

Sugarcane is an important industrial crop with a high sugar yield that has become a leading energy crop worldwide. It is widely cultivated in tropical and subtropical regions. Various diseases beset the cultivation of sugarcane. The molecular study of disease resistance in sugarcane is limited by its complicated genome. In our study, RNA-seq was employed to detect the mechanism of twisted leaf disease

Sucrose accumulation and decreased photosynthesis are early symptoms of yellow canopy syndrome (YCS) in sugarcane (Saccharum spp.), and precede the visual yellowing of the leaves. To investigate broad-scale gene expression changes during YCS-onset, transcriptome analyses coupled to metabolome analyses were performed. Across leaf tissues, the greatest number of differentially expressed genes related

Cedrela fissilis Vell. has a wide distribution in South and Central America, and in neotropical forests the species occurs at a low density. Its wood is one of the most valued around the world, and the species is currently at risk of extinction due to both habitat fragmentation and illegal logging. Considering the need for conservation strategies, this study aims to investigate the genetic structure

The megabiodiversity of Brazil created opportunities for the domestication of a number of crop species, including some of major global importance. Considering the economic value of many Brazilian native crops, the genetic characterization of their populations is fundamental to support the utilization and conservation of their genetic resources, currently threatened by deforestation and the intensification

Sugarcane is a major sugar-producing crop, which contributed 80% of the world’s sugar in 2010. Saccarhum officinarum is a domestic species with high sugar content, while, Saccarhum spontaneum is a wild species with stress tolerance. The highly complex polyploid genome of modern sugarcane cultivars arose from the interspecific hybridization between S. officinarum and S. spontaneum. Sucrose synthase

Artemisinins, as a class of bioactive molecules, are mainly derived from the extracts of Artemisia annua L. and are the mainstay for malaria treatment, including severe malaria, uncomplicated malaria and multi-drug resistant malaria. They are well-known for their good tolerability, safety and rapid onset of action. Their efficacy is not only limited to malaria but also extends to a variety of human

NAC [no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF1/2) and cup-shaped cotyledon (CUC2)] proteins is one of the largest classes of plant specific transcription factors and plays a critical role in plant growth, development process, and abiotic/biotic stresses. In this study, 73 NAC genes (AcNACs) were identified from the pineapple genome. Phylogenetic analysis showed that

The tassel architecture of maize (Zea mays L.), which plays an important role in F1 hybrid seed production and yield performance, is genetically controlled by quantitative trait loci (QTLs). Here, we constructed a high-density SNP-based genetic map using an F2 population containing 148 individuals. This genetic map included 7613 SNPs whose average genetic distance was 0.19 cM. On account of the F2

Starch is one of two crucial products of photosynthetic carbon-assimilation and mainly functions as the unit of energy storage in most crops such as rice, maize and sorghum, whereas interestingly in sugarcane that unit of energy storage is sucrose. Mature sugarcane stalk tissue has a very large apoplastic volume and contains nearly 700 mM sucrose—which is among the highest recorded sucrose concentrations

The Cytochrome P450 gene family is one of the largest in plants. Cytochrome P450 sequences have been annotated in the Saccharum spontaneum genome and they make up 1.3% of the known alleles. 394 genes have been identified in this family after mining two releases of the S. spontaneum AP85–441 genome. The P450 sequences are most similar to those of sorghum. The 45 CYP families in sugarcane have been compared

VQ protein, contain a conserved and short FxxxVQxLTG amino acid sequence motif. Some VQ proteins play important roles in development process and abiotic/biotic stress in plants. However, there has not been a systematic study of the VQ family in plants. The results revealed that Group I genes are conserved in plant development in angiosperms; Group IV and Group X in eudicots and Group I, Group VI and

The aim of this work was to study the regulation of coffee DREB-like genes in leaves of C. arabica subjected to cold, heat, low relative humidity, exogenous abscisic acid and high light stress, as well as in leaves and roots of drought-tolerant and drought-susceptible clones of Coffea canephora subjected to water limitation. In C. arabica, CaERF017 was the most expressed gene under low temperatures