Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions.

BACKGROUND: Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations. RESULTS: This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population. CONCLUSION: The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.

Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis.

Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.

In Silico Comparison of WRKY Transcription Factors in Wild and Cultivated Soybean and Their Co-expression Network Arbitrating Disease Resistance.

WRKY Transcription factors (TFs) play critical roles in plant defence mechanisms that are activated in response to biotic and abiotic stresses. However, information on the Glycine soja WRKYs (GsoWRKYs) is scarce. Owing to its importance in soybean breeding, here we identified putative WRKY TFs in wild soybean, and compared the results with Glycine max WRKYs (GmaWRKYs) by phylogenetic, conserved motif, and duplication analyses. Moreover, we explored the expression trends of WRKYs in G. max (oomycete, fungi, virus, bacteria, and soybean cyst nematode) and G. soja (soybean cyst nematode), and identified commonly expressed WRKYs and their co-expressed genes. We identified, 181 and 180 putative WRKYs in G. max and G. soja, respectively. Though the number of WRKYs in both studied species is almost the same, they differ in many ways, i.e., the number of WRKYs on corresponding chromosomes, conserved domain structures, WRKYGQK motif variants, and zinc-finger motifs. WRKYs in both species grouped in three major clads, i.e., I-III, where group-II had sub-clads IIa-IIe. We found that GsoWRKYs expanded mostly through segmental duplication. A large number of WRKYs were expressed in response to biotic stresses, i.e., Phakospora pachyrhizi, Phytoplasma, Heterodera glycines, Macrophomina phaseolina, and Soybean mosaic virus; 56 GmaWRKYs were commonly expressed in soybean plants infected with these diseases. Finally, 30 and 63 GmaWRKYs and GsoWRKYs co-expressed with 205 and 123 non-WRKY genes, respectively, indicating that WRKYs play essential roles in biotic stress tolerance in Glycine species.

A natural non-synonymous single nucleotide polymorphism in GmbHLH113 negates its inhibitory effect on root hair elongation in soybean.

Root hair length (RHL) is an important character that affects nutrient acquisition in plants. The regulatory network in soybean controlling RHL is yet to be fully understood. In this study, we identified a quantitative trait locus (QTL) regulating RHL. One candidate causal gene in this QTL (GmbHLH113), preferentially expressed in root hairs, was annotated as encoding a basic helix-loop-helix transcription factor. In wild soybeans, the allelic type of GmbHLH113 with a glycine in the 13th residue, which was associated with a reduction in RHL, was shown to localize in the nucleus and activate gene transcription. Another allelic type with a single nucleotide polymorphism that resulted in a glutamate in the 13th residue is fixed in cultivated soybeans, and it lost the ability to localize to the nucleus or negatively regulate RHL. The ectopic expression of GmbHLH113 from W05 in Arabidopsis root hairs resulted in shorter RHL and reduced phosphorus (P) accumulation in shoots. Hence, a loss-of-function allele in cultivated soybeans might have been selected during domestication due to its association with a longer RHL and improved nutrient acquisition.

Magnesium- a Forgotten Element: Phenotypic Variation and Genome Wide Association Study in Turkish Common Bean Germplasm.

Magnesium (Mg) is the fourth most abundant element in the human body and plays the role of cofactor for more than 300 enzymatic reactions. In plants, Mg is involved in various key physiological and biochemical processes like growth, development, photophosphorylation, chlorophyll formation, protein synthesis, and resistance to biotic and abiotic stresses. Keeping in view the importance of this element, the present investigation aimed to explore the Mg contents diversity in the seeds of Turkish common bean germplasm and to identify the genomic regions associated with this element. A total of 183 common bean accessions collected from 19 provinces of Turkey were used as plant material. Field experiments were conducted according to an augmented block design during 2018 in two provinces of Turkey, and six commercial cultivars were used as a control group. Analysis of variance depicted that Mg concentration among common bean accessions was statistically significant (p < 0.05) within each environment, however genotype × environment interaction was non-significant. A moderate level (0.60) of heritability was found in this study. Overall mean Mg contents for both environments varied from 0.33 for Nigde-Dermasyon to 1.52 mg kg-1 for Nigde-Derinkuyu landraces, while gross mean Mg contents were 0.92 mg kg-1. At the province level, landraces from Bolu were rich while the landraces from Bitlis were poor in seed Mg contents respectively. The cluster constellation plot divided the studied germplasm into two populations on the basis of their Mg contents. Marker-trait association was performed using a mixed linear model (Q + K) with a total of 7,900 DArTseq markers. A total of six markers present on various chromosomes (two at Pv01, and one marker at each chromosome i.e., Pv03, Pv07, Pv08, Pv11) showed statistically significant association for seed Mg contents. Among these identified markers, the DArT-3367607 marker present on chromosome Pv03 contributed to maximum phenotypic variation (7.5%). Additionally, this marker was found within a narrow region of previously reported markers. We are confident that the results of this study will contribute significantly to start common bean breeding activities using marker assisted selection regarding improved Mg contents.

Molecular characterization and validation of sunflower (Helianthus annuus L.) hybrids through SSR markers.

Genetic purity is a prerequisite for exploiting the potential of hybrids in cross-pollinated crops, such as sunflower. In this regard DNA-based study was conducted using 110 simple sequence repeat (SSR) markers to check the genetic purity of 23 parents and their 60 hybrids in sunflower. The polymorphism was shown in 92 markers with value 83.63%. The SSR markers ORS-453 and CO-306 showed the highest PIC values of 0.76 and 0.74, respectively. The primer ORS-453 amplified allele size of 310 base pairs (bp) for female parent L6 and 320 bp for L11, while for male parents, T1 and T2 had allele size 350 bp and 340 bp, respectively. The hybrids from these parents showed a similar size of alleles with parents, including hybrids L6×T1 (310 bp and 350 bp), L6×T2 (310 bp and 340 bp), and L11×T2 (320 bp and 340 bp). Similarly, the primer CO-306 amplified allele size 350 bp and 330 bp for female parents L6 and L11, respectively, while, allele size 300 bp and 310 bp for male parents T1 and T2, respectively. The hybrids' allele size was like the parents viz., L6×T1 (350 bp and 300 bp), L6×T2 (350 bp and 310 bp), and L11×T2 (330 bp and 310 bp). All 60 hybrids and their 23 parents were grouped into three main clusters (A, B and C) based upon DARWIN v.6.0 and STRUCTURE v.2.3 Bayesian analyses using genotypic data. Further, each main cluster was divided into two sub-divisions. Each sub-division showed the relatedness of parents and their hybrids, thus authenticating the genetic purity of hybrids. In conclusion, this study provides useful for accurate and effective identification of hybrids, which will help to improve seed genetic purity testing globally.

Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean.

The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.

Whole-genome resequencing of Sorghum bicolor and S. bicolor × S. halepense lines provides new insights for improving plant agroecological characteristics.

Sorghum (Sorghum bicolor L. (Moench)) is the world's fifth economically most important cereal and is a staple particularly in the semi-arid tropics of Africa and Asia. Genetic gains in this crop can benefit from wild relatives such as Sorghum halepense. Genome sequences including those from this wild species can boost the study of genome-wide and intraspecific variation for dissecting the genetic basis and improving important traits in sorghum. The whole-genome resequencing carried out in this work on a panel of 172 populations of S. bicolor and S. bicolor × S. halepense (SbxSh) advanced lines generated a total of 567,046,841 SNPs, 91,825,474 indels, 1,532,171 SVs, and 4,973,961 CNVs. Clearly, SbxSh accumulated more variants and mutations with powerful effects on genetic differentiation. A total of 5,548 genes private to SbxSh mapped to biological process GO enrichment terms; 34 of these genes mapped to root system development (GO: 0022622). Two of the root specific genes i.e., ROOT PRIMORDIUM DEFECTIVE 1 (RPD1; GeneID: 8054879) and RETARDED ROOT GROWTH (RRG, GeneID: 8072111), were found to exert direct effect on root growth and development. This is the first report on whole-genome resequencing of a sorghum panel that includes S. halepense genome. Mining the private variants and genes of this wild species can provide insights capable of boosting sorghum genetic improvement, particularly the perenniality trait that is compliant with agroecological practices, sustainable agriculture, and climate change resilience.

The Tiny Companion Matters: The Important Role of Protons in Active Transports in Plants.

In plants, the translocation of molecules, such as ions, metabolites, and hormones, between different subcellular compartments or different cells is achieved by transmembrane transporters, which play important roles in growth, development, and adaptation to the environment. To facilitate transport in a specific direction, active transporters that can translocate their substrates against the concentration gradient are needed. Examples of major active transporters in plants include ATP-binding cassette (ABC) transporters, multidrug and toxic compound extrusion (MATE) transporters, monosaccharide transporters (MSTs), sucrose transporters (SUTs), and amino acid transporters. Transport via ABC transporters is driven by ATP. The electrochemical gradient across the membrane energizes these secondary transporters. The pH in each cell and subcellular compartment is tightly regulated and yet highly dynamic, especially when under stress. Here, the effects of cellular and subcellular pH on the activities of ABC transporters, MATE transporters, MSTs, SUTs, and amino acid transporters will be discussed to enhance our understanding of their mechanics. The relation of the altered transporter activities to various biological processes of plants will also be addressed. Although most molecular transport research has focused on the substrate, the role of protons, the tiny counterparts of the substrate, should also not be ignored.

Nanobionics in Crop Production: An Emerging Approach to Modulate Plant Functionalities.

The "Zero Hunger" goal is one of the key Sustainable Development Goals (SDGs) of the United Nations. Therefore, improvements in crop production have always been a prime objective to meet the demands of an ever-growing population. In the last decade, studies have acknowledged the role of photosynthesis augmentation and enhancing nutrient use efficiency (NUE) in improving crop production. Recently, the applications of nanobionics in crop production have given hope with their lucrative properties to interact with the biological system. Nanobionics have significantly been effective in modulating the photosynthesis capacity of plants. It is documented that nanobionics could assist plants by acting as an artificial photosynthetic system to improve photosynthetic capacity, electron transfer in the photosystems, and pigment content, and enhance the absorption of light across the UV-visible spectrum. Smart nanocarriers, such as nanobionics, are capable of delivering the active ingredient nanocarrier upon receiving external stimuli. This can markedly improve NUE, reduce wastage, and improve cost effectiveness. Thus, this review emphasizes the application of nanobionics for improving crop yield by the two above-mentioned approaches. Major concerns and future prospects associated with the use of nanobionics are also deliberated concisely.

The Poly-Glutamate Motif of GmMATE4 Regulates Its Isoflavone Transport Activity.

Multidrug and toxic compound extrusion (MATE) transporters in eukaryotes have been characterized to be antiporters that mediate the transport of substrates in exchange for protons. In plants, alkaloids, phytohormones, ion chelators, and flavonoids have been reported to be the substrates of MATE transporters. Structural analyses have been conducted to dissect the functional significance of various motifs of MATE proteins. However, an understanding of the functions of the N- and C-termini has been inadequate. Here, by performing phylogenetic analyses and protein sequence alignment of 14 representative plant species, we identified a distinctive N-terminal poly-glutamate motif among a cluster of MATE proteins in soybean. Amongst them, GmMATE4 has the most consecutive glutamate residues at the N-terminus. A subcellular localization study showed that GmMATE4 was localized at the vacuolar membrane-like structure. Protein charge prediction showed that the mutation of the glutamate residues to alanine would reduce the negative charge at the N-terminus. Using yeast as the model, we showed that GmMATE4 mediated the transport of daidzein, genistein, glycitein, and glycitin. In addition, the glutamate-to-alanine mutation reduced the isoflavone transport capacity of GmMATE4. Altogether, we demonstrated GmMATE4 as an isoflavone transporter and the functional significance of the N-terminal poly-glutamate motif of GmMATE4 for regulating the isoflavone transport activity.

Pharmacological properties and preliminary phytochemical analysis of Pseudocaryopteris foetida (D.Don) P.D. Cantino leaves.

Medicinal plants have significant contribution in pharmaceutical industries being producers of compounds utilized as precursors for drug development. A plant of Lamiaceae family; Pseudocaryopteris foetida had not been investigated for its biomedical potential. Current research was aimed to investigate phytochemical analysis, cytotoxic potential and antioxidant activity of crude methanolic extract and fractions of Pseudocaryopteris foetida (leaves). The preliminary phytochemical analysis of crude methanolic extracts and fractions of Pseudocaryopteris foetida revealed that plant is rich in phenolic and flavonoid classes of secondary metabolites while presence of tannin was observed only in crude methanolic extract. The cytotoxicity was determined using brine shrimp lethality test. Different concentrations (25, 50, 100, 150, 200 and 250 µg/mL) of crude methanolic extract and fractions exhibited dose dependent cytotoxicity. However, The LD50 for all the extracts was more than 200 µg/mL indicating weak cytotoxic potential of Pseudocaryopteris foetida. The antioxidant capabilities of crude methanolic extract and fraction of Pseudocaryopteris foetida were analyzed by in vitro bio assays including DPPH, ABTS, Reducing power and phosphomolybdate antioxidant assays using ascorbic acid as standard. The crude methanolic extract showed IC50 (256.38 ± 0.6 and 314.95 ± 1.1 µg/mL) for DPPH and ABTS respectively, while total antioxidant capacity was calculated as 55.79 ± 0.5 µg/mL for crude methanolic extract of Pseudocaryopteris foetida while ascorbic acid indicated total antioxidant capacity of 71.89 ± 2.3 µg/mL. Study concluded that leaves of Pseudocaryopteris foetida were the rich source of antioxidant phytochemicals. Based on preliminary investigations further research should be focused to isolate bioactive phytochemicals as leading source of clinical medicines in future.

The Identification of MATE Antisense Transcripts in Soybean Using Strand-Specific RNA-Seq Datasets.

Natural antisense transcripts (NATs) have been generally reported as negative regulators of their sense counterparts. Multidrug and toxic compound extrusion (MATE) proteins mediate the transport of various substrates. Although MATEs have been identified genome-wide in various plant species, their transcript regulators remain unclear. Here, using the publicly available strand-specific RNA-seq datasets of Glycine soja (wild soybean) which have the data from various tissues including developing pods, developing seeds, embryos, cotyledons and hypocotyls, roots, apical buds, stems, and flowers, we identified 35 antisense transcripts of MATEs from 28 gene loci after transcriptome assembly. Spearman correlation coefficients suggested the positive expression correlations of eight MATE antisense and sense transcript pairs. By aligning the identified transcripts with the reference genome of Glycine max (cultivated soybean), the MATE antisense and sense transcript pairs were identified. Using soybean C08 (Glycine max), in developing pods and seeds, the positive correlations between MATE antisense and sense transcript pairs were shown by RT-qPCR. These findings suggest that soybean antisense transcripts are not necessarily negative transcription regulators of their sense counterparts. This study enhances the existing knowledge on the transcription regulation of MATE transporters by uncovering the previously unknown MATE antisense transcripts and their potential synergetic effects on sense transcripts.

Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses.

The two-component signal transduction system (TCS) acts in a variety of physiological processes in lower organisms and has emerged as a key signaling system in both prokaryotes and eukaryotes, including plants. TCS genes assist plants in processes such as stress resistance, cell division, nutrition signaling, leaf senescence, and chloroplast division. In plants, this system is composed of three types of proteins: response regulators (RRs), histidine kinases (HKs), and histidine phosphotransfer proteins (HPs). We aimed to study the Sorghum bicolor genome and identified 37 SbTCS genes consisting of 13 HKs, 5 HPs, and 19 RRs (3 type-A RRs, 7 type-B RRs, 2 type-C RRs, and 7 pseudo-RRs). The structural and phylogenetic comparison of the SbTCS members with their counterparts in Arabidopsis thaliana, Oryza sativa, Cicer arietinum, and Glycine max showed group-specific conservations and variations. Expansion of the gene family members is mostly a result of gene duplication, of both the tandem and segmental types. HKs and RRs were observed to be originated from segmental duplication, while some HPs originated from tandem duplication. The nuclear genome of S. bicolor contain 10 chromosomes and these SbTCS genes are randomly distributed on all the chromosomes. The promoter sequences of the SbTCS genes contain several abiotic stress-related cis-elements. RNA-seq and qRT-PCR-based expression analysis demonstrated most of the TCS genes were responsive to drought and salt stresses in leaves, which suggest their role in leaf development. This study lays a foundation for further functional study of TCS genes for stress tolerance and developmental improvement in S. bicolor.

Determination of ROS Scavenging, Antibacterial and Antifungal Potential of Methanolic Extract of Otostegia limbata (Benth.) Boiss.

Wide spectrum medicinal significance augments plant utilization as the primary source of significant pharmaceutical agents. In vitro investigation of antioxidant and antimicrobial activity highlights the therapeutic potential of Otostegia limbata. Methanol extract of the plant (MEP) shows considerable dose dependent antioxidant ability at six concentrations (7.81 µg/mL to 250 µg/mL) in 2.2-diphenyl-1-picrylhydrazyl (DPPH) assay, phosphomolybdate assay (PMA) and reducing power assay (RPA). The plant capability to scavenge free radicals in the mixture ranged from 37.89% to 63.50% in a concentration-dependent manner. MEP was active against five tested bacterial strains in the agar-well diffusion method. Staphylococcus aureus, gram-positive bacteria was found to be most susceptible followed by S. epidermidis with 18.80 mm and 17.47 mm mean zone of inhibition. The mean inhibition zone against gram-negative strains Klebsiella pneumonia, Pseudomonas spp. and Escherichia coli were 15.07 mm, 14.73 mm, and 12.17 mm. MEP revealed potential against Alternaria spp. and Aspergillus terreus fungal strains evaluated through agar-tube dilution assay. Aspergillus terreus was more sensitive than Alternaria spp. with an average 78.45% and 68.0% inhibition. These findings can serve as a benchmark for forthcoming scrutiny such as bioactive components discovery and drug development.

MATE-Type Proteins Are Responsible for Isoflavone Transportation and Accumulation in Soybean Seeds.

Soybeans are nutritionally important as human food and animal feed. Apart from the macronutrients such as proteins and oils, soybeans are also high in health-beneficial secondary metabolites and are uniquely enriched in isoflavones among food crops. Isoflavone biosynthesis has been relatively well characterized, but the mechanism of their transportation in soybean cells is largely unknown. Using the yeast model, we showed that GmMATE1 and GmMATE2 promoted the accumulation of isoflavones, mainly in the aglycone forms. Using the tobacco BrightYellow-2 (BY-2) cell model, GmMATE1 and GmMATE2 were found to be localized in the vacuolar membrane. Such subcellular localization supports the notion that GmMATE1 and GmMATE2 function by compartmentalizing isoflavones in the vacuole. Expression analyses showed that GmMATE1 was mainly expressed in the developing soybean pod. Soybean mutants defective in GmMATE1 had significantly reduced total seed isoflavone contents, whereas the overexpression of GmMATE1 in transgenic soybean promoted the accumulation of seed isoflavones. Our results showed that GmMATE1, and possibly also GmMATE2, are bona fide isoflavone transporters that promote the accumulation of isoflavones in soybean seeds.

Using HPLC-DAD and GC-MS Analysis Isolation and Identification of Anticandida Compounds from Gui Zhen Cao Herbs (Genus Bidens): An Important Chinese Medicinal Formulation.

Gui Zhen Cao is an herbal formulation that has been documented in Chinese traditional medicine as a remedy for diarrhea, dysentery, inflammation, and toxicity. The sources of this formulation (Bidens pilosa L., Bidens biternata (Lour.) Merr. & Sherff, Bidens bipinnata L.) are also listed in ethnomedicinal reports all over the world. In this study, all these plants are tested for in vitro anticandida activity. A quantitative evaluation of the phytochemicals in all these plants indicated that their vegetative parts are rich in tannins, saponins, oxalates, cyanogenic glycoside and lipids; moreover, the roots have high percentages of alkaloids, flavonoids, and phenols. The results indicated significant anticandida activity, especially for the hexane extract of B. bipinnata leaves which inhibited C. albicans (42.54%), C. glabrata (46.98%), C. tropicalis (50.89%), C. krusei (40.56%), and C. orthopsilosis (50.24%). The extract was subjected to silica gel chromatography and 220 fractions were obtained. Purification by High Performance Liquid Chromatography with Diode-Array Detection (HPLC-DAD) and Gas Chromatography tandem Mass Spectrometry (GC-MS/MS) analysis led to the identification of two anticandida compounds: dehydroabietic and linoleic acid having an inhibition of 85 and 92%, respectively.

Increased copy number of gibberellin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication.

Copy number variations (CNVs) play important roles in crop domestication. However, there is only very limited information on the involvement of CNVs in soybean domestication. Trailing growth and long shoots are soybean adaptations for natural habitats but cause lodging that hampers yield in cultivation. Previous studies have focused on Dt1/2 affecting the indeterminate/determinate growth habit, whereas the possible role of the gibberellin pathway remained unclear. In the present study, quantitative trait locus (QTL) mapping of a recombinant inbred population of 460 lines revealed a trailing-growth-and-shoot-length QTL. A CNV region within this QTL was identified, featuring the apical bud-expressed gibberellin 2-oxidase 8A/B, the copy numbers of which were positively correlated with expression levels and negatively with trailing growth and shoot length, and their effects were demonstrated by transgenic soybean and Arabidopsis thaliana. Based on the fixation index, this CNV region underwent intense selection during the initial domestication process.

Efficiency of plant growth promoting bacteria for growth and yield enhancement of maize (Zea mays) isolated from rock phosphate reserve area Hazara Khyber Pakhtunkhwa, Pakistan.

The usage of novel Plant Growth-Promoting Rhizobacteria (PGPR) as bioinoculant is a good opportunity for ecological farming practices to improve soil condition, quality of grain, crops' yield and biodiversity conservation. The purpose of recent research was focused to examine, isolate and characterize PGP bacteria that colonize the rhizosphere for the duration of the maize plant's seedling. For this purpose, 14 samples of soils and roots in the maize rhizosphere were collected from rock phosphate area of Hazara, Pakistan. Forty morphologically natural bacterial colonies have been extracted and tested for their PGP innovations and biocontrol residences and further recognized as plant production advancing rhizobacteria. To find the effective PGPR strains with numerous activities, an aggregate of 150 bacterial colonies were sequestered from different rhizospheric soils of the Hazara Pakistan rock phosphate area. These tested bacterial strains were subjected to biochemical description and in vitro screening for their plant growth-promoting qualities like generation of indole acetic acid (IAA), alkali (NH3), hydrogen cyanide (HCN), siderophores, catalases, proteases and pectinases. All the isolates of rhizobacteria showed IAA producing capacity, as well as found positive for catalase and HCN. The above results suggested that, in addition to biocontrol marketers, PGPR could be used as biofertilizers to substitute agro-chemicals in order to increase crop production. These microorganisms can therefore be further developed and used for greenhouse and discipline packages.

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses.

Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants' dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes.