Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea ( Cajanus cajan L.)

Haplotype-based breeding, a recent promising breeding approach to develop tailor-made crop varieties, deals with identification of superior haplotypes and their deployment in breeding programmes. In this context, whole genome re-sequencing data of 292 genotypes from pigeonpea reference set were mined to identify the superior haplotypes for 10 droughtresponsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene-based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker-trait associations (MTAs) in five genes influencing seven drought-responsive component traits. Haplo-pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. The haplotype C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight (TW), the haplotype C. cajan_30211-H6 for PW, FW, TW and dry weight (DW), the haplotype C. cajan_26230-H11 for FW and DW and the haplotype C. cajan_26230-H5 for relative water content (RWC) were identified as superior haplotypes under drought stress condition. Furthermore, 17 accessions containing superior haplotypes for three drought-responsive genes were identified. The identified superior haplotypes and the accessions carrying these superior haplotypes will be very useful for deploying haplotype-based breeding to develop nextgeneration tailor-made better drought-responsive pigeonpea cultivars

Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains

Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding

Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared

Tracking down carbon inputs underground from an arid zone Australian calcrete.

Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwater systems. However, despite the growing concerns related to increasing anthropogenic pressure and effects of global change to groundwater environments, our understanding of the dynamics regulating subterranean carbon flows is still sparse. We traced carbon composition and transformations in an arid zone calcrete aquifer using a novel multidisciplinary approach that combined isotopic analyses of dissolved organic carbon (DOC) and inorganic carbon (DIC) (δ13CDOC, δ13CDIC, 14CDOC and 14CDIC) with fluorescence spectroscopy (Chromophoric Dissolved OM (CDOM) characterisation) and metabarcoding analyses (taxonomic and functional genomics on bacterial 16S rRNA). To compare dynamics linked to potential aquifer recharge processes, water samples were collected from two boreholes under contrasting rainfall: low rainfall ((LR), dry season) and high rainfall ((HR), wet season). Our isotopic results indicate limited changes and dominance of modern terrestrial carbon in the upper part (northeast) of the bore field, but correlation between HR and increased old and 13C-enriched DOC in the lower area (southwest). CDOM results show a shift from terrestrially to microbially derived compounds after rainfall in the same lower field bore, which was also sampled for microbial genetics. Functional genomic results showed increased genes coding for degradative pathways-dominated by those related to aromatic compound metabolisms-during HR. Our results indicate that rainfall leads to different responses in different parts of the bore field, with an increase in old carbon sources and microbial processing in the lower part of the field. We hypothesise that this may be due to increasing salinity, either due to mobilisation of Cl- from the soil, or infiltration from the downstream salt lake during HR. This study is the first to use a multi-technique assessment using stable and radioactive isotopes together with functional genomics to probe the principal organic biogeochemical pathways regulating an arid zone calcrete system. Further investigations involving extensive sampling from diverse groundwater ecosystems will allow better understanding of the microbiological pathways sustaining the ecological functioning of subterranean biota

Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains

Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome (RG) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD1‐H8 with haplotype frequency (HF) of 30.13% in 3K RG panel, MOC1‐H9 (HF: 23.08%), IPA1‐H14 (HF: 6.64%), DEP3‐H2 (HF: 5.59%), DEP1‐H2 (HF: 37.53%), SP1‐H3 (HF: 5.05%), LAX1‐H5 (HF: 1.56%), LP‐H13 (3.64%), OSH1‐H4 (5.52%), PHD1‐H14 (HF: 15.21%), AGO7‐H15 (HF: 3.33%), ROC5‐H2 (31.42%), RSR1‐H8 (HF: 4.20%) and OsNAS3‐H2 (HF: 1.00%). For heading date, Ghd7‐H8 (HF: 3.08%), TOB1‐H10 (HF: 4.60%) flowered early, Ghd7‐H14 (HF: 42.60%), TRX1‐H9 (HF: 27.97%), OsVIL3‐H14 (HF: 1.72%) for medium duration flowering, while Ghd7‐H6 (HF: 1.65%), SNB‐H9 (HF: 9.35%) were late flowering. GS5‐H4 (HF: 65.84%) attributed slender, GS5‐H5 (HF: 29.00%), GW2‐H2 (HF: 4.13%) were medium slender and GS5‐H9 (HF: 2.15%) for bold grains. Furthermore, haplotype analysis explained possible genetic basis for superiority of selected mega‐varieties. Overall, this study suggests the possibility for developing next‐generation tailor‐made rice with superior haplotype combinations of target genes suiting future food and nutritional demands via haplotype‐based breeding

Unraveling candidate genomic regions responsible for delayed leaf senescence in rice

Photosynthates generated after heading contributes to 60% - 80% of grain yield in rice. Delay in leaf senescence can contribute to a long grain-filling period and thereby increased yield. The objective of this study was to identify genomic region(s) responsible for delayed leaf senescence (DLS) and validate the role of underlying candidate genes in controlling target traits. 302 BC2F4 backcross-derived lines (BILs) developed from a cross between Swarna and Moroberekan were phenotyped for two seasons (DS2016 and WS2017) for chlorophyll content and yield parameters. KASPar-SNP assays based genotyping data with 193 SNPs of mapping population was used to identify the targeted genomic region(s). Significant positive correlation was observed between the two most important determinants of DLS traits viz., RDCF (reduced decline degree of chlorophyll content of flag leaf) and RDCS (reduced decline degree of chlorophyll content of second leaf) with plant height (PH), grain number per panicle (GPN), panicle length (PL), number of tiller (NT) and grain yield (GY). A total of 41 and 29 QTLs with phenotypic variance (PVE) ranging from 8.2 to 25.1% were detected for six DLS traits during DS2016 and WS2017, respectively. Out of these identified QTLs, 19 were considered as stable QTLs detected across seasons. 17 of the identified stable QTLs were found to be novel. In-silico analysis revealed five key genes regulating chlorophyll metabolism. Expression analysis of these genes confirmed their strong association with the senescence pattern in leaf tissue of parents as well as selected phenotypically extreme lines. The identified stable QTLs regulating DLS traits and validation of potential candidate genes provides insight into genetic basis of delayed senescence and is expected to contribute in enhancing grain yield through genomics-assisted breeding (GAB)

Green synthesis of multifunctional silver and gold nanoparticles from the oriental herbal adaptogen: Siberian ginseng

Ragavendran Abbai,1,* Ramya Mathiyalagan,1,* Josua Markus,1 Yeon-Ju Kim,2 Chao Wang,2 Priyanka Singh,2 Sungeun Ahn,2 Mohamed El-Agamy Farh,2 Deok Chun Yang1,2 1Ginseng Bank, Graduate School of Biotechnology, 2Department of Oriental Medicinal Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea *These authors contributed equally to this work Abstract: Pharmacologically active stem of the oriental herbal adaptogen, Siberian ginseng, was employed for the ecofriendly synthesis of Siberian ginseng silver nanoparticles (Sg-AgNPs) and Siberian ginseng gold nanoparticles (Sg-AuNPs). First, for metabolic characterization of the sample, liquid chromatography-tandem mass spectrometry analysis (indicated the presence of eleutherosides A and E), total phenol content, and total reducing sugar were analyzed. Second, the water extract of the sample mediated the biological synthesis of both Sg-AgNPs and Sg-AuNPs that were crystalline face-centered cubical structures with a Z-average hydrodynamic diameter of 126 and 189 nm, respectively. Moreover, Fourier transform infrared analysis indicated that proteins and aromatic hydrocarbons play a key role in the formation and stabilization of Sg-AgNPs, whereas phenolic compounds accounted for the synthesis and stability of Sg-AuNPs. 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H tetrazolium bromide (MTT) assay determined that Sg-AgNPs conferred strong cytotoxicity against MCF7 (human breast cancer cell line) and was only slightly toxic to HaCaT (human keratinocyte cell line) at 10 µg·mL-1. However, Sg-AuNPs did not display cytotoxic effects against both of the cell lines. The disc diffusion assay indicated a dose-dependent increase in the zone of inhibition of Staphylococcus aureus (ATCC 6538), Bacillus anthracis (NCTC 10340), Vibrio parahaemolyticus (ATCC 33844), and Escherichia coli (BL21) treated with Sg-AgNPs, whereas Sg-AuNPs did not show inhibitory activity. In addition, the 2,2-diphenyl-1-picrylhydrazyl assay demonstrated that both Sg-AgNPs and Sg-AuNPs possess strong antioxidant activity. To the best of our knowledge, this is the first report unraveling the potential of Eleutherococcus senticosus for silver and gold nanoparticle synthesis along with its biological applications, which in turn would promote widespread usage of the endemic Siberian ginseng. Keywords: Siberian ginseng, eleutheroside E, eleutheroside A, green synthesis, cytotoxicity, antibacterial activity, antioxidant efficac

Ginseng-berry-mediated gold and silver nanoparticle synthesis and evaluation of their in vitro antioxidant, antimicrobial, and cytotoxicity effects on human dermal fibroblast and murine melanoma skin cell lines

Zuly Elizabeth Jiménez Pérez,1 Ramya Mathiyalagan,1 Josua Markus,1 Yeon-Ju Kim,2 Hyun Mi Kang,3 Ragavendran Abbai,1 Kwang Hoon Seo,2 Dandan Wang,2 Veronika Soshnikova,2 Deok Chun Yang1,21Department of Biotechnology and Ginseng Bank, 2Department of Oriental Medicine Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea; 3Advanced Cosmeceutical Technology R&D Center, Suwon, Republic of KoreaAbstract: There has been a growing interest in the design of environmentally affable and biocompatible nanoparticles among scientists to find novel and safe biomaterials. Panax ginseng Meyer berries have unique phytochemical profile and exhibit beneficial pharmacological activities such as antihyperglycemic, antiobesity, antiaging, and antioxidant properties. A comprehensive study of the biologically active compounds in ginseng berry extract (GBE) and the ability of ginseng berry (GB) as novel material for the biosynthesis of gold nanoparticles (GBAuNPs) and silver nanoparticles (GBAgNPs) was conducted. In addition, the effects of GBAuNPs and GBAgNPs on skin cell lines for further potential biological applications are highlighted. GBAuNPs and GBAgNPs were synthesized using aqueous GBE as a reducing and capping agent. The synthesized nanoparticles were characterized for their size, morphology, and crystallinity. The nanoparticles were evaluated for antioxidant, anti-tyrosinase, antibacterial, and cytotoxicity activities and for morphological changes in human dermal fibroblast and murine melanoma skin cell lines. The phytochemicals contained in GBE effectively reduced and capped gold and silver ions to form GBAuNPs and GBAgNPs. The optimal synthesis conditions (ie, temperature and v/v % of GBE) and kinetics were investigated. Polysaccharides and phenolic compounds present in GBE were suggested to be responsible for stabilization and functionalization of nanoparticles. GBAuNPs and GBAgNPs showed increased scavenging activity against 2,2-diphenyl-1-picrylhydrazyl free radicals compared to GBE. GBAuNPs and GBAgNPs effectively inhibited mushroom tyrosinase, while GBAgNPs showed antibacterial activity against Escherichia coli and Staphylococcus aureus. In addition, GBAuNPs were nontoxic to human dermal fibroblast and murine melanoma cell lines, and GBAgNPs showed cytotoxic effect on murine melanoma cell lines. The current results evidently suggest that GBAgNPs can act as potential agents for antioxidant, anti-tyrosinase, and antibacterial activities. In addition, GBAuNPs can be further developed into mediators in drug delivery and as antioxidant, anti-tyrosinase, and protective skin agents in cosmetic products. Consequently, the study showed the advantages of using nanotechnology and green chemistry to enhance the natural properties of GBs.Keywords: ginseng berry, nanoparticles, antibacterial, antioxidant, anti-tyrosinase, cytotoxicit

Ginseng-berry-mediated gold and silver nanoparticle synthesis and evaluation of their in vitro antioxidant, antimicrobial, and cytotoxicity effects on human dermal fibroblast and murine melanoma skin cell lines

Zuly Elizabeth Jiménez Pérez,1 Ramya Mathiyalagan,1 Josua Markus,1 Yeon-Ju Kim,2 Hyun Mi Kang,3 Ragavendran Abbai,1 Kwang Hoon Seo,2 Dandan Wang,2 Veronika Soshnikova,2 Deok Chun Yang1,21Department of Biotechnology and Ginseng Bank, 2Department of Oriental Medicine Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea; 3Advanced Cosmeceutical Technology R&D Center, Suwon, Republic of KoreaAbstract: There has been a growing interest in the design of environmentally affable and biocompatible nanoparticles among scientists to find novel and safe biomaterials. Panax ginseng Meyer berries have unique phytochemical profile and exhibit beneficial pharmacological activities such as antihyperglycemic, antiobesity, antiaging, and antioxidant properties. A comprehensive study of the biologically active compounds in ginseng berry extract (GBE) and the ability of ginseng berry (GB) as novel material for the biosynthesis of gold nanoparticles (GBAuNPs) and silver nanoparticles (GBAgNPs) was conducted. In addition, the effects of GBAuNPs and GBAgNPs on skin cell lines for further potential biological applications are highlighted. GBAuNPs and GBAgNPs were synthesized using aqueous GBE as a reducing and capping agent. The synthesized nanoparticles were characterized for their size, morphology, and crystallinity. The nanoparticles were evaluated for antioxidant, anti-tyrosinase, antibacterial, and cytotoxicity activities and for morphological changes in human dermal fibroblast and murine melanoma skin cell lines. The phytochemicals contained in GBE effectively reduced and capped gold and silver ions to form GBAuNPs and GBAgNPs. The optimal synthesis conditions (ie, temperature and v/v % of GBE) and kinetics were investigated. Polysaccharides and phenolic compounds present in GBE were suggested to be responsible for stabilization and functionalization of nanoparticles. GBAuNPs and GBAgNPs showed increased scavenging activity against 2,2-diphenyl-1-picrylhydrazyl free radicals compared to GBE. GBAuNPs and GBAgNPs effectively inhibited mushroom tyrosinase, while GBAgNPs showed antibacterial activity against Escherichia coli and Staphylococcus aureus. In addition, GBAuNPs were nontoxic to human dermal fibroblast and murine melanoma cell lines, and GBAgNPs showed cytotoxic effect on murine melanoma cell lines. The current results evidently suggest that GBAgNPs can act as potential agents for antioxidant, anti-tyrosinase, and antibacterial activities. In addition, GBAuNPs can be further developed into mediators in drug delivery and as antioxidant, anti-tyrosinase, and protective skin agents in cosmetic products. Consequently, the study showed the advantages of using nanotechnology and green chemistry to enhance the natural properties of GBs.Keywords: ginseng berry, nanoparticles, antibacterial, antioxidant, anti-tyrosinase, cytotoxicit