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  • Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps.

    Shan, Danting; Ali, Mohsin; Shahid, Mohammed; Arif, Anjuman; Waheed, Muhammad Qandeel; Xia, Xianchun; Trethowan, Richard; Tester, Mark A.; Poland, Jesse; Ogbonnaya, Francis C; Rasheed, Awais; He, Zhonghu; Li, Huihui (TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, Springer Science and Business Media LLC, 2022-08-01) [Article]
    A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.
  • The Gardenia Carotenoid Cleavage Dioxygenase 4a is an efficient tool for biotechnological production of crocins in green and non-green plant tissues

    Zheng, Xiongjie; Mi, Jianing; Balakrishna, Aparna; Liew, Kit Xi; Ablazov, Abdugaffor; Sougrat, Rachid; Al-Babili, Salim (Plant Biotechnology Journal, Wiley, 2022-07-29) [Article]
    Crocins are beneficial antioxidants and potential chemotherapeutics that give raise, together with picrocrocin, to the color and taste of saffron, the most expensive spice, respectively. Crocins are formed from crocetin dialdehyde that is produced in Crocus sativus from zeaxanthin by the Carotenoid Cleavage Dioxygenase 2L (CsCCD2L), while GjCCD4a from Gardenia jasminoides, another major source of crocins, converted different carotenoids, including zeaxanthin, into crocetin dialdehyde in bacterio. To establish a biotechnological platform for sustainable production of crocins, we investigated the enzymatic activity of GjCCD4a, in comparison to CsCCD2L, in citrus callus engineered by Agrobacterium-mediated super-transformation of multi genes and in transiently transformed Nicotiana benthamiana leaves. We demonstrate that co-expression of GjCCD4a with phytoene synthase and β-carotene hydroxylase genes is an optimal combination for heterologous production of crocetin, crocins and picrocrocin in citrus callus. By profiling apocarotenoids and using in vitro assays, we show that GjCCD4a cleaved β-carotene, in planta, and produced crocetin dialdehyde via C30 β-apocarotenoid intermediate. GjCCD4a also cleaved C27 β-apocarotenoids, providing a new route for C17-dialdehyde biosynthesis. Callus lines overexpressing GjCCD4a contained higher number of plastoglobuli in chromoplast-like plastids and increased contents in phytoene, C17:0 fatty acid (FA), and C18:1 cis-9 and C22:0 FA esters. GjCCD4a showed a wider substrate specificity and higher efficiency in Nicotiana leaves, leading to the accumulation of up to 1.6 mg/g dry weight crocins. In summary, we established a system for investigating CCD enzymatic activity in planta and an efficient biotechnological platform for crocins production in green and non-green crop tissues/organs.
  • Synergistic Practicing of Rhizobacteria and Silicon Improve Salt Tolerance: Implications from Boosted Oxidative Metabolism, Nutrient Uptake, Growth and Grain Yield in Mung Bean

    Mahmood, Sajid; Daur, Ihsanullah; Yasir, Muhammad; Waqas, Muhammad; Hirt, Heribert (Plants, MDPI AG, 2022-07-29) [Article]
    Plant growth promoting rhizobacteria (PGPR) and silicon (Si) are known for alleviating abiotic stresses in crop plants. In this study, Bacillus drentensis and Enterobacter cloacae strains of PGPR and foliar application of Si were tested for regulating the antioxidant metabolism and nutrient uptake on grain yield of mung bean under irrigation of saline water (3.12 and 7.81 dS m−1). Bacterial inoculation and supplemental Si (1 and 2 kg ha−1) reduced salinity-induced oxidative stress in mung bean leaves. The improved salt stress tolerance was achieved by enhancing the activities of catalase (45%), peroxidase (43%) and ascorbate peroxidase (48%), while decreasing malondialdehyde levels (57%). Enhanced nutrient uptake of magnesium 1.85 mg g−1, iron 7 mg kg−1, zinc 49.66 mg kg−1 and copper 12.92 mg kg−1 in mung bean seeds was observed with foliar application of Si and PGPR inoculation. Biomass (7.75 t ha−1), number of pods per plant (16.02) and 1000 seed weight (60.95 g) of plants treated with 2 kg Si ha−1 and B. drentensis clearly outperformed treatments with Si or PGPR alone. In conclusion, application of Si and PGPR enhances mung bean productivity under saline conditions, thereby helping exploitation of agriculture in low productive areas.
  • Zaxinone Synthase controls arbuscular mycorrhizal colonization level in rice

    Votta, Cristina; Fiorilli, Valentina; Haider, Imran; Wang, Jian You; Balestrini, Raffaella; Petřík, Ivan; Tarkowská, Danuše; Novak, Ondrej; Serikbayeva, Akmaral; Bonfante, Paola; Al-Babili, Salim; Lanfranco, Luisa (The Plant Journal, Wiley, 2022-07-25) [Article]
    The rice carotenoid cleavage dioxygenase OsZAS was described to produce zaxinone, a novel plant-growth promoting apocarotenoid. A zas mutant line showed a reduced arbuscular mycorrhizal (AM) colonization but the mechanisms underlying this behavior are unknown. Here, we investigated how OsZAS and exogenous zaxinone treatment regulate mycorrhization. Micromolar exogenous supply of zaxinone rescued the root growth but not the mycorrhizal defects of the zas mutant and even reduced mycorrhization in wild type and zas genotypes. The zas line did not display an increase in strigolactones (SLs) level as observed in wild type plants at 7 day post inoculation with the AM fungus. Moreover, an exogenous treatment with the synthetic SLs analog, GR24, rescued the zas mutant mycorrhizal phenotype, indicating that the lower AM colonization rate of zas is due to a SLs deficiency at the early stages of the interaction and pointing out that, during this phase, OsZAS activity is required to induce SLs production, possibly mediated by the Dwarf14-Like (D14L) signaling pathway. OsZAS is expressed in arbuscule-containing cells and OsPT11prom
  • ZAXINONE SYNTHASE 2 regulates growth and arbuscular mycorrhizal symbiosis in rice

    Ablazov, Abdugaffor; Votta, Cristina; Fiorilli, Valentina; Wang, Jian You; Aljedaani, Fatimah R.; Jamil, Muhammad; Balakrishna, Aparna; Balestrini, Raffaella; Liew, Kit Xi; Rajan, Chakravarthy; Berqdar, Lamis; Blilou, Ikram; Lanfranco, Luisa; Al-Babili, Salim (Cold Spring Harbor Laboratory, 2022-07-23) [Preprint]
    Carotenoid cleavage, catalyzed by CAROTENOID CLEAVAGE DIOXYGENASES (CCDs), provides signaling molecules and precursors of plant hormones. Recently, we showed that zaxinone, a novel apocarotenoid metabolite formed by the CCD Zaxinone Synthase (ZAS), is a growth regulator required for normal rice growth and development. The rice genome encodes three OsZAS homologs, called here OsZAS1b, OsZAS1c, and OsZAS2, with unknown functions. Here, we investigated the enzymatic activity, expression pattern, and subcellular localization of OsZAS2, and generated and characterized loss-of-function CRISPR/Cas9-Oszas2 mutants. We show that OsZAS2 formed zaxinone in vitro. OsZAS2 is a plastid-localized enzyme mainly expressed in the root cortex under phosphate starvation. Moreover, OsZAS2 expression increased during mycorrhization, specifically in arbuscule-containing cells. Oszas2 mutants contained lower zaxinone content in roots and exhibited reduced root and shoot biomass, less productive tiller, and higher strigolactone (SL) levels. Exogenous zaxinone application repressed SL biosynthesis and partially rescued the growth retardation of Oszas2 mutant. Consistent with the OsZAS2 expression pattern, Oszas2 mutants displayed a lower frequency of AM colonization. In conclusion, OsZAS2 encodes a further zaxinone-forming enzyme that determines rice growth and architecture and strigolactone content and is required for optimal mycorrhization.
  • Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

    Patiranage, Dilan Sarange Rajapaksha; Rey, Elodie; Emrani, Nazgol; Wellman, Gordon; Schmid, Karl; Schmöckel, Sandra M; Tester, Mark A.; Jung, Christian (eLife, eLife Sciences Publications, Ltd, 2022-07-08) [Article]
    Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study using multi-year phenotyping trials uncovered 600 SNPs stably associated with 17 traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits important for adaptation. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.
  • Minimally-invasive, real-time, non-destructive, species-independent phytohormone biosensor for precision farming

    Bu Khamsin, Abdullah; Ait Lahcen, Abdellatif; Filho, Jose De Oliveira; Shetty, Saptami; Blilou, Ikram; Kosel, Jürgen; Salama, Khaled N. (Biosensors and Bioelectronics, Elsevier BV, 2022-07-06) [Article]
    To keep up with population growth, precision farming technologies must be implemented to sustainably increase agricultural output. The impact of such technologies can be expanded by monitoring phytohormones, such as salicylic acid. In this study, we present a plant-wearable electrochemical sensor for in situ detection of salicylic acid. The sensor utilizes microneedle-based electrodes that are functionalized with a layer of salicylic acid selective magnetic molecularly imprinted polymers. The sensor's capability to detect the phytohormone is demonstrated both in vitro and in vivo with a limit of detection of 2.74 μM and a range of detection that can reach as high as 150 μM. Furthermore, the selectivity of the sensor is verified by testing the sensor on commonly occurring phytohormones. Finally, we demonstrate the capability of the sensor to detect the onset of fungal infestation in Tobacco 5 min post-inoculation. This work shows that the sensor could serve as a promising platform for continuous and non-destructive monitoring in the field and as a fundamental research tool when coupled with a portable potentiostat.
  • LEAfing through literature: Late embryogenesis abundant proteins coming of age – achievements and perspectives

    Hernández-Sánchez, Itzell E; López, Israel Maruri; Martinez-Martinez, Coral; Janis, Brett; Bremont, Juan Francisco Jiménez; Covarrubias, Alejandra A; Menze, Michael A; Graether, Steffen P; Thalhammer, Anja (Journal of Experimental Botany, Oxford University Press (OUP), 2022-07-06) [Article]
    To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review we recap the current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, posttranslational modifications or water deprivation, we give a detailed summary of the current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil-to-helix transitions, self-assembly and their recently discovered ability to undergo liquid-liquid phase separation (LLPS). We point out the promising potential of LEA proteins in biotechnological and agronomic applications and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity.
  • An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

    Wang, Yajun; Abrouk, Michael; Gourdoupis, Spyridon; Koo, Dal-Hoe; Karafiátová, Miroslava; Molnár, István; Doležel, Jaroslav; Athiyannan, Naveenkumar; Cavalet-Giorsa, Emile; Jaremko, Lukasz; Poland, Jesse; Krattinger, Simon G. (Research Square Platform LLC, 2022-07-05) [Preprint]
    The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with novel disease resistance genes. Here, we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease resistance genes for breeding.
  • The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

    Matny, Oadi; Gourdoupis, Spyridon; Johnson, Ryan; Aljedaani, Fatimah R.; Blilou, Ikram; Gardener, Catherine Helen; Yue, Yajuan; Kangara, Ngoni; Steuernagel, Burkhard; Hayta, Sadiye; Smedley, Mark A.; Harwood, Wendy; Patpour, Mehran; Wu, Shuangye; Poland, Jesse; Jones, Jonathan; Reuber, Lynne; Ronen, Moshe; Sharon, Amir; Rouse, Matthew; Xu, Steven; Holušová, Kateřina; Bartos, Jan; Molnár, István; Karafiátová, Miroslava; Jaremko, Lukasz; Doležel, Jaroslav; Steffenson, Brian J.; Wulff, Brande B. H. (Research Square Platform LLC, 2022-07-05) [Preprint]
    To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum. Sr43 encodes a protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
  • NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis

    Alshareef, Nouf Owdah Hameed; Otterbach, Sophie L.; Allu, Annapurna Devi; Woo, Yong; de Werk, Tobias; Kamranfar, Iman; Mueller-Roeber, Bernd; Tester, Mark A.; Balazadeh, Salma; Schmoeckel, Sandra Manuela (Scientific Reports, Springer Science and Business Media LLC, 2022-07-04) [Article]
    Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. ‘Thermomemory’ is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Arabidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like ataf1, anac055 mutants show improved thermomemory, revealing a potential co-control of both NAC TFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
  • Genome-Wide Association Mapping Identifies Key Genomic Regions for Grain Zinc and Iron Biofortification in Bread Wheat.

    Juliana, Philomin; Govindan, Velu; Crespo-Herrera, Leonardo; Mondal, Suchismita; Huerta-Espino, Julio; Shrestha, Sandesh; Poland, Jesse; Singh, Ravi P (Frontiers in plant science, Frontiers Media SA, 2022-06-30) [Article]
    Accelerating breeding efforts for developing biofortified bread wheat varieties necessitates understanding the genetic control of grain zinc concentration (GZnC) and grain iron concentration (GFeC). Hence, the major objective of this study was to perform genome-wide association mapping to identify consistently significant genotyping-by-sequencing markers associated with GZnC and GFeC using a large panel of 5,585 breeding lines from the International Maize and Wheat Improvement Center. These lines were grown between 2018 and 2021 in an optimally irrigated environment at Obregon, Mexico, while some of them were also grown in a water-limiting drought-stressed environment and a space-limiting small plot environment and evaluated for GZnC and GFeC. The lines showed a large and continuous variation for GZnC ranging from 27 to 74.5 ppm and GFeC ranging from 27 to 53.4 ppm. We performed 742,113 marker-traits association tests in 73 datasets and identified 141 markers consistently associated with GZnC and GFeC in three or more datasets, which were located on all wheat chromosomes except 3A and 7D. Among them, 29 markers were associated with both GZnC and GFeC, indicating a shared genetic basis for these micronutrients and the possibility of simultaneously improving both. In addition, several significant GZnC and GFeC associated markers were common across the irrigated, water-limiting drought-stressed, and space-limiting small plots environments, thereby indicating the feasibility of indirect selection for these micronutrients in either of these environments. Moreover, the many significant markers identified had minor effects on GZnC and GFeC, suggesting a quantitative genetic control of these traits. Our findings provide important insights into the complex genetic basis of GZnC and GFeC in bread wheat while implying limited prospects for marker-assisted selection and the need for using genomic selection.
  • Genetic architecture and QTL selection response for Kernza perennial grain domestication traits

    Crain, Jared; Larson, Steve; Dorn, Kevin; DeHaan, Lee; Poland, Jesse (Theoretical and Applied Genetics, Springer Science and Business Media LLC, 2022-06-28) [Article]
    Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8–5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.
  • Characterization of a thermostable Cas13 enzyme for one-pot detection of SARS-CoV-2

    Mahas, Ahmed; Maršić, Tin; Masson, Mauricio Lopez Portillo; Wang, Qiaochu; Aman, Rashid; Zheng, Cheng; Ali, Zahir; Alsanea, Madain; Al-Qahtani, Ahmed; Ghanem, Bernard; Alhamlan, Fatimah Saeed; Mahfouz, Magdy M. (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2022-06-28) [Article]
    Type VI CRISPR-Cas systems have been repurposed for various applications such as gene knockdown, viral interference, and diagnostics. However, the identification and characterization of thermophilic orthologs will expand and unlock the potential of diverse biotechnological applications. Herein, we identified and characterized a thermostable ortholog of the Cas13a family from the thermophilic organism Thermoclostridium caenicola (TccCas13a). We show that TccCas13a has a close phylogenetic relation to the HheCas13a ortholog from the thermophilic bacterium Herbinix hemicellulosilytica and shares several properties such as thermostability and inability to process its own pre-CRISPR RNA. We demonstrate that TccCas13a possesses robust cis and trans activities at a broad temperature range of 37 to 70 °C, compared with HheCas13a, which has a more limited range and lower activity. We harnessed TccCas13a thermostability to develop a sensitive, robust, rapid, and one-pot assay, named OPTIMA-dx, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. OPTIMA-dx exhibits no cross-reactivity with other viruses and a limit of detection of 10 copies/μL when using a synthetic SARS-CoV-2 genome. We used OPTIMA-dx for SARS-CoV-2 detection in clinical samples, and our assay showed 95% sensitivity and 100% specificity compared with qRT-PCR. Furthermore, we demonstrated that OPTIMA-dx is suitable for multiplexed detection and is compatible with the quick extraction protocol. OPTIMA-dx exhibits critical features that enable its use at point of care (POC). Therefore, we developed a mobile phone application to facilitate OPTIMA-dx data collection and sharing of patient sample results. This work demonstrates the power of CRISPR-Cas13 thermostable enzymes in enabling key applications in one-pot POC diagnostics and potentially in transcriptome engineering, editing, and therapies.
  • Mutational signatures on ischemic stroke-associated genes in Saudi human genome

    Vijayakumar, Rajendran; Manikandan, Palanisamy; Alfaiz, Faiz; Al Aboodi, Mohammad Saleh; Kannaiyan, Moorthy; Mickymaray, Suresh; Banoth, Balaji; Veluchamy, Alaguraj (Journal of King Saud University - Science, Elsevier BV, 2022-06-27) [Article]
    Stroke is a neurological syndrome, and it leads to 5.8 million mortalities worldwide annually. In the Kingdom of Saudi Arabia (KSA), stroke was predicted to have 57%-67% incidence rate against a population growth rate of 12.8%. Current state of the art in stroke research in KSA is limited to epidemiological, prevalence data and there is a lack of genetic basis of stroke among Saudi individuals and their risk for disease traits. Despite the better health care services in KSA, a genetic approach is needed for stroke, as it is a manifestation of both monogenic Mendelian and polygenic disorder. Here, we propose to analyze and annotate Saudi specific genome variations associated with stroke. In this study, we explored the non-coding and genic regions using 28 whole genomes of individuals from Saudi population. We explored stroke susceptible genes for additional variation. Analysis of 49 genes which are stroke-associated for single nucleotide polymorphism (SNPs), obtained from whole genomes, reveals variations in atleast 13 candidate genes. In conclusion, whole genome sequencing and annotation of SNPs in the population of Saudi Arabia provide an insight into genetics of stroke. This analysis furnish a list of probable novel Saudi specific mutations that could be associated with stroke, once a cohort of disease data can beobtained. In addition, we conjecture that, by identifying these mutational signatures, stroke subtype and susceptibility to stroke can be uncovered in the future.
  • Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS)

    Terraneo, Tullia Isotta; Mariappan, Kiruthiga; Forsman, Zac; Arrigoni, Roberto (Methods in molecular biology (Clifton, N.J.), Springer US, 2022-06-22) [Book Chapter, Protocol]
    Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.
  • The diversity of quinoa morphological traits and seed metabolic composition

    Tabatabaei, Iman; Alseekh, Saleh; Shahid, Mohammad; Leniak, Ewa; Wagner, Mateusz; Mahmoudi, Henda; Thushar, Sumitha; Fernie, Alisdair R.; Murphy, Kevin M.; Schmöckel, Sandra M.; Tester, Mark A.; Mueller-Roeber, Bernd; Skirycz, Aleksandra; Balazadeh, Salma (Scientific Data, Springer Science and Business Media LLC, 2022-06-20) [Article]
    Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography – mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
  • Evaluation of the Biostimulant Activity of Zaxinone Mimics (MiZax) in Crop Plants

    Wang, Jian You; Jamil, Muhammad; Hossain, Md. Golap; Chen, Guan-Ting Erica; Berqdar, Lamis; Ota, Tsuyoshi; Blilou, Ikram; Asami, Tadao; Al-Solimani, Samir Jamil; Mousa, Magdi Ali Ahmed; Al-Babili, Salim (Frontiers in Plant Science, Frontiers Media SA, 2022-06-16) [Article]
    Global food security is a critical concern that needs practical solutions to feed the expanding human population. A promising approach is the employment of biostimulants to increase crop production. Biostimulants include compounds that boost plant growth. Recently, mimics of zaxinone (MiZax) were shown to have a promising growth-promoting effect in rice (Oryza sativa). In this study, we investigated the effect of MiZax on the growth and yield of three dicot horticultural plants, namely, tomato (Solanum lycopersicum), capsicum (Capsicum annuum), and squash (Cucurbita pepo) in different growth environments, as well as on the growth and development of the monocot date palm (Phoenix dactylifera), an important crop in the Middle East. The application of MiZax significantly enhanced plant height, flower, and branch numbers, fruit size, and total fruit yield in independent field trials from 2020 to 2021. Importantly, the amount of applied MiZax was far less than that used with the commercial compound humic acid, a widely used biostimulant in horticulture. Our results indicate that MiZax have significant application potential to improve the performance and productivity of horticultural crops.
  • Gene fusion as an important mechanism to generate new genes in the genus Oryza

    Zhou, Yanli; Zhang, Chengjun; Zhang, Li; Ye, Qiannan; Liu, Ningyawen; Wang, Muhua; Long, Guangqiang; Fan, Wei; Long, Manyuan; Wing, Rod Anthony (Genome biology, Springer Science and Business Media LLC, 2022-06-15) [Article]
    Background: Events of gene fusion have been reported in several organisms. However, the general role of gene fusion as part of new gene origination remains unknown. Results: We conduct genome-wide interrogations of four Oryza genomes by designing and implementing novel pipelines to detect fusion genes. Based on the phylogeny of ten plant species, we detect 310 fusion genes across four Oryza species. The estimated rate of origination of fusion genes in the Oryza genus is as high as 63 fusion genes per species per million years, which is fixed at 16 fusion genes per species per million years and much higher than that in flies. By RNA sequencing analysis, we find more than 44% of the fusion genes are expressed and 90% of gene pairs show strong signals of purifying selection. Further analysis of CRISPR/Cas9 knockout lines indicates that newly formed fusion genes regulate phenotype traits including seed germination, shoot length and root length, suggesting the functional significance of these genes. Conclusions: We detect new fusion genes that may drive phenotype evolution in Oryza. This study provides novel insights into the genome evolution of Oryza.
  • Editorial: Plant Epigenetics and Climate Change.

    Rayapuram, Naganand; De Zelicourt, Axel; Satbhai, Santosh B; Arteaga-Vazquez, Mario Alberto (Frontiers in plant science, Frontiers Media SA, 2022-06-14) [Article]

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