Formerly the "Center for Desert Agriculture"

Recent Submissions

  • Digital insights: bridging the phenotype-to-genotype divide

    McCabe, Matthew; Tester, Mark A. (Journal of Experimental Botany, Oxford University Press (OUP), 2021-04-02) [Article]
    The convergence of autonomous platforms for field-based phenotyping with advances in machine learning for big data analytics and rapid sequencing for genome description herald the promise of new insights and discoveries in the plant sciences. Han et al. (2021) leverage these emerging tools to navigate the challenging path from field-based mapping of phenotypic features to identifying specific genetic loci in the laboratory: in this case, loci responsible for regulating daily flowering time in lettuce. While their contribution neatly illustrates these exciting technological developments, it also highlights the work that remains to bridge these multidisciplinary fields to more fully deliver upon the promise of digital agriculture.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (NCBI, 2021-03-22) [Bioproject, Dataset]
    We report the transcriptome composition of ahl13-1 compared to WT (col-0) plant without treatment and after Pst hrcC-application Overall design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of col0 and ahl13-1 under treated and untreated conditions. col0 samples are in GEO Series GSE118854.
  • Microbial communities of wheat plants inoculated with endophytic bacterium Enterobacter sp. SA187

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
    Global warming has become a critical challenge to food safety, causing severe yield losses of major crops worldwide. Here, we report that the endophytic bacterium Enterobacter sp. SA187 induces thermotolerance of crops in a sustainable manner. Microbiome diversity of wheat plants is positively influenced by SA187 in open field agriculture, indicating that beneficial microbes can be a powerful tool to enhance agriculture in open field agriculture. Overall design: We examined the effect the SA187 inoculation on the root endosphere microbiome of wheat plant growing under desert farming condition.
  • Molecular mechanisms of Enterobacter sp. SA187 induced thermotolerance in Arabidopsis thaliana

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (NCBI, 2021-03-16) [Bioproject, Dataset]
    Global warming and heat stress belong to the most critical environmental challenges to agriculture worldwide, causing severe losses of major crop yields. In present study we report that the endophytic bacterium Enterobacter sp. SA187 protects Arabidopsis thaliana to heat stress. To understand the mechanisms at molecular level we performed RNA-seq Overall design: mRNA seq to elucidate the SA187 mediated thermotolerance in Arabidopsis thaliana inoculated with entrobacter sp SA187
  • LAMP-Coupled CRISPR–Cas12a Module for Rapid and Sensitive Detection of Plant DNA Viruses

    Mahas, Ahmed; Hassan, Norhan; Aman, Rashid; Maršić, Tin; Wang, Qiaochu; Ali, Zahir; Mahfouz, Magdy M. (Viruses, MDPI AG, 2021-03-12) [Article]
    One important factor for successful disease management is the ability to rapidly and accurately identify the causal agent. Plant viruses cause severe economic losses and pose a serious threat to sustainable agriculture. Therefore, optimization of the speed, sensitivity, feasibility, portability, and accuracy of virus detection is urgently needed. Here, we developed a clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid diagnostic method utilizing the CRISPR–Cas12a system for detecting two geminiviruses, tomato yellow leaf curl virus (TYLCV) and tomato leaf curl New Delhi virus (ToLCNDV), which have single-stranded DNA genomes. Our assay detected TYLCV and ToLCNDV in infected plants with high sensitivity and specificity. Our newly developed assay can be performed in ~1 h and provides easy-to-interpret visual readouts using a simple, low-cost fluorescence visualizer, making it suitable for point-of-use applications.
  • Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Hirt, Heribert; Saad, Maged (Current Microbiology, Springer Science and Business Media LLC, 2021-03-08) [Article]
    Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18′s genome with type strains from the same genus, using digital DNA–DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.
  • Chemical activation of Arabidopsis SnRK2.6 by pladienolide B

    Punkkinen, Matleena; Mahfouz, Magdy M.; Fujii, Hiroaki (Plant Signaling & Behavior, Informa UK Limited, 2021-03-08) [Article]
    Abscisic acid (ABA) is an important phytohormone mediating osmotic stress responses. SUCROSE NONFERMENTING 1 (SNF1)-RELATED PROTEIN KINASE 2.6 (SnRK2.6, also named OPEN STOMATA1 and SNF1-RELATED KINASE 2E) is central in the ABA signaling pathway; therefore, manipulating its activity may be useful to confer stress tolerance in plants. Pladienolide B (PB) is an mRNA splicing inhibitor and enhances ABA responses. Here, we analyzed the effect of PB on Arabidopsis SnRK2.6. PB enhanced the activity of recombinant SnRK2.6 in vitro through direct physical interaction as predicted by molecular docking simulations followed by mutation experiments and isothermal titration calorimetry. Structural modeling predicted probable interaction sites between PB and SnRK2.6, and experiments with mutated SnRK2.6 revealed that Leu-46 was the most essential amino acid residue for SnRK2.6 activation by PB. This study demonstrates the feasibility of SnRK2.6 chemical manipulation and paves the way for the modification of plant osmotic stress responses.
  • The role of PQL genes in response to salinity tolerance in Arabidopsis and barley

    Alqahtani, Mashael Daghash Saeed; Lightfoot, Damien; Lemtiri-Chlieh, Fouad; Bukhari, Ebtihaj; Pardo, José M.; Julkowska, Magdalena M.; Tester, Mark A. (Plant Direct, Wiley, 2021-02-10) [Article]
    While soil salinity is a global problem, how salt enters plant root cells from the soil solution remains underexplored. Non-selective cation channels (NSCCs) are suggested to be the major pathway for the entry of sodium ions (Na+), yet their genetic constituents remain unknown. Yeast PQ loop (PQL) proteins were previously proposed to encode NSCCs, but the role of PQLs in plants is unknown. The hypothesis tested in this research is that PQL proteins constitute NSCCs mediating some of the Na+ influx into the root, contributing to ion accumulation and the inhibition of growth in saline conditions. We identified plant PQL homologues, and studied the role of one clade of PQL genes in Arabidopsis and barley. Using heterologous expression of AtPQL1a and HvPQL1 in HEK293 cells allowed us to resolve sizable inwardly directed currents permeable to monovalent cations such as Na+, K+, or Li+ upon membrane hyperpolarization. We observed that GFP-tagged PQL proteins localized to intracellular membrane structures, both when transiently over-expressed in tobacco leaf epidermis and in stable Arabidopsis transformants. Expression of AtPQL1a, AtPQL1b, and AtPQL1c was increased by salt stress in the shoot tissue compared to non-stressed plants. Mutant lines with altered expression of AtPQL1a, AtPQL1b, and AtPQL1c developed larger rosettes in saline conditions, while altered levels of AtPQL1a severely reduced development of lateral roots in all conditions. This study provides the first step toward understanding the function of PQL proteins in plants and the role of NSCC in salinity tolerance.
  • LC–MS-Based Profiling Provides New Insights into Apocarotenoid Biosynthesis and Modifications in Citrus Fruits

    Zheng, Xiongjie; Mi, Jianing; Deng, Xiuxin; Al-Babili, Salim (Journal of Agricultural and Food Chemistry, American Chemical Society (ACS), 2021-02-05) [Article]
    Apocarotenoids contribute to fruit color and aroma, which are critical quality and marketability attributes. Previously, we reported that the red peels of citrus fruits, which are characterized by higher expression levels of a <i>carotenoid cleavage dioxygenase</i> 4<i>b</i> (<i>CitCCD</i>4<i>b</i>) gene, accumulate higher levels of β-citraurin and β-citraurinene than yellow peels. Here, we identified and quantified 12 apocarotenoids, either volatile or nonvolatile, in citrus peel using liquid chromatography-mass spectrometry (LC-MS). Our results show that red peels contain also dramatically higher amounts of β-apo-8'-carotenal, crocetin dialdehyde known from saffron, β-citraurol, β-cyclocitral, and 3-OH-β-cyclocitral and up to about 17-fold higher levels of 3-OH-β-cyclocitral glucoside (picrocrocin isomer). The content of these apocarotenoids was also significantly increased in different <i>CitCCD</i>4<i>b</i>-overexpressing transgenic callus lines, compared with corresponding controls. Transient expression of <i>CitCCD</i>4<i>b</i> in <i>Nicotiana benthamiana</i> leaves resulted in a striking increase in the 3-OH-β-cyclocitral level and the accumulation of picrocrocin. Thus, our work reinforces the specific function of CitCCD4b in producing C<sub>10</sub> apocarotenoid volatiles and C<sub>30</sub> pigments in citrus peel and uncovers its involvement in the biosynthesis of picrocrocin, C<sub>20</sub> dialdehyde, and C<sub>30</sub> alcohol apocarotenoids, suggesting the potential of this enzyme in metabolic engineering of apocarotenoids and their derivatives.
  • Practical strategies to mitigate ruminant greenhouse gas emissions

    Ortega, Alejandra; Tester, Mark A.; Lauersen, Kyle J. (Research Square, 2021-02-05) [Preprint]
    Abstract Livestock contributes to 14.5 percent of global greenhouse gas emissions, with ruminants being the largest contributor through enteric methane emissions. Although several mitigation strategies are available to reduce livestock methane, no consensus exists on which methods are the most effective. Here, the mitigation impact of the most pragmatic strategies to reduce enteric methane has been projected to 2050, using cattle emissions as a model. The projection shows that supplementing ruminant feed with anti-methanogenic seaweed and converting grassland into silvopasture offer the greatest potential to reduce emissions. With a synergic combination of strategies, the livestock sector in Europe and most of Asia can reach carbon neutrality by 2035 and 2038, respectively. However, global cattle CO2-eq emissions will be reduced by no more than 34 percent by 2050, remaining far above the carbon neutrality target. Mitigation strategies alone are insufficient to lower emissions, and reducing the demand for ruminant products is also necessary – particularly in Africa and Western Asia.
  • Superhydrophobic sand mulches increase agricultural productivity in arid regions

    Gallo Junior, Adair; Odokonyero, Kennedy; Mousa, Magdi A. A.; Reihmer, Joel W.; Almashharawi, Samir; Marasco, Ramona; Manalastas, Edelberto; Morton, Mitchell J. L.; Daffonchio, Daniele; McCabe, Matthew; Tester, Mark A.; Mishra, Himanshu (arXiv, 2021-01-31) [Preprint]
    Excessive evaporative loss of water from the topsoil in arid-land agriculture is compensated via irrigation, which exploits massive freshwater resources. The cumulative effects of decades of unsustainable freshwater consumption in many arid regions are now threatening food-water security. While plastic mulches can reduce evaporation from the topsoil, their cost and non-biodegradability limit their utility. In response, we report on superhydrophobic sand (SHS), a bio-inspired enhancement of common sand with a nanoscale wax coating. When SHS was applied as a 5 mm-thick mulch over the soil, evaporation dramatically reduced and crop yields increased. Multi-year field trials of SHS application with tomato (Solanum lycopersicum), barley (Hordeum vulgare), and wheat (Triticum aestivum) under normal irrigation enhanced yields by 17%-73%. Under brackish water irrigation (5500 ppm NaCl), SHS mulching produced 53%-208% higher fruit yield and grain gains for tomato and barley. Thus, SHS could benefit agriculture and city-greening in arid regions.
  • Lycopene β-cyclase expression influences plant physiology, development and metabolism in tobacco plants

    Kossler, Stella; Armarego-Marriott, Tegan; Tarkowska, Danuse; Tureckova, Veronika; Agrawal, Shreya; Mi, Jianing; Perez da Sousa, Leonardo; Aurel Schottler, Mark; Schadach, Anne; Frohlich, Anja; Bock, Ralph; Al-Babili, Salim; Ruf, Stephanie; Sampathkumar, Arun; Moreno, Juan C (Journal of Experimental Botany, Oxford University Press (OUP), 2021-01-23) [Article]
    Abstract Carotenoids are important isoprenoids produced in the plastids of photosynthetic organisms that play key roles in photoprotection and antioxidative processes. β-carotene is generated from lycopene by the lycopene β-cyclase (LCYB). Previously, we demonstrated that the introduction of the Daucus carota (carrot) DcLCYB1 gene into tobacco (cultivar Xanthi) resulted in increased levels of abscisic acid (ABA) and especially gibberellins (GAs), resulting in increased plant yield. In order to understand this phenomenon prior exporting this genetic strategy to crops, we generated tobacco (cultivar Petit Havana) mutants that exhibited a wide range of LCYB expression. Transplastomic plants expressing DcLCYB1 at high levels showed a wild-type-like growth, even though their pigment content was increased, and their leaf GA content was reduced. RNAi NtLCYB lines showed different reductions in NtLCYB transcript abundance, correlating with reduced pigment content and plant variegation. Photosynthesis (leaf absorptance, Fv/Fm, and ETRII) and plant growth were impaired. Remarkably, drastic changes in phytohormone content also occurred in the RNAi lines. However, external application of phytohormones was not sufficient to rescue their phenotypes, suggesting that altered photosynthetic efficiency might be another important factor explaining their reduced biomass. These results show that LCYB expression influences plant biomass by different mechanisms and suggests thresholds for LCYB expression levels that might be beneficial/detrimental for plant growth.
  • A type dependent effect of treated wastewater matrix on seed germination and food production.

    Zaouri, Noor A.; Cheng, Hong; Khairunnisa, Fatin; Alahmed, Abdulelah; Blilou, Ikram; Hong, Pei-Ying (The Science of the total environment, Elsevier BV, 2021-01-21) [Article]
    Municipal wastewater treated by membrane bioreactor, either aerobically (AeMBR) or anaerobically (AnMBR), can be reused to irrigate crops. However, post-AeMBR and post-AnMBR effluent have different water quality that may impact crop growth and yield. This study aims to assess for differences in water quality from both AeMBR and AnMBR, and determine if the type of treated wastewater matrix would impact seed germination and crop yield. Compared to post-AeMBR and control, post-AnMBR effluent had a negative impact on seed germination for both tomatoes and lettuces. The use of post-AnMBR but not post-AeMBR effluent also resulted in a higher number of unripe tomato fruits at the time of harvesting. However, when post-AnMBR effluent was diluted to 25% and 75% v/v with tap water, higher lettuce biomass was harvested compared to the same concentrations of post-AeMBR effluent and control. The observed differences in germination and yield were likely due to differences in the concentrations of heavy metals (e.g. Zn) and steroids or phytohormones (e.g. testosterone, gibberellic acid) present in both post-MBR effluents. This study demonstrated that the type of treated wastewater generated from different upstream treatment technologies can potentially impact crop yield based on the crop type. By understanding how the type of treated wastewater affect downstream agricultural activities, changes in management practices can be made accordingly.
  • Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci

    Shekhawat, Kirti; Saad, Maged; Sheikh, Arsheed Hussain; Mariappan, Kiruthiga; Al-Mahmoudi, Henda; abdulhakim, fatimah; Eida, Abdul Aziz; Jalal, Rewaa S.; Masmoudi, Khaled; Hirt, Heribert (EMBO reports, EMBO, 2021-01-10) [Article]
    Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.
  • Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

    Rayapuram, Naganand; Jarad, Mai; Alhoraibi, Hanna; Bigeard, Jean; Abulfaraj, Aala A.; Volz, Ronny; Mariappan, Kiruthiga; Almeida-Trapp, Marilia; Schlöffel, Maria; Lastrucci, Emmanuelle; Bonhomme, Ludovic; Gust, Andrea A.; Mithöfer, Axel; Arold, Stefan T.; Pflieger, Delphine; Hirt, Heribert (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2021-01-08) [Article]
    In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
  • Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

    Patiranage, Dilan S. R.; Rey, Elodie; Emrani, Nazgol; Wellman, Gordon; Schmid, Karl; Schmöckel, Sandra M.; Tester, Mark A.; Jung, Christian (Dryad, 2021) [Dataset]
    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 fast LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study uncovered 600 SNPs stably associated with 17 agronomic 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 that are highly responding to photoperiod hence important for the adaptation to different environments. 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.
  • Carotenoid Biofortification of Crops in the CRISPR Era

    Zheng, Xiongjie; Kuijer, Hendrik N.J.; Al-Babili, Salim (Trends in Biotechnology, Elsevier BV, 2020-12-29) [Article]
    Carotenoids are micronutrients important for human health. The continuous improvements in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing techniques make rapid, DNA/transgene-free and targeted multiplex genetic modification a reality, thus promising to accelerate the breeding and generation of ‘golden’ staple crops. We discuss here the progress and future prospects of CRISPR/Cas9 applications for carotenoid biofortification.
  • Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii

    Aragon-Raygoza, Alejandro; Vasco, Alejandra; Blilou, Ikram; Herrera-Estrella, Luis Rafael; Cruz-Ramírez, Alfredo (Genes, MDPI AG, 2020-12-09) [Article]
    Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
  • A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina

    Friis, Guillermo; Vizueta, Joel; Smith, E. G.; Nelson, David R; Khraiwesh, Basel; Qudeimat, Enas; Salehi-Ashtiani, Kourosh; Ortega, Alejandra; Marshell, Alyssa; Duarte, Carlos M.; Burt, John A (G3 Genes|Genomes|Genetics, Oxford University Press (OUP), 2020-12-08) [Article]
    Abstract The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.
  • Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history

    Patiranage, Dilan S. R.; Rey, Elodie; Emrani, Nazgol; Wellman, Gordon; Schmid, Karl; Schmöckel, Sandra M.; Tester, Mark A.; Jung, Christian (Cold Spring Harbor Laboratory, 2020-12-04) [Preprint]
    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 fast LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study uncovered 600 SNPs stably associated with 17 agronomic 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 that are highly responding to photoperiod hence important for the adaptation to different environments. 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.

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