Molecular Research in Rice: Agronomically Important Traits 2.0

This volume presents recent research achievements concerning the molecular genetic basis of agronomic traits in rice. Rice (Oryza sativa L.) is the most important food crop in the world, being a staple food for more than half of the world’s population. Recent improvements in living standards have increased the worldwide demand for high-yielding and high-quality rice cultivars. To develop novel cultivars with superior agronomic performance, we need to understand the molecular basis of agronomically important traits related to grain yield, grain quality, disease resistance, and abiotic stress tolerance. Decoding the whole rice genome sequence revealed that ,while there are more than 37,000 genes in the ~400 Mbp rice genome, there are only about 3000 genes whose molecular functions are characterized in detail. We collected in this volume the continued research efforts of scholars that elucidate genetic networks and the molecular mechanisms controlling agronomically important traits in rice

Cross-Kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses

High-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. We showed previously that Arabidopsis (Arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. To recognize low-oxygen responses that are evolutionarily conserved versus species specific, we compared the transcriptomic reconfiguration in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). Sorting of organism proteomes into clusters of putative orthologs identified broadly conserved responses associated with glycolysis, fermentation, alternative respiration, metabolite transport, reactive oxygen species amelioration, chaperone activity, and ribosome biogenesis. Differ-entially regulated genes involved in signaling and transcriptional regulation were poorly conserved across kingdoms. Strikingly, nearly half of the induced mRNAs of Arabidopsis seedlings encode proteins of unknown function, of which over 40% had up-regulated orthologs in poplar (Populus trichocarpa), rice (Oryza sativa), or Chlamydomonas reinhardtii. Sixteen HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes, including four that are Arabidopsis specific, were ectopically overexpressed and evaluated for their effect on seedling tolerance to oxygen deprivation. This allowed the identification of HUPs coregulated with genes associated with anaerobic metabolism and other processes that significantly enhance or reduce stress survival when ectopically overexpressed. These findings illuminate both broadly conserved and plant-specific low-oxygen stress responses and confirm that plant-specific HUPs with limited phylogenetic distribution influence low-oxygen stress endurance.Instituto de Biotecnologia y Biologia Molecula

Techniques against Distinct Abiotic Stress of Rice

Plants cannot physically escape environmental stresses because they are sessile organisms, which can stunt their growth. As a result, plants have had to evolve distinct strategies to deal with abiotic stress. Indeed, responding to and eventually adapting to abiotic stress may be a driving force in speciation. Because of the complexity of stress, multiple sensors, rather than a single sensor, are more likely to be responsible for stress perception. Stress-induced gene issues can be divided into two categories: those involved in stress tolerance and those involved in signal transduction. Stress-tolerance genes help plants cope with stress in both short- and long-term responses. These can include the synthesis of chaperones and enzymes for osmolyte biosynthesis. And, as with cold stress, detoxification causes a change in the composition of membrane lipids. Gene products can also function as transcription regulators, controlling groups of stress-related genes, or as components in the production of regulatory molecules. It has been shown that multiple signaling pathways can be activated during stress, resulting in similar responses to different triggers

Ethylene Response Factor VII Transkriptionsfaktoren steuern die Umformung der Wurzelsystemarchitektur als Antwort auf Hypoxie

Upon flooding, roots are the first organs to encounter oxygen shortage due to decreased gas diffusion and depletion of oxygen by microorganisms in the soil. Root performance is crucial for plant survival during hypoxia. Arabidopsis thaliana, with its intermediate tolerance to flooding, is a well-suited model organism to characterize adaptation to hypoxia at the level of root system architecture and its underlying molecular regulation. This work revealed distinct changes in the root system which are hypothesized to contribute low oxygen stress adaptation. ERFVIIs antagonize hypoxiainduced root bending and enhance lateral and adventitious root elongation highlighting their regulatory role in the developmental reprogramming of the root system. The study further revealed a, yet unknown, ERFVII-independent sensing mechanism for low oxygen.Staunässe und Überflutung führen bei Pflanzen zu Sauerstoffmangel und damit zu einem Verlust der mitochondrialen ATP Bildung. Wurzeln sind die ersten Organe, die dabei Sauerstoffmangel erfahren, weil Gasdiffusion in Wasser vermindert ist und Sauerstoff im Boden durch aerobe Mikroorganismen aufgebraucht wird. Wurzeln sind aber entscheidend für das Überleben der Pflanze bei Hypoxie. Arabidopsis thaliana, mit seiner mittleren Toleranz gegenüber Überflutung, wurde als Modellorganismus gewählt, um Veränderungen der Wurzelarchitektur bei Hypoxie zu untersuchen, und die zugrundeliegenden molekularen Regulationsmechanismen aufzuklären. In dieser Arbeit wurden spezifische Veränderungen der Wurzelarchitektur in Anwort auf und wahrscheinlich in Anpassung an Sauerstoffmangel beschrieben und teilweise mechanistisch aufgeklärt. ERFVIIs fungieren als Gegenspieler zu der durch Hypoxie ausgelösten Krümmung der Wurzel. Gleichzeitig fördern sie das Wachstum von Sekundärwurzeln, was zu einer insgesamt veränderten Wurzelarchitektur führt. Darüber hinaus wurde deutlich, dass es einen bisher unbekannten, ERFVII unabhängigen, Mechanismus zur Wahrnehmung geringer Sauerstoffkonzentration gibt

Salt stress response in rice: genetics, molecular biology, and comparative genomics

Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers. Salt-tolerant transgenic rice plants have been produced using a host of different genes and transcript profiling by micro- and macroarray-based methods has opened the gates for the discovery of novel salt stress mechanisms in rice, and comparative genomics is turning out to be a critical input in this respect. In this paper, we present a comprehensive review of the genetic, molecular biology, and comparative genomics effort towards the generation of salt-tolerant rice. From the data on comprehensive transcript expression profiling of clones representing salt-stress-associated genes of rice, it is shown that transcriptional and translational machineries are important determinants in controlling salt stress response, and gene expression response in tolerant and susceptible rice plants differs mainly in quantitative terms

Potential Role of Plant Growth Regulators in Administering Crucial Processes Against Abiotic Stresses

Plant growth regulators are naturally biosynthesized chemicals in plants that influence physiological processes. Their synthetic analogous trigger numerous biochemical and physiological processes involved in the growth and development of plants. Nowadays, due to changing climatic scenario, numerous biotic and abiotic stresses hamper seed germination, seedling growth, and plant development leading to a decline in biological and economic yields. However, plant growth regulators (PGRs) can potentially play a fundamental role in regulating plant responses to various abiotic stresses and hence, contribute to plant adaptation under adverse environments. The major effects of abiotic stresses are growth and yield disturbance, and both these effects are directly overseen by the PGRs. Different types of PGRs such as abscisic acid (ABA), salicylic acid (SA), ethylene (ET), and jasmonates (JAs) are connected to boosting the response of plants to multiple stresses. In contrast, PGRs including cytokinins (CKs), gibberellins (GAs), auxin, and relatively novel PGRs such as strigolactones (SLs), and brassinosteroids (BRs) are involved in plant growth and development under normal and stressful environmental conditions. Besides, polyamines and nitric oxide (NO), although not considered as phytohormones, have been included in the current review due to their involvement in the regulation of several plant processes and stress responses. These PGRs are crucial for regulating stress adaptation through the modulates physiological, biochemical, and molecular processes and activation of the defense system, upregulating of transcript levels, transcription factors, metabolism genes, and stress proteins at cellular levels. The current review presents an acumen of the recent progress made on different PGRs to improve plant tolerance to abiotic stress such as heat, drought, salinity, and flood. Moreover, it highlights the research gaps on underlying mechanisms of PGRs biosynthesis under stressed conditions and their potential roles in imparting tolerance against adverse effects of suboptimal growth conditions.Fil: Sabagh, Ayman EL. Kafrelsheikh University; EgiptoFil: Mbarki, Sonia. National Institute Of Research In Rural Engineering; TúnezFil: Hossain, Akbar. Bangladesh Agricultural Research Institute; BangladeshFil: Iqbal, Muhammad Aamir. University Of Poonch Rawalakot; PakistánFil: Islam, Mohammad Sohidul. Hajee Mohammad Danesh And Technology University; BangladeshFil: Raza, Ali. Fujian Agriculture And Forestry University; ChinaFil: Llanes, Analia Susana. Universidad Nacional de Rio Cuarto. Facultad de Cs.exactas Fisicoquimicas y Naturales. Instituto de Investigaciones Agrobiotecnologicas. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Cordoba. Instituto de Investigaciones Agrobiotecnologicas.; ArgentinaFil: Reginato, Mariana Andrea. Universidad Nacional de Rio Cuarto. Facultad de Cs.exactas Fisicoquimicas y Naturales. Instituto de Investigaciones Agrobiotecnologicas. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Cordoba. Instituto de Investigaciones Agrobiotecnologicas.; ArgentinaFil: Rahman, Md Atikur. Grassland And Forage Division National Institute; Corea del SurFil: Mahboob, Wajid. Nuclear Institute Of Agriculture,; PakistánFil: Singhal, Rajesh Kumar. Indian Council Of Agricultural Research; IndiaFil: Kumari, Arpna. Guru Nanak Dev University; IndiaFil: Rajendran, Arvind. Vellore Institute Of Technology; IndiaFil: Wasaya, Allah. Bahauddin Zakariya University; PakistánFil: Javed, Talha. Fujian Agriculture And Forestry University; JapónFil: Shabbir, Rubab. University Of Poonch Rawalakot; PakistánFil: Rahim, Junaid. University Of Çukurova; PakistánFil: Barutçular, Celaleddin. Institute Of Crop Science And Resource Conservation; AlemaniaFil: Habib Ur Rahman, Muhammad. Sichuan Agricultural University; ChinaFil: Raza, Muhammad Ali. Sichuan Agricultural University; ChinaFil: Ratnasekera, Disna. University Of Ruhuna; Sri LankaFil: Konuskan l, Ömer. Mustafa Kemal University; TurquíaFil: Hossain, Mohammad Anwar. Bangladesh Agricultural Research Institute; BangladeshFil: Meena, Vijay Singh. Indian Council Of Agricultural Research; IndiaFil: Ahmed, Sharif. Bangladesh Agricultural Research Institute; BangladeshFil: Ahmad, Zahoor. Bangladesh Wheat And Maize Research Institute; BangladeshFil: Mubeen, Muhammad. Sichuan Agricultural University; ChinaFil: Singh, Kulvir. Punjab Agricultural University; IndiaFil: Skalicky, Milan. Czech University Of Life Sciences Prague; República ChecaFil: Brestic, Marian. Slovak University Of Agriculture; EslovaquiaFil: Sytar, Oksana. Slovak University Of Agriculture; EsloveniaFil: Karademir, Emine. Siirt University; TurquíaFil: Karademir, Cetin. Siirt University; TurquíaFil: Erman, Murat. Siirt University; TurquíaFil: Farooq, Muhammad. College Of Agricultural And Marine Sciences Sultan; Omá

Genetic and Physiological Analyses of the Tolerance Mechanisms to Ferrous Iron Toxicity in Rice (<em>Oryza sativa</em> L.)

Rice is a widely consumed staple food for more than half of the world population. Iron (Fe) toxicity is a major nutrient disorder affecting rice production. The understanding of the genetic and physiological basis of Fe tolerance mechanisms can provide useful information for the breeding of tolerant varieties. This thesis is structured into three major parts: (I) Quantitative trait locus (QTL) mapping using two bi-parental populations exposed to an acute Fe stress (1,000 ppm Fe2+ for 5 days). QTLs were detected on several chromosomes (1, 2, 3, 4, 7, 8 and 12) indicating a complex genetic structure for Fe toxicity tolerance. Some QTLs were co-localized with previously reported QTLs on chromosome 1 and 2. One tolerant recombinant inbred line (RIL) FL510 showing an Fe exclusion mechanism was investigated along with two parental lines regarding root oxidizing power. It was found that the root architecture favored the root oxidizing ability in FL510. (II) In a second chapter, a tolerant RIL carrying a shoot-based tolerance mechanism was subjected to in-depth physiological analysis comprising both transcriptomic and biochemical approaches. Three hypotheses were tested to elucidate the roles of (1) Fe uptake, transport and partitioning, (2) biosynthesis of antioxidants and (3) antioxidant enzymes in shoot-based tolerance. It was found that the tolerance in FL483 was conferred by relatively lower ascorbate redox state controlled by dehydroascorbate reductase and ascorbate oxidase activity. A pro-oxidant activity of ascorbate was demonstrated in planta for the first time. (III) In a third chapter, a genome-wide association study (GWAS) was employed to investigate the genetic basis of Fe tolerance with a diverse panel consisting of 329 rice accessions genotyped by 44,100 single nucleotide polymorphism (SNP) markers. Among the different rice sub-populations, temperate japonica and aromatic showed more tolerance than indica and tropical japonica while aus showed intermediate tolerance. Two glutathione-S-transferase genes in one locus co-localized with previously detected QTLs on chromosome 1 for the trait of leaf bronzing score. Contrasting haplotypes at this locus showed sequence polymorphism in the two candidate genes. The tolerance underlying the locus was associated with low ascorbate redox state controlled by dehydroascorbate reductase in shoots. In summary, these efforts will contribute to the breeding of more adapted varieties and to a better understanding of Fe toxicity tolerance mechanisms in plants.Reis (Oryza sativa L.) ist das wichtigste Grundnahrungsmittel für mehr als die Hälfte der Weltbevölkerung. Die übermäßige Aufnahme von Eisen (Fe) führt zu einem schwerwiegenden Nährstoffungleichgewicht, das den Reisanbau weltweit beeinträchtigen kann. Für die Züchtung von toleranten Reissorten ist es essentiell, die genetischen und physiologischen Toleranzmechanismen gegen Eisentoxizität zu verstehen. Die vorliegende Arbeit gliedert sich in drei Teile: (I) Bestimmung von quantitative trait locus (QTL) in einer biparentalen Population, die akutem Eisenstress ausgesetzt wurde (1,000 ppm Fe2+ für 5 Tage). QTLs wurden auf etlichen Chromosomen entdeckt (1, 2, 3, 4, 7, 8 und 12), was auf eine komplexe genetische Struktur des Toleranzmechanismus hindeutet. Einige der QTLs co-lokalisierten mit bereits beschriebenen QTLs auf den Chromosomen 1 und 2. Die tolerante rekombinante Inzuchtlinie (RIL) FL510 zeichnete sich durch einen Wurzel-basierten Fe Exklusionsmechanismus aus, woraufhin die Oxidationskraft der Wurzeln untersucht wurde. Dabei zeigte sich, dass die Wurzelarchitektur der Linie FL510 deren Oxidationskraft begünstigte. (II) Im zweiten Kapitel wurde eine RIL mit Spross-basiertem Toleranzmechanismus mit Hilfe von transkriptionellen und biochemischen Analysen eingehend physiologisch charakterisiert. Die Rolle von (1) Eisenaufnahme, -transport und –verteilung; (2) Biosynthese von Antioxidantien und (3) antioxidativen Enzymen in Spross-basierten Toleranzmechanismen wurde untersucht. Es konnte gezeigt werden, dass die Toleranz der Linie FL483 gegenüber Eisenstress auf einem niedrigeren Ascorbat-Redox-Status basiert, der durch die Enzymaktivität der Dehydroascorbatreduktase und Ascorbatoxidase reguliert wird. Hierbei wurde erstmalig in planta eine prooxidative Aktivität von Ascorbat nachgewiesen. (III) Im dritten Kapitel wurde eine genomweite Assoziationsstudie (GWAS) durchgeführt um die genetische Grundlage von Eisen Toleranz in einem Panel von 329 diversen Reislinien zu untersuchen, die mit jeweils 44,100 Einzelnukleotid-Polymorphismen (englisch: single nucleotide polymorphisms, SNPs) genotypisiert sind. Dabei waren die temperate japonica und aromatischen Subpopulationen toleranter als indica und tropische japonica, während aus intermediär tolerant war. Das typische Verfärben der Blätter bei Fe Stress (“leaf bronzing”) wurde mit zwei Glutathion-S-Transferase Genen assoziiert, die mit einem bereits beschriebenen QTL auf Chromosom 1 co-lokalisierten. Gegensätzliche Haplotypen für diesen Locus zeigten Sequenzunterschiede innerhalb der beiden Kandidatengene. Damit wurde der niedrigere Ascorbat-Redox-Status aufgrund von veränderter Dehydroascorbatreduktase Aktivität im Spross in Zusammenhang gebracht. Diese Arbeit trägt zum grundlegenden Verständnis von Fe Toleranzmechanismen in Pflanzen bei sowie zur erfolgreichen Züchtung von besser angepassten Reissorten bei