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Genetic Variation of Traits Related to Salt Stress Response in Wheat (Triticum Aestivum L.)

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Genetic Variation of Traits Related to Salt Stress Response in Wheat (Triticum Aestivum L.) Institut für Nutzpflanzenwissenschaften und Ressourcenschutz Genetic variation of traits related to salt stress response in Wheat (Triticum aestivum L.) Dissertation zur Erlangung des Grades Doktor der Agrarwissenschaften (Dr. agr.) der Landwirtschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Oyiga Benedict Chijioke aus Enugu-Ezike, Nigeria Bonn 2017 Referent: Prof. Dr. Jens Léon Plant Breeding, INRES, University of Bonn Korreferent: Prof. Dr. Heiner Goldbach Plant Nutrition, INRES, University of Bonn Tag der Mündlichen Prüfung: 14.12. 2016 This research work was financially supported by the “Bundesministerium fur wirtschaftliche Zusammenarbeit und Entwicklung (BMZ)” in collaboration with the German Agency for International Cooperation (GIZ), Germany (Project number: 09.7860.1-001.00), the International Centre for Research in Dryland Agriculture (ICARDA) and the Center for Development Research (ZEF), Friedrich-Wilhelms-University, Bonn, Germany. Angefertigt mit Genehmigung der Landwirtschaftlichen Fakultät der Universität Bonn ii GENERAL SUMMARY (English) Salinity is one of the most severe abiotic stresses perceived by plants, and is continuously increasing due to climatic change and poor irrigation management practices. It is currently affecting ~800 million hectares of land worldwide, including over 20% of the world’s irrigated arable land. Salinity causes significant growth reduction and crop yield losses. With the predicted geometric increase in the global population, improving the salt tolerance (ST) of crops has become an important challenge and target for plant breeders. Several approaches have been exhaustively exploited to ameliorate the impact of salinity on crop plants, but because of the complex nature of ST in crop plant, these approaches have not been optimally translated into the desired results. It is well known that ST is difficult to breed due to its interaction with many physiological processes that are controlled by many genes, plant growth stage and are influenced by environmental factors. Wheat is moderately salt tolerant which means that the grain yield is significantly affected under soil saline condition of ~10 dS m-1. Therefore, improving wheat adaptation under high salinity is seen as the most efficient and economical approach to address the salinity problem and increase its grain yield especially in the poor resource wheat producing countries that are prone to soil salinity. This thesis applies several morphological and physiological evaluations, genetic and molecular approaches to elucidate the genetic and physiological mechanisms underlying natural variation for ST in wheat and to find ways to explore the inherent genetic variation, with the ultimate aim of finding new candidate genes that can be used to improve ST in wheat. The performance of 150 genetically diverse wheat genotypes were evaluated under different salinity conditions at germination, seedling and adult plant field growth stages, to identify heritable variation for salt tolerance in the measured traits. In addition, the amount of Na+, K+ and K+/Na+ ratio in the different shoot parts such as third leaves, stem and remaining leaf parts were determined for each genotypes after 24 days of stress under 150 mM/L NaCl. Results revealed genotype and salt treatment effects across all the growth stages, and the salt stress applied caused 33%, 51% and 82% reductions in germination vigour, seedling biomass and grain yield, respectively. The ability of wheat to conserve water in both root and shoot tissues was positively correlated with the K+ uptake under exposure to salinity. The wide-spectrum of responses to salt stress observed among the genotypes was exploited to identify genotypes with most consistent ST status across growth stages. Among the outstanding genotypes identified, four genotypes including Altay2000, 14IWWYTIR-19 and UZ- 11CWA-8 (tolerant) and Bobur (sensitive) showed consistent ST status across the three growth stages iii including germination, seedling and adult-plant field growth stages. Further evaluation of the identified genotypes using several physiological parameters showed that the tolerant genotypes possess better adaptation characteristics than the sensitive ones (Bobur and UZ-11CWA-24) which allowed them to sustain growth and reproduce under high salinity. A high density molecular map with ~18,000 SNPs (average distance between markers of 0.49 cM cM) and all the morpho-physiological and seed quality data collected were used to map QTLs for ST in the studied population. The LD decayed moderately fast (10 cM, 11 cM and 14 cM (r2 > 0.1) for the A, B and D-genome, respectively). By applying mixed linear modeling (MLM) while correcting for the effects of population structure and the kinship resulted in the detection of 302 SNPs (representing 50 distinct QTL regions) that were significantly associated with various ST traits. They explained between 2.00 and 63.45 % of the genetic variance. Most of the associated SNPs/loci showed pleiotropic effect on several traits and/or were detected across several independent experiments/growth stages. For instance, a single locus (at 90.04 cM) on 6AL was found to be strongly associated with ABS/RC, DIo/RC and shoot Na+ traits. An important (about 1.8 cM interval) region on 2BL was also found to strongly contribute to the variation in ST in various salt stress related traits (ST_DRW, shoot Na+, Fv/Fm, grain yield and seed crude protein). Five novel ST QTL regions were also detected on 1BS, 1DL, 5BS, 6AL and 5BL genomic regions. All the identified QTL have been discussed in this thesis. By analyzing sequences of the associated SNPs, several key genes involved in salt and abiotic stress tolerance were identified. Among the categories of genes identified (Chapter 3 and 4), the genes involved in the stress response (24%), antiporter and transmembrane (18%), transcription and translation (14%), and redox homeostasis and detoxification (11%) related activities occurred predominantly. The transcriptome and RT-PCR expression analyses performed with the genes linked to the significant MTAs revealed differential expressions between the contrasting ST wheat genotypes. Moreover, the amino acid sequence analyses of the putative genes uncovered many sites of non-synonymous/missense mutation that may have contributed to the observed variable salt stress responses in the contrasting wheat genotypes. This study provides new insights towards understanding the traits and mechanisms related to ST. Thus, the underlying genetic and molecular response as presented in this thesis can be directly exploited by the breeders and scientists to improve salt tolerance in wheat. iv ALLGEMEINE ZUSAMMENFASSUNG Die Versalzung des Bodens zählt zu den größten abiotischen Stressfaktoren für Pflanzen, und steigt durch den Klimawandel und ein schlechtes Wassermanagement kontinuierlich. Zur Zeit sind etwa 800 Millionen Hektar weltweit und 20 % der künstlich bewässerten Flächen von Versalzung betroffen. Diese führt zu einer signifikanten Reduktion des Pflanzenwachstums und ist mitverantwortlich für Ertragseinbußen. Durch das weltweite Bevölkerungswachstum wird die Erhöhung der Salztoleranz (ST) von Nutzpflanzen eine immer wichtigere Aufgabe und ein anzustrebendes Ziel für die Pflanzenzüchtung. Verschiedene Forschungsansätze wurden verfolgt, um die Salztoleranz von Pflanzen zu verbessern, jedoch führten viele dieser Ansätze aufgrund der komplexen Natur der ST nicht zu verwertbaren Ergebnissen. Es ist bekannt, dass ST aufgrund der Interaktion zwischen vielen physiologischen Prozessen, den unterschiedliche Genen und der Umwelt, schwierig in die Züchtung zu integrieren ist. Weizen gilt als mäßig salztolerant und der Ertrag wird ab einem Bodensalzgehalt von ~10 dS m-1 signifikant beeinflusst. Gerade die landwirtschaftlich schwächer entwickelten Regionen sind für Bodenversalzung anfällig und eine Erhöhung der Salztoleranz wäre ein probates wirtschaftliches Mittel um den Weizenertrag zu steigern. Diese Dissertation nutzt mehrere morphologische und physiologische Auswertungen, genetische und molekulare Ansätze, um die genetischen und physiologischen Mechanismen zu erklären, die der ST des Weizens zugrunde liegen. Dabei soll die eigene genetische Variation des Weizens erklärt und schlussendlich neue Kandidatengene gefunden werden, welche die ST des Kulturweizens erhöhen. Die Leistung von 150 genetisch verschiedenen Weizengenotypen wurde während der Keimung, dem Sämlingsstadium und an der adulten Pflanze unter unterschiedlichen Salzbedingungen geprüft, um die erbliche Variation des ST in unterschiedlichen Merkmalen oder Wachstumsstadien zu identifizieren. Nach 24 Stunden unter Stressbedingungen mit 150 mM/L NaCl wurde der Na+-, K+- Gehalt und des K+/Na+ - Verhältnis in verschiedenen Sprossteilen, wie dem dritten Blatt, dem Stängel und den übrigen Blättern für alle Genotypen bestimmt. Die Ergebnisse zeigten Interaktionen der Genotypen und der Salzbehandlung in allen Wachstumsstadien. Die Salzapplikation verursachte einen Rückgang von 33% bei der Keimfähigkeit, von 51 % der Sämlingsbiomasse und von 82% beim Kornertrag. Die Eigenschaft des Weizens, Wasser in Wurzel- und Sprossteilen zu speichern war positiv mit der K+ -Aufnahme unter Stressbedingungen korreliert. Das beobachtete breite Spektrum der Pflanzenreaktionen auf die Salzstressapplikation wurde genutzt um die beständigsten, v beziehungsweise die salztolerantesten Genotypen über alle Wachstumsstadien zu identifizieren. Es wurden vier extreme
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