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Resistance (R) Genes; a Natural Resource of Plant-Pathogen Resistance

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Resistance (R) Genes; a Natural Resource of Plant-Pathogen Resistance DEPARTMENT OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES Resistance (R) genes; a natural resource of plant-pathogen resistance Iman Abbas Degree project for Bachelor of Science with a major in Biology BIO602 Biology; Degree project 15 Hec Second cycle Semester/year: Autumn 2018 Supervisor: Mats Andersson, Department of Biological and Environmental Science Examiner: Cornelia Spetea-Wiklund, Department of Biological and Environmental Science TABLE OF CONTENTS Abstract ...................................................................................................................................... 2 Sammanfattning ......................................................................................................................... 3 Forewords ................................................................................................................................... 4 Introduction ................................................................................................................................ 5 Plant immunity ........................................................................................................................ 5 R genes and R proteins ........................................................................................................... 6 Aim .......................................................................................................................................... 7 Material and methods ................................................................................................................. 8 Study design ............................................................................................................................ 8 Datamining and article selections .......................................................................................... 8 Article review .......................................................................................................................... 9 Results ........................................................................................................................................ 9 Recognition mechanisms ...................................................................................................... 10 Direct and indirect interactions ......................................................................................... 11 Evolution and diversifying mechanisms of R genes .............................................................. 11 Breeding for more resistant plants ....................................................................................... 13 Discussion and conclusions ...................................................................................................... 16 Acknowledgments .................................................................................................................... 19 References ................................................................................................................................ 20 Appendix 1, Search Schedule ................................................................................................... 22 1 ABSTRACT Breeding for more disease-resistant plants has been an important subject to secure global food production. Focus has been on breeding of crops such as maize, rice, and wheat, which are consumed widely and form the basis of staple foods for many people. This literature study discusses the possibility to control and improve plant disease resistance by the use of resistance (R) genes in modern crop-breeding programs. PubMed Central provides scientific articles for this literature study. The majority of R proteins belong to the NB-LRR family consisting of two domains, NB-ARC and LRR. Both these domains play a central role in the activation of plant- pathogen recognition inducing a defense response in the plant cell. The dynamics of plant- pathogen interaction suggests a great variation and diversity of R genes in the plant kingdom. Protein Data Bank provides 3D structures of NB-ARC Apfa-1 (1Z6T), the LRR homodimer Lr10 (4V2D), TIR and CC domains of the L6 (3OZI) and Mla10 (3QFL). The organization of R proteins is well preserved throughout generations in coevolved populations. They are therefore considered to be a great natural resource of resistance to control and improve plant disease resistance. The use of a single R gene-mediated resistance in traditional crop-breeding programs has its limitations and is therefore not durable as a long-term solution. The conclusion that a single R gene-mediated resistance is not durable shed light on the inherited quantitative traits of these genes. Combining the quantitative traits of these genes in a sustainable way with other development strategies in customized crop-breeding programs may provide a long-term solution. The involvement of multiple R gene-mediated resistance has shown great potential as an environmentally friendly way to improve and control plant disease resistance. Keywords: Plant immunity, R genes, NB-LRR, Breeding program, Development strategies. 2 SAMMANFATTNING För att säkra den globala livsmedelsproduktionen har förädling av mer sjukdomsresistenta växter blivit ett viktigt ämne. Fokus har varit på grödor som konsumeras globalt och utgör basfödan för många människor, såsom majs, ris och vete. Denna litteraturstudie kommer därför att diskutera möjligheten att använda resistans (R) gener i moderna förädlings-program med syfte att kontrollera samt förbättra motståndet hos växter gentemot patogener. PubMed Central har försett denna litteraturstudie med vetenskapliga artiklar. Majoriteten av R proteiner tillhör familjen NB- LRR vilket består av två huvuddomäner, NB-ARC och LRR. Båda spelar en central roll i aktiveringen av växt-patogenigenkänningen som inducerar växtcellensförvar. Dynamiken i växt- patogeninteraktionerna antyder på att det finns en stor variation och mångfald av R gener i växtriket. Protein Data Bank har försett denna litteraturstudie med tredimensionella strukturer av NB-ARC Apfa-1 (1Z6T), LRR homodimer Lr10 (4V2D), TIR- och CC-domänen av L6 (3OZI) och Mla10 (3QFL). Strukturen hos R proteiner är väl bevarade inom den genetiska polen i samevolutionära populationer. Därför anses de vara en stor naturlig resurs för kontroll och förbättring av växternas resistens. Användning av traditionella förädlings-program som medför R-genmedierat försvar bestående av en singel R-gen har visats ha sina begränsningar och leder därför till kortsiktig resistens gentemot patogener. Slutsatsen att en singel R-genmedierat försvar inte är hållbart uppmärksammade R-geners kvantitativa egenskaper. Egenskaperna i en multipel R-genmedierat försvar kan kombineras med andra förädlingsutvecklingsstrategier för att uppnå ett hållbart samt långsiktig resistens gentemot växtsjukdomar. En multipel R-genmedierat försvar har därför visats ha stor potential som ett miljövänligt sätt för att kontrollera samt förbättra växtresistensen. Nyckelord: Växtimmunitet, R-gener, NBS-LRR, Förädlingsprogram, Utvecklingsstrategier. 3 FOREWORDS “Go back young man and gather up your weary and defeated genes of the past, take your currently successful genes, find some new ones if you can, and build yourself a highly durable strategy.” Richard R. Nelson 4 INTRODUCTION PLANT IMMUNITY Plants have developed a two-layered immune system to defend themselves against pathogens in the agricultural ecosystems. The two-layered plant immunity contains several disease resistance components. The first-layer includes physical barriers and pattern recognition receptors (PRRs). A defense response triggered by the activation of PRRs is led by a system known as the pattern- triggered immunity. The second-layer includes proteins encoded by R genes, which recognize specific pathogen effectors. A defense response triggered by R proteins results in a strong and rapid response leading to a localized effector-triggered immunity. The recognition induces the synthesis of antimicrobial enzymes and other metabolites that generate downstream signaling. These pathways activate the defense in neighboring cells surrounding the site of the infection and often lead to programmed cell death (Dangl et al. 2013). The need for matched specificity between the R protein and pathogen avirulence effector (Avr) was first presented by Flor’s gene-for-gene hypothesis. Flor describe correlation between the inherited resistance and pathogenicity in linseed rust caused by fungus (Melampsora lini). He described the correlation with “for each gene conditioning rust reaction in the host there is a specific gene conditioning pathogenicity in the parasite” (Flor, 1971). The concept has been applied to various degree of proof to other host-pathogen interactions including bacteria, viruses, fungi and nematodes (Sasaki, 2000). Different schools of thought later expanded the gene-for- gene hypothesis. According to Vanderplank (Vanderplank, 1978) the specificity in gene-for-gene lies in the susceptibility. Later on, he elaborated the protein-for-protein hypothesis as a biochemical explanation of the gene-for-gene hypothesis. The biochemical explanation states that in gene-for-gene diseases the mutual recognition of host and pathogen is not by their genes themselves but by their encoded proteins. Vanderplank hypothesized that in susceptibility the pathogen injects an Avr effector into the host cell, that interacts with a complementary R protein triggering a defense response. The induced defense response in plant-pathogen recognition is described
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