PLANT-­‐PATHOGEN INTERACTION CONCLUSIONS FROM

Many  of  the  LRRs  found  to  possess  signatures  of  selection  have  been  reported  to   be   involved   in   defence   against   pathogens.   A   significant   range   of   pathogens   are  

represented   via   their  R   genes   or   PRRs   within   the   loci   marked   by   SelectionFinder,   spanning   bacteria   (AT1G55020   –  Xanthomonas   campestris   campestris   resistance   (Montillet  et  al.  2013);  AT3G20600  –  component  of  systemic  acquired  resistance  to   many  bacteria,  incl.  Pseudomonas  syringae  (Lewis  et  al.  2010)),  viruses  (AT1G05760   –   tobacco   etch   virus   resistance   (Cosson   &   Sofer   2010);   AT5G16000   –   antiviral   signalling   (Sakamoto   et   al.   2012)),   nematodes   (AT1G75820   –   detection   of   nematode  effectors  (Replogle  et  al.  2013)),  fungi  (AT1G71830  –  resistance  against  

Verticillium   spp.   (Fradin   et   al.   2011);   AT1G72300   –   resistance   to   Alternaria  

brassicicola   (Mosher   et   al.   2013))   and   oomycetes   (AT4G20380   –   resistance   to  

Hyaloperonospora  arabidopsidis  (Cooper  et  al.  2008)).  Two  genes  –  AT1G74360  and  

AT3G14840  –  are  also  triggered  by  the  detection  of  oviposition  by  butterflies  of  the   Pieridae   family   (Little   et   al.   2007).   A   number   of   genes   involved   in   regulating   the   hypersensitive  response  are  also  present.    

One  candidate  TIR-­‐NBS-­‐LRR  gene  described  by  Kim  et  al.  (Kim  et  al.  2012)  and   named  VICTR   (AT5G46520)  is   of   particular   interest.     This   gene   encodes   a   receptor   protein   that   responds   to   treatment   with   a   small   signaling   molecule   DPFM   (5-­‐(3,4-­‐dichlorophenyl)furan-­‐2-­‐yl]-­‐piperidine-­‐1-­‐ylmethanethione),   and   causes  a  localised  arrest  of  primary  growth  in  the  root  meristem  upon  detection   of  that  compound.    

Activation  of  defence  pathways  and  restriction  of  root  growth  is  likely  to  limit   the  potential  damage  caused  to  a  plant  encountering  soil-­‐borne  pathogens,  and   could  therefore  be  a  significant  determinant  of  fitness.  The  specific  response  of   a  local  cessation  of  root  growth  (rather  than  hypersensitive  cell  death)  may  also   be   adaptive,   since   programmed   death   of   root   cells   may   have   a   greater   detrimental  effect  on  the  ability  of  the  plant  to  flourish  in  adulthood  than  attack   by   pathogens.   Alternatively,   the   cessation   of   growth   may   simply   limit   further   exposure   to   pathogen   attack   though   the   simple   expedient   of   avoiding   placing   vulnerable  tissues  in  areas  found  to  contain  pathogens.  As  such,  it  may  be  that   the   response   mediated   by  VICTR   can   be   regarded   as   an   optimal   point   in   an  

evolutionary   trade-­‐off.     Interestingly,  VICTR   was   also   noted   to   share   a   high   degree   of   homology   with   other   genes   known   to   confer   pathogen-­‐specific   resistance,  including  the  R  gene  RPS6  (which  detects  the  presence  of  the  hopA1   effector   from  P.   syringae  pv.  syringae   (Kim   et   al.   2009))   and   the   white   rust   resistance  gene  WRR1  (previously  RAC1)  (Kim  et  al.  2009;  Borhan  et  al.  2004).     An   important   membrane-­‐bound   receptor-­‐like   gene   named  EFR   (AT5G20480)   (Zipfel  et  al.  2006)  was  also  identified  in  the  SelectionFinder  analysis.    This  gene   encodes   a   homolog   of   the   PRR   kinase  FLS2,   which   confers   recognition   of   a   pathogen-­‐associated   molecular   pattern   (PAMP)   in   bacterial   flagellin.   Upon   detection   of   the   EF-­‐Tu   PAMP   produced   by   the   pathogenic   bacterium  

Agrobacterium  tumefaciens,  EFR  induces  a  similar  response  to  that  induced  by  

FLS2  (Zipfel  et  al.  2006).    

The  lack  of  detection  for  positive  selection  in  genes  found  to  be  associated  with   either   total   or   partial   white   rust   resistance   (WRR1/RAC1,  WRR4,  WRR5   and  

WRR6)  by  MAGIC  mapping  (see  Chapter  4.3.1)  suggests  that  Albugo  candida  is   not  imposing  a  significant  selection  pressure  in  the  temporal  and  spatial  scales   of   A.   thaliana  populations   that   were   sampled   in   this   study.   However,   the   possibility  cannot  yet  be  ruled  out  that  white  rust  resistance  instead  follows  the   pattern  of  small,  quantitative  changes  across  a  large  number  of  genes  leading  to   small  overall  changes  in  phenotype.  For  example,  DAR5  is  one  member  of  the   family  that  was  identified  by  SelectionFinder  and  may  play  a  role  in  response  to  

Albugo   candida.     This   gene   is   located   in   a   locus   designated  WRR7   which   is  

associated  with  a  weak  ‘loss-­‐of-­‐turgidity’  response  that  permits  colonization  of   tissue   by   A.   candida  but   impedes   asexual   reproduction   (Taylor,   Cevik   and   Holub,   unpublished).   Another   locus   -­‐   AT4G20380   -­‐   was   reported   in   previous   experiments  (Cooper  et  al.  2008)  to  be  suppressed  by  Albugo  infection,  leaving   the  host  vulnerable  to  extensive  infection  by  other  biotrophic  pathogens,  such   as   Hyaloperonospora   arabidopsis,   that   would   normally   be   halted   by   the   hypersensitive   response   regulated   by   this   gene's   protein   product.   Along   with  

further   findings   discussed   below,   this   underscores   that   a   complete   picture   of   plant-­‐pathogen   interactions   must   come   from   viewing   the   whole   system   as   a   complex  network  of  interactions,    as  proposed  in  Chapter  1.7.1.  

Most  notably,  some  18  of  the  62  loci  marked  by  SelectionFinder  are  part  of  a   complex   web   of   interactions   that   was   found   to   be   activated   in   response   to   infection  by  geminivirus  infection  (Ascencio-­‐Ibáñez  et  al.  2008).  Many  of  these   genes  are  also  known  to  be  associated  other  functions,  including  responses  to   stress   and   development.   In   order   to   gain   a   complete   understanding   of   the   interactions  between  plants  and  pathogens,  and  to  understand  the  outcomes  of   pathogen   attacks   in   the   real   world   and   the   ultimate   success   or   failure   of   genotypes  in  the  face  of  these  attacks,  it  is  now  clear  that  we  need  to  examine   more  than  direct  interactions  between  pathogen  effectors  and  host  R  genes.  It  is   necessary   to   view   these   interactions   in   the   wider   context   of   the   entire   molecular  machinery,  developmental  processes  and  ecological  circumstances  of   the  host  and  pathogen.    

Given   the   relative   adaptability   of   this   approach   to   next-­‐generation   resequencing  data  such  as  that  produced  by  the  1001  Genomes  Project,  future   analyses  along  the  lines  laid  out  in  this  chapter  may  be  employed  to  answer  a   very  broad  range  of  questions  relating  to  ecology  and  evolution.  Whole-­‐genome   analyses  of  the  described  in  this  chapter  remain  one  possibility;  however,  the   approach   may   also   be   used   simply   to   investigate   the   possibility   of   selection   acting  upon  specific  loci  already  suspected,  through  other  work,  to  be  subject  to   selection.