Rice  is   the  principle  food  crop  of  Nepal.   Similarly,  barley   is   another  important  crop  in mountain  areas  of  the  Nepal.   Increased  yield  productivity  and yield  stability  of  these  two crops  are  always  challenging  in  context  of the  unpredictable climate   change.  Nepal   always lacks  suitable  cultivars  in  these crops  which  can challenge  the biotic  and abiotic threats  from the   climate   change.   Blast  and   bacterial  blight   resistant  and   submergence   tolerant   rice varieties;   and  leaf  rust  and  stripe  rust  resistant  barley   varieties   are  highly   demanding  in Nepalese  fanning  community.   Nepalese  rice  and   barley  landraces   have   many   important genes  for biotic  and abiotic  stress  resistance.  Therefore, we used  144 rice  accessions for blast and bacterial  leaf blight (BLB)  resistance in rice,  313  rice accessions for flash  flood  tolerance and  241  barley  accessions for  leaf and  yellow/stripe rust resistance characteristics  for agro morphological  and  physiological  screening  during   2011/12  in  Nepal   Agriculture  Research Council  Farm  Khumaltar,  Lalitpur.  Similarly,  we  have  used 92 rice  accessions for blast and 94 accessions  for BLB  resistance in  rice,  46  accessions for flash  flood  tolerance in  rice  and 109  accessions  for  leaf  and yellow/stripe rust resistance  in  barley  for  molecular screening based  on their  morphological  and  physiological  screening.  We  have  used  six  microsatellite (SSR)  markers  for leaf rust and  11  SSR  markers  for stripe  rust  resistance in  barley,   12  SSR markers  for Blast and  eight  SSR  markers  for BLB  resistance in  rice  and  eight  SSR  markers for flash  flood  tolerance  characteristics  in  rice.  Blast resistant genes  Pi-54,  Pi-y2(t), Pi-d(t)l, Pi-z,  Pi-a,  Pi-k,  Pi-yl(t),  Pi-44, Pi-b,  Pi-g(t),  Pi-29,  Pi-11,  Pi-ta and  Pi20(t)  were  detected among Nepalese rice gene pool.  Similarly,  BLB resistance genes  Xa-10, Xa-13, Xa-7,  Xa-10, Xa-3, Xa-4,  Xa-5,  Xa-8  were  detected.  Presence  of  SublA-1   and  SNORKEL  genes  also found  in Nepalese rice landraces.  Leaf rust resistance gene Rphl,  Rph2, Rph3, Rph7,  QBLR• p and QTL  on 5HS  was  detected on Nepalese barley  accessions.  Similarly,  barley  stripe  rust resistance genes  QTL  on  1  H, QTL5  on  lH, QTL  on 4H,  QTL  on  SH,  QTL  on 6H,  QTL  on 7H,  YrpstYl   and  Rpsx   were   also  detected.   This   output  is   highly   important  for  use  of Nepalese rice and barley  germplasm as donor parents for marker  assisted breeding programs.

Rice  is   the  principle  food  crop  of  Nepal.   Similarly,  barley   is   another  important  crop  in mountain  areas  of  the  Nepal.   Increased  yield  productivity  and yield  stability  of  these  two crops  are  always  challenging  in  context  of the  unpredictable climate   change.  Nepal   always lacks  suitable  cultivars  in  these crops  which  can challenge  the biotic  and abiotic threats  from the   climate   change.   Blast  and   bacterial  blight   resistant  and   submergence   tolerant   rice varieties;   and  leaf  rust  and  stripe  rust  resistant  barley   varieties   are  highly   demanding  in Nepalese  fanning  community.   Nepalese  rice  and   barley  landraces   have   many   important genes  for biotic  and abiotic  stress  resistance.  Therefore, we used  144 rice  accessions for blast and bacterial  leaf blight (BLB)  resistance in rice,  313  rice accessions for flash  flood  tolerance and  241  barley  accessions for  leaf and  yellow/stripe rust resistance characteristics  for agro morphological  and  physiological  screening  during   2011/12  in  Nepal   Agriculture  Research Council  Farm  Khumaltar,  Lalitpur.  Similarly,  we  have  used 92 rice  accessions for blast and 94 accessions  for BLB  resistance in  rice,  46  accessions for flash  flood  tolerance in  rice  and 109  accessions  for  leaf  and yellow/stripe rust resistance  in  barley  for  molecular screening based  on their  morphological  and  physiological  screening.  We  have  used  six  microsatellite (SSR)  markers  for leaf rust and  11  SSR  markers  for stripe  rust  resistance in  barley,   12  SSR markers  for Blast and  eight  SSR  markers  for BLB  resistance in  rice  and  eight  SSR  markers for flash  flood  tolerance  characteristics  in  rice.  Blast resistant genes  Pi-54,  Pi-y2(t), Pi-d(t)l, Pi-z,  Pi-a,  Pi-k,  Pi-yl(t),  Pi-44, Pi-b,  Pi-g(t),  Pi-29,  Pi-11,  Pi-ta and  Pi20(t)  were  detected among Nepalese rice gene pool.  Similarly,  BLB resistance genes  Xa-10, Xa-13, Xa-7,  Xa-10, Xa-3, Xa-4,  Xa-5,  Xa-8  were  detected.  Presence  of  SublA-1   and  SNORKEL  genes  also found  in Nepalese rice landraces.  Leaf rust resistance gene Rphl,  Rph2, Rph3, Rph7,  QBLR• p and QTL  on 5HS  was  detected on Nepalese barley  accessions.  Similarly,  barley  stripe  rust resistance genes  QTL  on  1  H, QTL5  on  lH, QTL  on 4H,  QTL  on  SH,  QTL  on 6H,  QTL  on 7H,  YrpstYl   and  Rpsx   were   also  detected.   This   output  is   highly   important  for  use  of Nepalese rice and barley  germplasm as donor parents for marker  assisted breeding programs.

Rice   diseases   are   the   major   problem   for   rice   production   and   blast   is   one   of  them. Development  of the  resistance  varieties  instead  of using chemical  and botanicals  to treat the rice blast disease in field  is most  important in Nepalese  context. Therefore,  identification of resistance rice accessions from Nepalese  rice germplasrn collection is very important for development  of blast  resistance  rice  varieties.  One  hundred  and  forty  four  Nepalese  rice landraces  were   screened   for  their  response   on  blast  pathogen   in   natural   condition   at Khumaltar, Lalitpur, Nepal.  Blast lesion type, disease severity, disease incidence and disease damage were  recorded  on 25  days  old  rice seedling.  Local  rice  varieties  Jumli  Marshi  and Masuli  were  used  as  susceptible  check whereas  Sabitri  was  used  as  resistant  check.  One hundred  and nine  rice  landraces  showed  resistance  reaction  with  blast.  Similarly,  sixty  four rice landraces  showed  no  blast disease symptom  during seedling stage.  Variation on origin  of rice  landraces  may  account  for  this  differential  reaction  in  blast  disease  development  at seedling stage. 

Rice   diseases   are   the   major   problem   for   rice   production   and   blast   is   one   of  them. Development  of the  resistance  varieties  instead  of using chemical  and botanicals  to treat the rice blast disease in field  is most  important in Nepalese  context. Therefore,  identification of resistance rice accessions from Nepalese  rice germplasrn collection is very important for development  of blast  resistance  rice  varieties.  One  hundred  and  forty  four  Nepalese  rice landraces  were   screened   for  their  response   on  blast  pathogen   in   natural   condition   at Khumaltar, Lalitpur, Nepal.  Blast lesion type, disease severity, disease incidence and disease damage were  recorded  on 25  days  old  rice seedling.  Local  rice  varieties  Jumli  Marshi  and Masuli  were  used  as  susceptible  check whereas  Sabitri  was  used  as  resistant  check.  One hundred  and nine  rice  landraces  showed  resistance  reaction  with  blast.  Similarly,  sixty  four rice landraces  showed  no  blast disease symptom  during seedling stage.  Variation on origin  of rice  landraces  may  account  for  this  differential  reaction  in  blast  disease  development  at seedling stage. 

Blast  (caused   by  Magnaporthe  oryzae)  is  the  major  yield   limiting  biotic  stress  for  rice farming  in  Nepal  that  is  prevalent  all  over  the  country.  Resistant variety  for  one  location becomes  susceptible  to another location  which  shows  the  need  of resistant gene  pyramiding for yield  stability. Identifying blast resistant genes  in Nepalese rice  germplasm and its use for varietal  development is very  important.  Ninety  two  Nepalese rice  accessions were  screened using 12 SSR markers  for presence of different  blast resistant genes.  IR-64  and  Sabitri  were used  as resistant check while  Masuli  and Jumli  Marshi  were  used  as susceptible check. Blast resistant genes  Pi-54,  Pi-y2(t), Pi-d(t) 1,  Pi-z,  Pi-a,  Pi-k,  Pi-yl (t)  and Pi-44  were  detected on seven,   seven,   nine,   11,  20  and  28 rice  accessions  respectively.  Eighteen  rice  accessions showed  presence Pi-b  and  Pi-g(t), 22  rice  accessions  showed  presence of Pi-29  and  Pi-11; and  two rice  accessions  showed  presence  of Pi-ta  and  Pi20(t).   Nepalese  rice  gene  pool doesn't  contain   resistant  gene  Pi-d(t)2   and  it  needs   to  incorporate from   exotic  sources. Therefore,  many  Nepalese rice  landraces  can  be  used  on  marker assisted gene  pyramiding program for development of durable  blast resistance varieties.

Blast  (caused   by  Magnaporthe  oryzae)  is  the  major  yield   limiting  biotic  stress  for  rice farming  in  Nepal  that  is  prevalent  all  over  the  country.  Resistant variety  for  one  location becomes  susceptible  to another location  which  shows  the  need  of resistant gene  pyramiding for yield  stability. Identifying blast resistant genes  in Nepalese rice  germplasm and its use for varietal  development is very  important.  Ninety  two  Nepalese rice  accessions were  screened using 12 SSR markers  for presence of different  blast resistant genes.  IR-64  and  Sabitri  were used  as resistant check while  Masuli  and Jumli  Marshi  were  used  as susceptible check. Blast resistant genes  Pi-54,  Pi-y2(t), Pi-d(t) 1,  Pi-z,  Pi-a,  Pi-k,  Pi-yl (t)  and Pi-44  were  detected on seven,   seven,   nine,   11,  20  and  28 rice  accessions  respectively.  Eighteen  rice  accessions showed  presence Pi-b  and  Pi-g(t), 22  rice  accessions  showed  presence of Pi-29  and  Pi-11; and  two rice  accessions  showed  presence  of Pi-ta  and  Pi20(t).   Nepalese  rice  gene  pool doesn't  contain   resistant  gene  Pi-d(t)2   and  it  needs   to  incorporate from   exotic  sources. Therefore,  many  Nepalese rice  landraces  can  be  used  on  marker assisted gene  pyramiding program for development of durable  blast resistance varieties.

Bacterial Leaf Blight (BLB)  is the most important yield limiting factor in Nepalese rice. BLB resistance rice varieties are highly demanding in the country. Breeding efforts for developing disease  resistant  depends  on  the  availability  and  use  of resistant  gene  donors.  Ninety  six Nepalese  rice  accessions  were  screened using  eight  SSR  markers  and  one STS  marker for presence  and  absence  of  BLB  resistance  gene.   We  detected  BLB  resistance  gene Xa-10  on two accessions,  Xa-13  on  six  accessions,  Xa-7  on  23  accessions, Xa-10  on  five accessions, Xa-3  and  Xa-4  on  52  accessions,  Xa-5  on 25  accessions,  Xa-8 on  30  rice  accessions.  No  any rice  accessions  have  Xa-21.  Similarly,   17  rice  accessions  showed  three  and  more than  three BLB    resistance   genes.  Presence  of  Xa-13   on   susceptible  check   variety  CNTRL-85033 confirmed  that different  BLB  pathotypes  are  active  in Nepalese rice field  and  need  of gene pyramiding for durable  resistance.

Bacterial Leaf Blight (BLB)  is the most important yield limiting factor in Nepalese rice. BLB resistance rice varieties are highly demanding in the country. Breeding efforts for developing disease  resistant  depends  on  the  availability  and  use  of resistant  gene  donors.  Ninety  six Nepalese  rice  accessions  were  screened using  eight  SSR  markers  and  one STS  marker for presence  and  absence  of  BLB  resistance  gene.   We  detected  BLB  resistance  gene Xa-10  on two accessions,  Xa-13  on  six  accessions,  Xa-7  on  23  accessions, Xa-10  on  five accessions, Xa-3  and  Xa-4  on  52  accessions,  Xa-5  on 25  accessions,  Xa-8 on  30  rice  accessions.  No  any rice  accessions  have  Xa-21.  Similarly,   17  rice  accessions  showed  three  and  more than  three BLB    resistance   genes.  Presence  of  Xa-13   on   susceptible  check   variety  CNTRL-85033 confirmed  that different  BLB  pathotypes  are  active  in Nepalese rice field  and  need  of gene pyramiding for durable  resistance.

Flooding  is  a  notorious  environmental  stresses   that  limits  the   rice   production   in  Asia significantly.  Rice  has  a unique   capacity  to  withstand  the  period of flooding  environment through   the   activation   of  coordinated  regulatory  efforts   at  morphological,  anatomical, biochemical   and   molecular  level.   Three hundred   and   thirteen   diverse    rice   collections including  selected  landraces  from  Nepal   were  completely  submerged  for  14  days  for  this study.  Rice accessions  had diverse  response to  submergence  with survival ity  ranging  from  0 to  100 % and differential elongation growth  response. Presence of Sub 1  A-1 and  SNORKEL genes    were    then    monitored    in    the    tolerant     landraces.    Four    landraces;    Bhaatsaar, Kariyaparewa  pakha,  Sauthari  and  Karangi  and  2  landraces;  NPGR   3501  and  NPGR   3503 showed  better  response than  FRl 3A  and Kalamon  113  respectively.  However, Kariyaparewa pakha  and Sauthari  were  found  lacking  the  presence  of Sub 1  A-1  allele.  In  addition,  eight landraces  with  Sub I A- I   allele  were  found  intolerant to  submergence. However,  the  SPAD reading  showed  that  FR 13A  had  the  highest  chlorophyll  retention  capacity.  Thus,  the  detail morpho-physiological  and  molecular analysis  showed   that  both  the  tolerant  and  intolerant landraces possessed the SublA-1  allele  and they  showed  both escape  and quiescence strategy to cope the flooding.  Therefore, SublA-1  allele  is  not the only ones  responsible  for tolerance but there  is the participation of other stress responsive factors.

Flooding  is  a  notorious  environmental  stresses   that  limits  the   rice   production   in  Asia significantly.  Rice  has  a unique   capacity  to  withstand  the  period of flooding  environment through   the   activation   of  coordinated  regulatory  efforts   at  morphological,  anatomical, biochemical   and   molecular  level.   Three hundred   and   thirteen   diverse    rice   collections including  selected  landraces  from  Nepal   were  completely  submerged  for  14  days  for  this study.  Rice accessions  had diverse  response to  submergence  with survival ity  ranging  from  0 to  100 % and differential elongation growth  response. Presence of Sub 1  A-1 and  SNORKEL genes    were    then    monitored    in    the    tolerant     landraces.    Four    landraces;    Bhaatsaar, Kariyaparewa  pakha,  Sauthari  and  Karangi  and  2  landraces;  NPGR   3501  and  NPGR   3503 showed  better  response than  FRl 3A  and Kalamon  113  respectively.  However, Kariyaparewa pakha  and Sauthari  were  found  lacking  the  presence  of Sub 1  A-1  allele.  In  addition,  eight landraces  with  Sub I A- I   allele  were  found  intolerant to  submergence. However,  the  SPAD reading  showed  that  FR 13A  had  the  highest  chlorophyll  retention  capacity.  Thus,  the  detail morpho-physiological  and  molecular analysis  showed   that  both  the  tolerant  and  intolerant landraces possessed the SublA-1  allele  and they  showed  both escape  and quiescence strategy to cope the flooding.  Therefore, SublA-1  allele  is  not the only ones  responsible  for tolerance but there  is the participation of other stress responsive factors.

Barley is  the major crop for the people living  in  the high hills and mountainous  region  of the Nepal.  Rust is  the major production  threat for barley  cultivation. However,  a lot of variation can be observed  on Nepalese  barley accessions  with respect  to rust resistance  characteristics. Two hundred and forty one barley accessions  were screened  for leaf rust ( caused by Puccinia hordei)  and  stripe  rust  ( caused  by P. striformis  f.sp.  hordei)  resistance  characteristics  on heading stage  at Khumaltar,   Lalitpur,  Nepal  during  normal  barley  growing  season  2011. Bonus  (origin  Sweden)  and  Local  Jau  (Nepalese   landrace)  were  used  as resistant  and susceptible check  respectively.  Seventeen  barley  accessions  showed  leaf rust  susceptibility but resistant with stripe rust.  Thirty barley accessions showed  resistant for both  leaf rust and strip  rust. Lower frequency  of the leaf rust infection  may be due to prevalent  resistance  gene for leaf rust resistant characteristics  in Nepalese  barley.

Barley is  the major crop for the people living  in  the high hills and mountainous  region  of the Nepal.  Rust is  the major production  threat for barley  cultivation. However,  a lot of variation can be observed  on Nepalese  barley accessions  with respect  to rust resistance  characteristics. Two hundred and forty one barley accessions  were screened  for leaf rust ( caused by Puccinia hordei)  and  stripe  rust  ( caused  by P. striformis  f.sp.  hordei)  resistance  characteristics  on heading stage  at Khumaltar,   Lalitpur,  Nepal  during  normal  barley  growing  season  2011. Bonus  (origin  Sweden)  and  Local  Jau  (Nepalese   landrace)  were  used  as resistant  and susceptible check  respectively.  Seventeen  barley  accessions  showed  leaf rust  susceptibility but resistant with stripe rust.  Thirty barley accessions showed  resistant for both  leaf rust and strip  rust. Lower frequency  of the leaf rust infection  may be due to prevalent  resistance  gene for leaf rust resistant characteristics  in Nepalese  barley.

Leaf rust ( caused  by Puccinia  hordei)  and  stripe/yellow  rust ( caused  by  P.  striformis  fsp. hordei  and P.  striformis fsp.  tritici)  are  the  major problem for  barley  cultivation in Nepal. Durable   resistant  variety   of the  barley   is  highly   important  for  this   country.  Barley  rust resistance  is   controlled  by   many   major   genes   and   quantitative  trait   loci   (QTLs)    and pyramiding  these  genes   into  varieties   is  the  most  important  barley   breeding  strategies  in Nepal.   Molecular  marker   assisted  breeding  (MAB)   is   the   only   option  for  this.   Marker assisted  screening  is  the primary stage  to initiate  the MAB.  One  hundred and nine  Nepalese barley  accessions were  screened  using  six  and  eleven  SSR  markers linked  to  leaf rust and stripe  rust  resistance genes  respectively.  Bonus  and  Local  Jau  was  used  as the resistant and susceptible  check  respectively.  Leaf rust resistance gene  Rphl,  Rph2,  Rph3, Rph7,  QBLR-P and QTL on 5HS was  detected on Nepalese barley  accessions using  respective SSR  markers. Similarly,  stripe  rust resistance genes  QTL  on  lH,  QTL5  on  lH,  QTL  on 4H,  QTL  on  SH, QTL on 6H, QTL on 7H, YrpstYl  and Rpsx  were  detected.  Eight Nepalese barley  accessions showed  presence of three  and more  leaf rust resistant genes  and twenty-five Nepalese barley accessions have  three  and  more  stripe rust resistance  genes.  Poor  relationship  between rust resistance gene  and  field  disease  may  be  due  to  the  less  relationship  between   the  pathogen type  on  field  and  rust  resistance  genes   detected  using   SSR  markers   on  Nepalese  barley germplasm.

Leaf rust ( caused  by Puccinia  hordei)  and  stripe/yellow  rust ( caused  by  P.  striformis  fsp. hordei  and P.  striformis fsp.  tritici)  are  the  major problem for  barley  cultivation in Nepal. Durable   resistant  variety   of the  barley   is  highly   important  for  this   country.  Barley  rust resistance  is   controlled  by   many   major   genes   and   quantitative  trait   loci   (QTLs)    and pyramiding  these  genes   into  varieties   is  the  most  important  barley   breeding  strategies  in Nepal.   Molecular  marker   assisted  breeding  (MAB)   is   the   only   option  for  this.   Marker assisted  screening  is  the primary stage  to initiate  the MAB.  One  hundred and nine  Nepalese barley  accessions were  screened  using  six  and  eleven  SSR  markers linked  to  leaf rust and stripe  rust  resistance genes  respectively.  Bonus  and  Local  Jau  was  used  as the resistant and susceptible  check  respectively.  Leaf rust resistance gene  Rphl,  Rph2,  Rph3, Rph7,  QBLR-P and QTL on 5HS was  detected on Nepalese barley  accessions using  respective SSR  markers. Similarly,  stripe  rust resistance genes  QTL  on  lH,  QTL5  on  lH,  QTL  on 4H,  QTL  on  SH, QTL on 6H, QTL on 7H, YrpstYl  and Rpsx  were  detected.  Eight Nepalese barley  accessions showed  presence of three  and more  leaf rust resistant genes  and twenty-five Nepalese barley accessions have  three  and  more  stripe rust resistance  genes.  Poor  relationship  between rust resistance gene  and  field  disease  may  be  due  to  the  less  relationship  between   the  pathogen type  on  field  and  rust  resistance  genes   detected  using   SSR  markers   on  Nepalese  barley germplasm.