Association mapping of resistance to rice blast in upland field conditions
Background: Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results: The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions: It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.
id |
dig-cirad-fr-582133 |
---|---|
record_format |
koha |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 |
spellingShingle |
H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 Raboin, Louis-Marie Ballini, Elsa Tharreau, Didier Ramanantsoanirina, Alain Frouin, Julien Courtois, Brigitte Ahmadi, Nourollah Association mapping of resistance to rice blast in upland field conditions |
description |
Background: Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results: The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions: It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties. |
format |
article |
topic_facet |
H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Raboin, Louis-Marie Ballini, Elsa Tharreau, Didier Ramanantsoanirina, Alain Frouin, Julien Courtois, Brigitte Ahmadi, Nourollah |
author_facet |
Raboin, Louis-Marie Ballini, Elsa Tharreau, Didier Ramanantsoanirina, Alain Frouin, Julien Courtois, Brigitte Ahmadi, Nourollah |
author_sort |
Raboin, Louis-Marie |
title |
Association mapping of resistance to rice blast in upland field conditions |
title_short |
Association mapping of resistance to rice blast in upland field conditions |
title_full |
Association mapping of resistance to rice blast in upland field conditions |
title_fullStr |
Association mapping of resistance to rice blast in upland field conditions |
title_full_unstemmed |
Association mapping of resistance to rice blast in upland field conditions |
title_sort |
association mapping of resistance to rice blast in upland field conditions |
url |
http://agritrop.cirad.fr/582133/ http://agritrop.cirad.fr/582133/1/2016_Rice_Raboinetal.pdf |
work_keys_str_mv |
AT raboinlouismarie associationmappingofresistancetoriceblastinuplandfieldconditions AT ballinielsa associationmappingofresistancetoriceblastinuplandfieldconditions AT tharreaudidier associationmappingofresistancetoriceblastinuplandfieldconditions AT ramanantsoanirinaalain associationmappingofresistancetoriceblastinuplandfieldconditions AT frouinjulien associationmappingofresistancetoriceblastinuplandfieldconditions AT courtoisbrigitte associationmappingofresistancetoriceblastinuplandfieldconditions AT ahmadinourollah associationmappingofresistancetoriceblastinuplandfieldconditions |
_version_ |
1806036982963372032 |
spelling |
dig-cirad-fr-5821332024-06-27T16:04:48Z http://agritrop.cirad.fr/582133/ http://agritrop.cirad.fr/582133/ Association mapping of resistance to rice blast in upland field conditions. Raboin Louis-Marie, Ballini Elsa, Tharreau Didier, Ramanantsoanirina Alain, Frouin Julien, Courtois Brigitte, Ahmadi Nourollah. 2016. Rice, 9 (59), 12 p.https://doi.org/10.1186/s12284-016-0131-4 <https://doi.org/10.1186/s12284-016-0131-4> Association mapping of resistance to rice blast in upland field conditions Raboin, Louis-Marie Ballini, Elsa Tharreau, Didier Ramanantsoanirina, Alain Frouin, Julien Courtois, Brigitte Ahmadi, Nourollah eng 2016 Rice H20 - Maladies des plantes F30 - Génétique et amélioration des plantes Oryza sativa Magnaporthe grisea résistance génétique résistance aux maladies génome génétique des populations analyse qualitative analyse quantitative marqueur génétique variété variation génétique chromosome locus des caractères quantitatifs Magnaporthe riz pluvial http://aims.fao.org/aos/agrovoc/c_5438 http://aims.fao.org/aos/agrovoc/c_37090 http://aims.fao.org/aos/agrovoc/c_35130 http://aims.fao.org/aos/agrovoc/c_2328 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_35284 http://aims.fao.org/aos/agrovoc/c_32660 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_8157 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_1598 http://aims.fao.org/aos/agrovoc/c_37974 http://aims.fao.org/aos/agrovoc/c_31827 http://aims.fao.org/aos/agrovoc/c_8076 Madagascar Sénégal Mali Philippines Inde France http://aims.fao.org/aos/agrovoc/c_4510 http://aims.fao.org/aos/agrovoc/c_6970 http://aims.fao.org/aos/agrovoc/c_4540 http://aims.fao.org/aos/agrovoc/c_5783 http://aims.fao.org/aos/agrovoc/c_3825 http://aims.fao.org/aos/agrovoc/c_3081 Background: Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. Results: The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. Conclusions: It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/582133/1/2016_Rice_Raboinetal.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/s12284-016-0131-4 10.1186/s12284-016-0131-4 info:eu-repo/semantics/altIdentifier/doi/10.1186/s12284-016-0131-4 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12284-016-0131-4 |