QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum”
Rice blast (BL) caused by <i>Magnaporthe oryzae</i> is a fungal disease causing significant yield losses in rice production worldwide. To overcome the breakdown of resistance by the rapid adaptation of pathogens, identifying resistance (<i>R</i>) genes or QTLs in indigenous r...
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MDPI AG
2022-08-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/8/1166 |
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| author | Chaiwat Netpakdee Sittiwut Mathasiripakorn Arthit Sribunrueang Sompong Chankaew Tidarat Monkham Siwaret Arikit Jirawat Sanitchon |
| author_facet | Chaiwat Netpakdee Sittiwut Mathasiripakorn Arthit Sribunrueang Sompong Chankaew Tidarat Monkham Siwaret Arikit Jirawat Sanitchon |
| author_sort | Chaiwat Netpakdee |
| collection | DOAJ |
| description | Rice blast (BL) caused by <i>Magnaporthe oryzae</i> is a fungal disease causing significant yield losses in rice production worldwide. To overcome the breakdown of resistance by the rapid adaptation of pathogens, identifying resistance (<i>R</i>) genes or QTLs in indigenous rice, which harbors the <i>R</i> genes that co-evolved with the local pathogen race, is necessary. In this study, a recombinant inbred line (RIL) population derived from a cross between RD6 and Phaladum (PLD) was used to map quantitative trait loci (QTL) for BL resistance through a QTL-seq approach. A single QTL (<i>qBLchr4</i>) associated with BL resistance at the seedling and maximum tillering stages was mapped on the long arm of chromosome 4. Five genes, <i>LOC_Os04g0616600, LOC_Os04g0617900 (OsGLP4-1), LOC_Os04g0619600 (OsRLCK161), LOC_Os04g0620800 (Pi63),</i> and <i>LOC_Os04g0621500</i>, were considered the candidate genes representing <i>qBLchr4</i>. Subsequently, the Kompetitive Allele-Specific PCR (KASP) markers specific for the SNP variant and position of each gene were designed for validation in the mapping population. These markers showed the high phenotypic variance explained (PVE) values in all testing methods and/or environments, signifying the major effect of <i>qBLchr4</i>. Among these markers, the <i>Pi63</i>-KASP marker explained the highest and most stable phenotypic variation across all testing methods and/or environments, with 84.18%, 80.34%, and 23.43% in the upland short row (USR) method, Sila environment, and Mueang environment, respectively. Therefore, <i>Pi63</i> was suggested to be the strongest candidate gene. These results represent the potential utility of future BL resistance breeding and/or pyramiding using marker-assisted selection (MAS). |
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| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-09T12:03:40Z |
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| spelling | doaj.art-624f738705794635972a4223f37a45022023-11-30T23:00:58ZengMDPI AGAgriculture2077-04722022-08-01128116610.3390/agriculture12081166QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum”Chaiwat Netpakdee0Sittiwut Mathasiripakorn1Arthit Sribunrueang2Sompong Chankaew3Tidarat Monkham4Siwaret Arikit5Jirawat Sanitchon6Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandDepartment of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, ThailandDepartment of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, ThailandRice blast (BL) caused by <i>Magnaporthe oryzae</i> is a fungal disease causing significant yield losses in rice production worldwide. To overcome the breakdown of resistance by the rapid adaptation of pathogens, identifying resistance (<i>R</i>) genes or QTLs in indigenous rice, which harbors the <i>R</i> genes that co-evolved with the local pathogen race, is necessary. In this study, a recombinant inbred line (RIL) population derived from a cross between RD6 and Phaladum (PLD) was used to map quantitative trait loci (QTL) for BL resistance through a QTL-seq approach. A single QTL (<i>qBLchr4</i>) associated with BL resistance at the seedling and maximum tillering stages was mapped on the long arm of chromosome 4. Five genes, <i>LOC_Os04g0616600, LOC_Os04g0617900 (OsGLP4-1), LOC_Os04g0619600 (OsRLCK161), LOC_Os04g0620800 (Pi63),</i> and <i>LOC_Os04g0621500</i>, were considered the candidate genes representing <i>qBLchr4</i>. Subsequently, the Kompetitive Allele-Specific PCR (KASP) markers specific for the SNP variant and position of each gene were designed for validation in the mapping population. These markers showed the high phenotypic variance explained (PVE) values in all testing methods and/or environments, signifying the major effect of <i>qBLchr4</i>. Among these markers, the <i>Pi63</i>-KASP marker explained the highest and most stable phenotypic variation across all testing methods and/or environments, with 84.18%, 80.34%, and 23.43% in the upland short row (USR) method, Sila environment, and Mueang environment, respectively. Therefore, <i>Pi63</i> was suggested to be the strongest candidate gene. These results represent the potential utility of future BL resistance breeding and/or pyramiding using marker-assisted selection (MAS).https://www.mdpi.com/2077-0472/12/8/1166multiple-stage resistancerice germplasmrapid generation advanceupland short rowSNP index |
| spellingShingle | Chaiwat Netpakdee Sittiwut Mathasiripakorn Arthit Sribunrueang Sompong Chankaew Tidarat Monkham Siwaret Arikit Jirawat Sanitchon QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” Agriculture multiple-stage resistance rice germplasm rapid generation advance upland short row SNP index |
| title | QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” |
| title_full | QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” |
| title_fullStr | QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” |
| title_full_unstemmed | QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” |
| title_short | QTL-Seq Approach Identified <i>Pi63</i> Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum” |
| title_sort | qtl seq approach identified i pi63 i conferring blast resistance at the seedling and tillering stages of thai indigenous rice variety phaladum |
| topic | multiple-stage resistance rice germplasm rapid generation advance upland short row SNP index |
| url | https://www.mdpi.com/2077-0472/12/8/1166 |
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