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QTL-Seq Approach Identified Pi63 Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum”

Author

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  • Chaiwat Netpakdee

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
    Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand)

  • Sittiwut Mathasiripakorn

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand)

  • Arthit Sribunrueang

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand)

  • Sompong Chankaew

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
    Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand)

  • Tidarat Monkham

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand)

  • Siwaret Arikit

    (Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand)

  • Jirawat Sanitchon

    (Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand)

Abstract

Rice blast (BL) caused by Magnaporthe oryzae 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 ( R ) genes or QTLs in indigenous rice, which harbors the R 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 ( qBLchr4 ) associated with BL resistance at the seedling and maximum tillering stages was mapped on the long arm of chromosome 4. Five genes, LOC_Os04g0616600, LOC_Os04g0617900 (OsGLP4-1), LOC_Os04g0619600 (OsRLCK161), LOC_Os04g0620800 (Pi63), and LOC_Os04g0621500 , were considered the candidate genes representing qBLchr4 . 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 qBLchr4 . Among these markers, the Pi63 -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, Pi63 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).

Suggested Citation

  • Chaiwat Netpakdee & Sittiwut Mathasiripakorn & Arthit Sribunrueang & Sompong Chankaew & Tidarat Monkham & Siwaret Arikit & Jirawat Sanitchon, 2022. "QTL-Seq Approach Identified Pi63 Conferring Blast Resistance at the Seedling and Tillering Stages of Thai Indigenous Rice Variety “Phaladum”," Agriculture, MDPI, vol. 12(8), pages 1-14, August.
    • Handle: RePEc:gam:jagris:v:12:y:2022:i:8:p:1166-:d:881210
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    References listed on IDEAS

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    1. Yunyu Wu & Ning Xiao & Ling Yu & Cunhong Pan & Yuhong Li & Xiaoxiang Zhang & Guangqing Liu & Zhengyuan Dai & Xuebiao Pan & Aihong Li, 2015. "Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.)," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-14, June.
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    1. Decha Songtoasesakul & Wanchana Aesomnuk & Sarinthip Pannak & Jonaliza Lanceras Siangliw & Meechai Siangliw & Theerayut Toojinda & Samart Wanchana & Siwaret Arikit, 2023. "QTL-seq Identifies Pokkali-Derived QTLs and Candidate Genes for Salt Tolerance at Seedling Stage in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 13(8), pages 1-15, August.

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