Identification and Characterization of a Large Effect QTL from Oryza Glumaepatula Revealed Pi68(t) As Putative Candidate Gene for Rice Blast Resistance

Overview

Journal Rice (N Y)

Date 2020 Mar 14

PMID 32166467

Citations 13

Authors

S J S Rama Devi

Kuldeep Singh

B Umakanth

B Vishalakshi

K Vijaya Sudhakara Rao

B Suneel

S K Sharma

Gopala Krishna Murthy Kadambari

M S Prasad

P Senguttvel

Divya P Syamaladevi

M S Madhav

Affiliations

Soon will be listed here.

Abstract

Background: Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast.

Results: Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards leaf and neck blast resistance, respectively and qBL7 contributing about 25% of phenotypic variance for leaf blast. Further, qBL3 was fine mapped, narrowed down to 300 kb region and a linked SNP maker was identified. By combining mapping with microarray analysis, a candidate gene, Os03g0281466 (malectin-serine threonine kinase), was identified in the fine mapped region and named as Pi68(t). The nucleotide variations in the coding as well as upstream region of the gene was identified through cloning and sequence analysis of Pi68(t) alleles. These significant variations led to the non-synonymous changes in the protein as well as variations (presence/absence) in four important motifs (W-box element; MYC element; TCP element; BIHD1OS) at promoter region those are associated with resistance and susceptible reactions. The effect of qBL3 was validated by its introgression into BPT5204 (susceptible variety) through marker-assisted selection and progeny exhibiting resistance to both leaf and neck blast was identified. Further, the utility of linked markers of Pi68(t) in the blast breeding programs was demonstrated in elite germplasm lines.

Conclusions: This is the first report on the identification and characterization of major effect QTL from O. glumaepatula, which led to the identification of a putative candidate gene, Pi68(t), which confers field resistance to leaf as well as neck blast in rice.

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References

McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M . Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 2003; 9(6):199-207. DOI: 10.1093/dnares/9.6.199. View

Wang X, Jia M, Ghai P, Lee F, Jia Y . Genome-Wide Association of Rice Blast Disease Resistance and Yield-Related Components of Rice. Mol Plant Microbe Interact. 2015; 28(12):1383-92. DOI: 10.1094/MPMI-06-15-0131-R. View

Xue M, Yang J, Li Z, Hu S, Yao N, Dean R . Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae. PLoS Genet. 2012; 8(8):e1002869. PMC: 3410873. DOI: 10.1371/journal.pgen.1002869. View

Peterson B, Weber J, Kay E, Fisher H, Hoekstra H . Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One. 2012; 7(5):e37135. PMC: 3365034. DOI: 10.1371/journal.pone.0037135. View

Onaga G, Wydra K, Koopmann B, Sere Y, von Tiedemann A . Population Structure, Pathogenicity, and Mating Type Distribution of Magnaporthe oryzae Isolates from East Africa. Phytopathology. 2015; 105(8):1137-45. DOI: 10.1094/PHYTO-10-14-0281-R. View

Mishra K, Vikram P, Yadaw R, Swamy B, Dixit S, Cruz M . qDTY12.1: a locus with a consistent effect on grain yield under drought in rice. BMC Genet. 2013; 14:12. PMC: 3616849. DOI: 10.1186/1471-2156-14-12. View

Zhu D, Kang H, Li Z, Liu M, Zhu X, Wang Y . A Genome-Wide Association Study of Field Resistance to Magnaporthe Oryzae in Rice. Rice (N Y). 2016; 9(1):44. PMC: 5005242. DOI: 10.1186/s12284-016-0116-3. View

Xiao N, Wu Y, Pan C, Yu L, Chen Y, Liu G . Improving of Rice Blast Resistances in by Pyramiding Major R Genes. Front Plant Sci. 2017; 7:1918. PMC: 5206849. DOI: 10.3389/fpls.2016.01918. View

Inoue H, Hayashi N, Matsushita A, Xinqiong L, Nakayama A, Sugano S . Blast resistance of CC-NB-LRR protein Pb1 is mediated by WRKY45 through protein-protein interaction. Proc Natl Acad Sci U S A. 2013; 110(23):9577-82. PMC: 3677490. DOI: 10.1073/pnas.1222155110. View

10.

Wang C, Yang Y, Yuan X, Xu Q, Feng Y, Yu H . Genome-wide association study of blast resistance in indica rice. BMC Plant Biol. 2014; 14:311. PMC: 4239320. DOI: 10.1186/s12870-014-0311-6. View

11.

Fang N, Wei X, Shen L, Yu Y, Li M, Yin C . Fine mapping of a panicle blast resistance gene Pb-bd1 in Japonica landrace Bodao and its application in rice breeding. Rice (N Y). 2019; 12(1):18. PMC: 6434012. DOI: 10.1186/s12284-019-0275-0. View

12.

Chomczynski P . A reagent for the single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques. 1993; 15(3):532-4, 536-7. View

13.

Rajaraman J, Douchkov D, Hensel G, Stefanato F, Gordon A, Ereful N . An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat. Front Plant Sci. 2016; 7:1836. PMC: 5156707. DOI: 10.3389/fpls.2016.01836. View

14.

Sirithunya P, Tragoonrung S, Vanavichit A, Vongsaprom C, Toojinda T . Quantitative trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice (Oryza sativa). DNA Res. 2002; 9(3):79-88. DOI: 10.1093/dnares/9.3.79. View

15.

Hayashi N, Inoue H, Kato T, Funao T, Shirota M, Shimizu T . Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication. Plant J. 2010; 64(3):498-510. DOI: 10.1111/j.1365-313X.2010.04348.x. View

16.

Soliman K, Jorgensen R, Allard R . Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci U S A. 1984; 81(24):8014-8. PMC: 392284. DOI: 10.1073/pnas.81.24.8014. View

17.

Kumar P, Sujatha K, Laha G, Rao K, Mishra B, Viraktamath B . Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas oryzae pv. oryzae. Phytopathology. 2011; 102(2):222-8. DOI: 10.1094/PHYTO-03-11-0075. View

18.

Bellande K, Bono J, Savelli B, Jamet E, Canut H . Plant Lectins and Lectin Receptor-Like Kinases: How Do They Sense the Outside?. Int J Mol Sci. 2017; 18(6). PMC: 5485988. DOI: 10.3390/ijms18061164. View

19.

Sakulkoo W, Oses-Ruiz M, Oliveira Garcia E, Soanes D, Littlejohn G, Hacker C . A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus. Science. 2018; 359(6382):1399-1403. DOI: 10.1126/science.aaq0892. View

20.

Sinha R, Gupta A, Senthil-Kumar M . Concurrent Drought Stress and Vascular Pathogen Infection Induce Common and Distinct Transcriptomic Responses in Chickpea. Front Plant Sci. 2017; 8:333. PMC: 5361651. DOI: 10.3389/fpls.2017.00333. View