Transcriptome analysis of rice upon rice blast infection and in silico development of microsatellite markers from multiple sequences

Name: Athipat Ngernmuen

LCSH: Kasetsart University -- Dissertations. Ph.D. (Genetics) 2019

Classification :.LCCS: SB608.R5

LCSH: Kasetsart University. -- Department of Genetics -- Dissertations

LCSH: Rice -- Jao Hom Nin -- Breeding

LCSH: Rice -- Jao Hom Nin -- Diseases and pests

Abstract: Rice is an important crop which is depleted by plant diseases including rice blast disease caused by rice blast fungus (Magnaporthe oryzae). Jao Hom Nin (JHN) is Thai rice conferring broad spectrum resistance and have been reported the occurrence of two rice blast resistant QTLs, which can be genetic resource for improvement by markerassisted selection. Firstly, the polymorphic InDel and SSR markers between JHN (resistant cultivar) and Kho Khor 6 (RD6) (susceptible cultivar) were used for graphical genotype construction of nine backcross inbred lines (BILs) containing RD6 background introgressed with JHN QTLs. Secondly, the transcriptome analysis of JHN, RD6 and two BILs containing QTL from JHN chromosome1 (Q1) and 11 (Q11) inoculated by rice blast isolate THL84 at 0 hour after inoculation (hai) and 24 hai was conducted by RNA-seq. The up and down differently expressed genes at 24 hai in Q1 and Q11 were examined. Ten candidate genes were validated by quantitative real time PCR. Thirdly, the in silico SSR polymorphsm was used for development of polymorphic SSR markers among Thai cultivars and Thai rice blasts. The result showed that 94 out of 363 markers were polymorphic markers between JHN and RD6. From graphical genotype, these nine BILs showed mostly RD6 background. In RNA-seq, there were 6,466 and 6,047 differently expressed genes of Q1 and Q11 at 24 hai respectively. The gene ontology analysis revealed signicant 119, 125 and 225 GO terms in up-regulation of Q1, Q11 and common of Q1 and Q11 respectively. Nine out of ten genes were relevant to the validation by RT-PCR. By in silico SSR development, 15 out of 24 rice SSRs showed polymorphism in 12 Thai rice cultivars and 10 out of 14 rice blast SSRs showed polymorphism in 58 rice blast isolates.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Chatchawan Jantasuriyarat

Role: Thesis Advisor

Name: Tanee Sreewongchai

Role: Thesis CO-Advisor

Created: 2019

Modified: 2025-07-01

Issued: 2025-07-01

วิทยานิพนธ์/Thesis

application/pdf

URL: https://www.lib.ku.ac.th/KUthesis/2562/athipat-nge-all.pdf

CallNumber: SB608.R5 .A83

eng

DegreeName: Doctor of Philosophy

Level: Doctoral Degree

Descipline: Genetics

Grantor: Kasetsart University

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