Unlocking the genetic secrets of heat tolerance in Malaysian weedy rice (Oryza spp.)
Abstract
Climate change has become a severe global threat to agricultural crops in recent decades. One of the most critical aspects of achieving sustainable crop yield is breeding crops that are highly tolerant of a wide range of biotic and abiotic stresses. Farming heat-tolerant rice is now in high demand, and candidate genes for the heat tolerance trait can potentially be found in weedy rice. In this study, a set of 180 weedy rice accessions were screened for heat stress tolerance. Five heat tolerant (HT) accessions (MU244, MU235, MU249, MU260, and MU237) and five selected heat susceptible (HS) accessions (MU100, MU114, MU264, MU251, and MU005) were subjected to relative electrical conductivity (REC) and reactive oxidative species assay (ROS). The comparative tests verified that the five putative HT accessions tolerated heat better than the five HS samples. In addition, the whole-genome sequences of three HT (MU060, MU235, and MU237) and four HS (MU100, MU114, MU022, and MU005) accessions were selected for genome-wide SNPs analyses. The analysis revealed beneficial mutation linked with some heat shock factors (HSFs) and heat shock protein (HSP) genes in HT, such as HSF2BC, HSP18, and HSFA2E. Interestingly, these genes also appeared in the lists of differentially expressed genes (DEGs) generated by transcriptome profiling of HT and HS accessions. When HT and HS rice transcriptomes were separately compared against their untreated control group, HT gave 3528 and 3543 DEGs, respectively, while HS showed 3487 and 3040 DEGs at the 2 and 4 hrs time points. Functionally relevant DEGs were investigated to identify putative heat stress tolerance genes that may produce adaptive stress functions in weedy rice. Among the DEGs identified, 88 common genes of the HSP20s, HSP40s, HSP70s, HSP90s, HSP101s, and HSFs were shared between HT and HS groups, and 72 DEGs were unique in both HT (30 genes) and HS (42 genes) types. HT samples were found to have higher expression of HSP20 (LOC Os01g04370), HSFA6 (LOC Os06g36930), HSP40 (LOC Os05g30130), OsBiP4/HSP70 (LOC Os05g35400), HSF1 (LOC Os04g48030) and HSFA2B (LOC Os07g08140) compared to HS rice. The latter four were absent in HS's DEGs list when the HT-HS comparison was performed. GA2OX7 (LOC Os01g11150), OsPDS (LOC Os03g08570), OsLFNR2 (LOC Os06g01850), and OsORC5 (LOC Os03g55200) were downregulated in HS and were considered vital candidates for heat tolerance in weedy rice. The differential involvement of critical pathways determined in the present study, such as oxidative phosphorylation, spliceosome, and protein processing in the endoplasmic reticulum under different treatment conditions, has provided a better understanding of the heat stress tolerance ability in weedy rice. Additionally, qRT-PCR was performed to verify the accuracy of RNA-seq expression patterns.
Home Country
Bangladesh
College
College of Public Health
Specialization
Health Sciences
Faculty Sponsor
Monica Uddin
Presentation Type
Event
Unlocking the genetic secrets of heat tolerance in Malaysian weedy rice (Oryza spp.)
Climate change has become a severe global threat to agricultural crops in recent decades. One of the most critical aspects of achieving sustainable crop yield is breeding crops that are highly tolerant of a wide range of biotic and abiotic stresses. Farming heat-tolerant rice is now in high demand, and candidate genes for the heat tolerance trait can potentially be found in weedy rice. In this study, a set of 180 weedy rice accessions were screened for heat stress tolerance. Five heat tolerant (HT) accessions (MU244, MU235, MU249, MU260, and MU237) and five selected heat susceptible (HS) accessions (MU100, MU114, MU264, MU251, and MU005) were subjected to relative electrical conductivity (REC) and reactive oxidative species assay (ROS). The comparative tests verified that the five putative HT accessions tolerated heat better than the five HS samples. In addition, the whole-genome sequences of three HT (MU060, MU235, and MU237) and four HS (MU100, MU114, MU022, and MU005) accessions were selected for genome-wide SNPs analyses. The analysis revealed beneficial mutation linked with some heat shock factors (HSFs) and heat shock protein (HSP) genes in HT, such as HSF2BC, HSP18, and HSFA2E. Interestingly, these genes also appeared in the lists of differentially expressed genes (DEGs) generated by transcriptome profiling of HT and HS accessions. When HT and HS rice transcriptomes were separately compared against their untreated control group, HT gave 3528 and 3543 DEGs, respectively, while HS showed 3487 and 3040 DEGs at the 2 and 4 hrs time points. Functionally relevant DEGs were investigated to identify putative heat stress tolerance genes that may produce adaptive stress functions in weedy rice. Among the DEGs identified, 88 common genes of the HSP20s, HSP40s, HSP70s, HSP90s, HSP101s, and HSFs were shared between HT and HS groups, and 72 DEGs were unique in both HT (30 genes) and HS (42 genes) types. HT samples were found to have higher expression of HSP20 (LOC Os01g04370), HSFA6 (LOC Os06g36930), HSP40 (LOC Os05g30130), OsBiP4/HSP70 (LOC Os05g35400), HSF1 (LOC Os04g48030) and HSFA2B (LOC Os07g08140) compared to HS rice. The latter four were absent in HS's DEGs list when the HT-HS comparison was performed. GA2OX7 (LOC Os01g11150), OsPDS (LOC Os03g08570), OsLFNR2 (LOC Os06g01850), and OsORC5 (LOC Os03g55200) were downregulated in HS and were considered vital candidates for heat tolerance in weedy rice. The differential involvement of critical pathways determined in the present study, such as oxidative phosphorylation, spliceosome, and protein processing in the endoplasmic reticulum under different treatment conditions, has provided a better understanding of the heat stress tolerance ability in weedy rice. Additionally, qRT-PCR was performed to verify the accuracy of RNA-seq expression patterns.
