The Differential Reaction of Rice Hybrids to Tungro Virus by Phenotyping and PCR Analysis

Twenty popular rice hybrids were used to screen for rice tungro virus (RTV) disease reaction. Virulent green leafhoppers (GLH) were used as vector to introduce RTV to the rice hybrids. Virus symptoms scores were recorded at 14, 21, 34, 41 and 59 days postinoculation (DPI), which suggested that virus symptoms are greatly influenced by growth stage of plants. To confirm the presence of virus, polymerase chain reaction (PCR)‐based detection of Rice tungro bacilliform virus (RTBV) was carried out at 7, 14, 21 and 59 DPI using virus genome‐specific primers. Virus presence was observed in all the rice hybrids and check varieties, particularly at later stages of infection. This study shows that phenotyping for tungro virus resistance in rice hybrids at 21 DPI gives most reliable results based on both virus symptoms and presence of virus. Further, to assess the relative difference in population of RTBV, quantitative PCR was performed in all the genotypes at 21 DPI. Yield data were also recorded from control and virus‐infected plants to estimate yield loss percentage due to tungro disease. This study is important to understand the response of rice hybrids to tungro virus disease. Results obtained in this study emphasize that molecular detection of virus is very important to screen the rice plants accurately for tungro disease reaction.     

Rhythm of a life within life: role of viral suppressors in hijacking the host cell

Virus–host interaction at cellular and intra-cellular level is a constantly evolving process which results either in the host to resist or the virus to break host immunity and to establish the disease. We have put extensive efforts to understand the genomic organization and gene functions of important viral proteins involved in resisting or avoiding host antiviral responses mediated by RNA interference or Ubiquitin–Proteasome Pathway. Nearly two decades of dedicated research on three agriculturally important viruses revealed genetic and epigenetic regulation of host to induce the defense/immunity responses. The microRNA and auxin regulated development of disease symptoms and the role of temperature in optimizing the interactions of viral protein with host small RNAs are intriguing observations. Owing to the complexity of the dynamic interactions between plant and virus, this research field will always be challenging and fascinating.

     

Regulatory non-coding RNAs: a new frontier in regulation of plant biology

Functional & Integrative Genomics - Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant...     

Genome editing of indica rice ASD16 for imparting resistance against rice tungro disease

Journal of Plant Biochemistry and Biotechnology - Rice tungro disease (RTD) is caused by the joint infection of rice tungro bacilliform virus and rice tungro spherical virus (RTSV) and is the most...     

Expression Dynamics of Genes and microRNAs at Different Growth Stages and Heat Treatments in Contrasting High Temperature Responsive Rice Genotypes

The global warming-driven climate change is becoming a major challenge for rice cultivation in Asia and Africa. High-temperature stress impairs the physiology and growth of rice plant, and ultimately results in reduced grain yield. This study was aimed to decipher the physiological and molecular changes occurring during different growth stages of heat-tolerant (N22) and -susceptible (Vandana) rice cultivars under three different heat treatments. Chlorophyll content, membrane integrity, gas exchange parameters and expression of genes and miRNAs were analyzed in N22 and Vandana at seedling, vegetative, and reproductive growth stages after exposing to short and long duration of high temperature stress, and recovery. A number of genes and miRNAs showed dynamic changes in their expression patterns at different growth stages and heat treatments, highlighting the necessity to understand gene regulation before employing the genes for modification through transgenic or gene editing approaches. Predominantly N22 showed distinct and unique capability to reprogram its physiological and molecular machinery during prolonged heat stress at reproductive stage, suggesting that the dynamics in gene regulation is crucial to determine its heat tolerant ability. The study has larger implications in deploying genes for the development of heat tolerant rice cultivars through breeding, transgenic, and genome editing approaches.

     

Field level evaluation of rice introgression lines for heat tolerance and validation of markers linked to spikelet fertility

Rice lines derived from wild species and mutants can serve as a good resource for favorable alleles for heat tolerance. In all, 48 stable lines including 17 KMR3/O. rufipogon introgression lines (KMR3 ILs), 15 Swarna/O. nivara ILs (Swarna ILs) along with their parents, Nagina 22 (N22) and its 4 EMS induced mutants and 7 varieties were evaluated for heat tolerance under irrigated conditions under field in two seasons, wet season 2012 using poly cover house method and dry season 2013 using late sown method. Spikelet fertility (SF), yield per plant (YP) and heat susceptibility index (HSI) for these two traits were considered as criteria to assess heat tolerance compared to control. Four KMR3 ILs and eight Swarna ILs were identified as heat tolerant based on SF and YP and their HSIs in both wet and dry seasons. S-65 and S-70 showed low SF and high YP consistently in response to heat in both seasons. We provide evidence that SF alone may not be the best criterion to assess heat tolerance and including YP is important as lines with low SF but high YP and vice versa were identified under heat stress. Out of 49 SSR markers linked to spikelet fertility, 18 were validated for five traits. RM229 in wet season and RM430 and RM210 in dry season were significantly associated with both SF and its HSI under heat stress. RM430 was also significantly associated with both YP and its HSI in dry season. Thirty two candidate genes were identified close to nine markers associated with traits under heat stress.     

Expression patterns of QTL based and other candidate genes in Madhukar × Swarna RILs with contrasting levels of iron and zinc in unpolished rice grains

Background

Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. Genome wide mapping showed 14 QTLs for iron and zinc concentration in unpolished rice grains of F7 RILs derived from Madhukar × Swarna. One line (HL) with high Fe and Zn and one line (LL) with low Fe and Zn in unpolished rice were compared with each other for gene expression using qPCR. 7 day old seedlings were grown in Fe + and Fe − medium for 10 days and RNA extracted from roots and shoots to determine the response of 15 genes in Fe − conditions.

Results

HL showed higher upregulation than LL in shoots but LL showed higher upregulation than HL in roots. YSL2 was upregulated only in HL roots and YSL15 only in HL shoots and both up to 60 fold under Fe − condition. IRT2 and DMAS1 were upregulated 100 fold and NAS2 1000 fold in HL shoot. NAS2, IRT1, IRT2 and DMAS1 were upregulated 40 to 100 fold in LL roots. OsZIP8, OsNAS3, OsYSL1 and OsNRAMP1 which underlie major Fe QTL showed clear allelic differences between HL and LL for markers flanking QTL. The presence of iron increasing QTL allele in HL was clearly correlated with high expression of the underlying gene. OsZIP8 and OsNAS3 which were within major QTL with increasing effect from Madhukar were 8 fold and 4 fold more expressed in HL shoot than in LL shoot. OsNAS1, OsNAS2, OsNAS3, OsYSL2 and OsYSL15 showed 1.5 to 2.5 fold upregulation in flag leaf of HL when compared with flag leaf of Swarna.

Conclusion

HL and LL differed in root length, Fe concentration and expression of several genes under Fe deficiency. The major distinguishing genes were NAS2, IRT2, DMAS1, and YSL15 in shoot and NAS2, IRT1, IRT2, YSL2, and ZIP8 in roots. The presence of iron increasing QTL allele in HL at marker locus close to genes also increased upregulation in HL.