Nimai Prasad Mandal

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

Summary This study discusses improvement of popular rice varieties under drought through the identification and marker-assisted introgression of drought yield QTLs without any adverse effect on yield under normal conditions.

Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.

Background Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. Methodology/Principal Findings Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the −QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/−QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha−1 over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. Conclusions/Significance Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought.

Characterization of the effect of a QTL for drought resistance in rice, qtl12.1, over a range of environments in the Philippines and eastern India

A large-effect QTL for grain yield under drought conditions (qtl12.1) was reported in a rice mapping population derived from Vandana and Way Rarem. Here, we measured the effect of qtl12.1 on grain yield and associated traits in 21 field trials: ten at IRRI in the Philippines and 11 in the target environment of eastern India. The relative effect of the QTL on grain yield increased with increasing intensity of drought stress, from having no effect under well-watered conditions to having an additive effect of more than 40% of the trial mean in the most severe stress treatments. The QTL improved grain yield in nine out of ten direct-seeded upland trials where drought stress was severe or moderate, but no effect was measured under well-watered aerobic conditions or under transplanted lowland conditions. These trials confirm that qtl12.1 has a large and consistent effect on grain yield under upland drought stress conditions, in a wide range of environments.

Drought yield index to select high yielding rice lines under different drought stress severities.

BackgroundDrought is the most severe abiotic stress reducing rice yield in rainfed drought prone ecosystems. Variation in intensity and severity of drought from season to season and place to place requires cultivation of rice varieties with different level of drought tolerance in different areas. Multi environment evaluation of breeding lines helps breeder to identify appropriate genotypes for areas prone to similar level of drought stress. From a set of 129 advanced rice (Oryza sativa L.) breeding lines evaluated under rainfed drought-prone situations at three locations in eastern India from 2005 to 2007, a subset of 39 genotypes that were tested for two or more years was selected to develop a drought yield index (DYI) and mean yield index (MYI) based on yield under irrigated, moderate and severe reproductive-stage drought stress to help breeders select appropriate genotypes for different environments.ResultsARB 8 and IR55419-04 recorded the highest drought yield index (DYI) and are identified as the best drought-tolerant lines. The proposed DYI provides a more effective assessment as it is calculated after accounting for a significant genotype x stress-level interaction across environments. For rainfed areas with variable frequency of drought occurrence, Mean yield index (MYI) along with deviation in performance of genotypes from currently cultivated popular varieties in all situations helps to select genotypes with a superior performance across irrigated, moderate and severe reproductive-stage drought situations. IR74371-70-1-1 and DGI 75 are the two genotypes identified to have shown a superior performance over IR64 and MTU1010 under all situations.ConclusionFor highly drought-prone areas, a combination of DYI with deviation in performance of genotypes under irrigated situations can enable breeders to select genotypes with no reduction in yield under favorable environments compared with currently cultivated varieties. For rainfed areas with variable frequency of drought stress, use of MYI together with deviation in performance of genotypes under different situations as compared to presently cultivated varieties will help breeders to select genotypes with superior performance under all situations.

Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers

Molecular screening and genetic diversity of major rice blast resistance (R) genes were determined in 32 accessions of rice germplasm from North East and Eastern India with ten gene based single nucleotide polymorphisms and sequence tagged sites (STS) markers, namely z56592, zt56591, k39512, k3957, candidate gene marker, Pita3, YL155/YL87, YL183/YL87, Pb28, 195R-1 which showed close-set linkage to nine major rice blast resistance (R) genes, Piz, Piz-t, Pik, Pik-p, Pik-h, Pita/Pita-2, Pib and Pi9 and one susceptible pita gene. Among the 32 accessions, 13 were positive for Piz gene and six for Piz-t gene. Six accessions were positive for Pik gene, seven for Pik-p and 16 for Pik-h gene. One accession, Atte thima, was positive for three of Pik multiple genes. Out of 32, only two germplasm, Dudhraj and Nepali dhan, were detected with both Pita3 and YL155/YL87 marker for Pita/Pita-2 gene. The Pib gene appeared to be omnipresent and was detected in 31 of 32 germplasm with marker Pb28. The gene specific STS marker, 195R-1, for Pi9 gene produced positive bands in only two germplasm, Kalchatti and Bachi thima. The Uniform Blast Nursery (UBN) analysis showed that out of 32, six germplasm was resistant, ten moderately resistant and 16 germplasm were susceptible. Presence of Piz-t, Pita/Pita-2 and Pi9 gene ensured a resistant reaction in outdoor blast nursery whereas germplasm carrying Pib was susceptible when present alone. Presence of multiple genes, however, contributed to slow blasting resistance in the field. These results are useful in identification and incorporation of resistant genes from the germplasm into elite cultivars through marker assisted selection in rice breeding programs.

Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought

Highlight Drought-yield QTLs qDTY 2.2 and qDTY 4.1 improved rice variety IR64 complementarily through peak QTL effects at distinct stress levels, and by increasing root hydraulic conductance and root growth at depth.

Grain yield and physiological traits of rice lines with the drought yield QTL qDTY12.1 showed different responses to drought and soil characteristics in upland environments

To improve yield in upland conditions, near-isogenic lines (NILs) of the major-effect drought yield quantitative trait locus qDTY12.1 in rice (Oryza sativa L.) were developed in the background of the upland variety Vandana. These NILs have shown greater water uptake a larger proportion of lateral roots, and higher transpiration efficiency under drought than Vandana, and one NIL (481-B) was selected as having the highest yield. In this study, the NILs were assessed in two greenhouse and 18 upland field trials for their response to drought and different soil textures. Performance of qDTY12.1 NILs was not affected by soil texture but showed a notable response to drought stress severity. The yield advantage of 481-B over Vandana was highest in field trials with intermittent drought stress, in which the mean trial yield was greater than 0.5tha-1, and in the least favourable well watered trial. The effects of qDTY12.1 on water uptake were most apparent under mild to moderate stress but not in very severe drought or well watered treatments, whereas the lateral root and transpiration efficiency responses were observed under a range of conditions. These results highlight the varying response of qDTY12.1 across upland environments and the complexity of multiple mechanisms acting together to confer an effect on rice yield under drought.

Advances in Molecular Mechanism Toward Understanding Plant-Microbe Interaction: A Study of M. oryzae Versus Rice

Rice blast, caused by the fungus Magnaporthe oryzae, is the most devastating disease of rice which causes considerable economic loss worldwide. The interaction between rice and M. oryzae is an important model system for studying host-pathogen interactions. Since genomes of both species are sequenced, research is more focused by exploiting modern genetics, genomics, proteomics and bioinformatics. Recent research on functional genomics and candidate gene identification has helped to elucidate the role of resistance (R) and avirulence (Avr) genes and their interactions. Over the years, many avirulence genes (Avr) involved in pathogenicity and resistance genes (R) of rice involved in pathogen signaling molecules and defence response have been identified and characterized. Recent development in cloning of Avr genes (13) and R genes (22) and identification of many quantitative trait loci (QTL) has improved our understanding of rice-M. oryzae interaction at molecular level. This chapter is focusses on the current R and Avr genes cloned and characterized their structure, function and co-evolution, and the future research directions to study and understand the molecular mechanism of rice-M. oryzae interactions for better targeting and exploitation of host plant resistance towards management of this disease.

Molecular Analysis of Indian Rice Germplasm Accessions with Resistance to Blast Pathogen

The present study was needed to understand the genetic constitution of indigenous rice (Oryza sativa L.) germplasm with respect to their resistance towards the blast pathogen Magnaporthe oryzae. Specifically, the objective was to identify landrace(s) of rice for the presence of effective rice blast resistance (R) gene(s) that can be employed in breeding programs for Eastern India. A set of 47 landraces that consistently showed resistant reaction to blast disease (Magnaporthe oryzae) in multi-season evaluations in outdoor blast nurseries at Hazaribag, Jharkhand, was probed for the presence of known R genes. Seven DNA-based single nucleotide polymorphism (SNP) markers, namely, z56592, zt56591, k39512, k3957, Pita3, PB8, and Pb28, were used to determine the presence of eight major R genes, Piz, Piz-t, Pik, Pik-p, Pita, Pita-2, Pi2, and Pib, in the rice accessions from North East and Eastern India. Among the 47 accessions, only one was positive for Piz, three for Piz-t, and six for Pi2. Three accessions were positive for Pik gene and 21 for Pik-p gene. One accession, 333039, was positive for both Pik and Pik-p genes. Out of 47, 16 accessions possessed the two closely linked Pita and Pita-2 genes. The Pib gene was commonly detected, with 45 out of 47 accessions amplifying the marker Pb28, whereas Piz, Piz-t, Pik, and Pi2 were less common. Many accessions carried multiple genes; one accession, 352766, amplified the markers for as many as six genes, viz., Pib, Piz-t, Pi2, Pik-p, Pita, and Pita-2. Because this core set of accessions was consistently resistant to blast in outdoor blast nurseries and had the added advantage of local adaptation, knowledge of their genetic constitution with respect to the detected R genes and availability of robust markers would be useful for resistance breeding programs.

Microbial interactions in plants: Perspectives and applications of proteomics.

The structure and function of proteins involved in plant-microbe interactions is investigated through large-scale proteomics technology in a complex biological sample. Since the whole genome sequences are now available for several plant species and microbes, proteomics study has become easier, accurate and huge amount of data can be generated and analyzed during plant-microbe interactions. Proteomics approaches are highly important and relevant in many studies and showed that only genomics approaches are not sufficient enough as much significant information are lost as the proteins and not the genes coding them are final product that is responsible for the observed phenotype. Novel approaches in proteomics are developing continuously enabling the study of the various aspects in arrangements and configuration of proteins and its functions. Its application is becoming more common and frequently used in plant-microbe interactions with the advancement in new technologies. They are more used for the portrayal of cell and extracellular destructiveness and pathogenicity variables delivered by pathogens. This distinguishes the protein level adjustments in host plants when infected with pathogens and advantageous partners. This review provides a brief overview of different proteomics technology which is currently available followed by their exploitation to study the plant-microbe interaction.