Jahangir Imam

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.

Identification of Rice Blast Resistance Gene Pi9 from Indian Rice Land Races with STS Marker and Its Verification by Virulence Analysis

The Pi9 gene in rice confers resistance to strains of blast pathogen Magnaporthe oryzae.Pi9 is a typical broad spectrum resistance gene containing nucleotide binding site, leucine rich repeat family of sequences. In the present study, presence of the Pi9 gene in 47 rice germplasm accessions was determined using dominant sequence tagged site marker 195R-1/195F-1 derived from the Nbs2-Pi9 candidate gene and resistance confirmed by inoculating rice germplasm with a mixture of aggressive isolates of M. oryzae namely Mo-ei-66, Mo-ei-79, Mo-ei-119, and Mo-ei-202. The Pi9 gene was found in six rice germplasm accessions from eastern India. Usefulness of this STS marker for determination of the genotype of rice germplasm was thus demonstrated. Rare occurrence of Pi9 gene in the evaluated rice germplasm suggests that its introgression is very less in indica rice. These results are useful for incorporating Pi9 gene into elite cultivars by marker assisted selection in rice breeding programs worldwide.

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.

Role of Enzymes and Proteins in Plant-Microbe Interaction: A Study of M. oryzae Versus Rice

The wall interface between rice and Magnaporthe oryzae plays an important role in the outcome of their interactions, i.e., resistance or susceptibility. A number of enzymes and proteins are involved in both external and internal interactions. The blast fungus secretes many enzymes which help in the plant cell wall degradation and the entry of fungus into the plant cell which results in the development of disease. To restrict the growth and development of blast fungus, the rice plants have also developed many defense mechanisms like generation of defense substances and hydrogen peroxide catalysis by the production of some enzymes in plant cells. These enzymes occur frequently in many isoforms and help in plant defense. Proteins also participate in the defense against blast fungus attack. These proteins are called as pathogenesis-related proteins (PRs). PR proteins have activities of both proteins and hydrolytic enzymes. Chitinase and β-1,3-glucanase are the most common PR proteins which can hydrolyze major components of blast fungal cell walls, chitin and β-1,3-glucan, respectively.

Biohydrogen as Biofuel: Future Prospects and Avenues for Improvements

Biological hydrogen production is one of the most imperative and demanding areas of research and technology development as a clean, efficient, and sustainable energy option to be considered as imminent fuel. The successful biohydrogen production needs technology improvement, use of updated microbial technologies to generate, and developing innovative proficient methods of biohydrogen production. This review explains the various possibilities toward the advancement of biohydrogen production methods, microbial technology involved in different methods with their benefits and shortcomings. It also spotlights on the avenues for enhancement in biohydrogen production and the future prospects of exploiting biohydrogen as prominent biofuel.

Molecular Screening of Blast Resistance Gene Pi2 in Indian Rice Landraces (Oryza sativa L.) and its Verification by Virulence Analysis

The Pi2 gene is a member of a multigene family which confers resistance to strains of blast pathogen Magnaporthe oryzae. The gene encodes a typical NBS-LRR type protein which confers broad spectrum resistance to a wide range of races of blast pathogen prevalent in eastern India. In the present study, the presence of Pi2 gene in 61 landraces was determined using a pair of primers NBS2P3 and NBS2R followed by restriction digestion and the results were further confirmed by pathotyping using M. oryzae isolates avirulent for Pi2 gene. The Pi2 gene was found in four rice landraces from Sikkim and one landrace from Jharkhand though the latter was susceptible to the isolate bearing corresponding avirulence gene. Presence of Pi2 gene in independent indica landraces from the eastern Indian region suggested that the gene might have originated and evolved in indica rice and exist in different allelic forms in blast endemic zones of eastern India. The present study not only identifies the presence of Pi2 gene in landraces but also demonstrates the usefulness of molecular markers and virulence analyses for rapid identification of resistant genes in rice landraces. These characterized landraces can be used for genetic studies and marker assisted breeding for improving blast resistance in rice.

Allele Mining and Selective Patterns of Pi9 Gene in a Set of Rice Landraces from India

Allelic variants of the broad-spectrum blast resistance gene, Pi9 (nucleotide binding site-leucine-rich repeat region) have been analyzed in Indian rice landraces. They were selected from the list of 338 rice landraces phenotyped in the rice blast nursery at central Rainfed Upland Rice Research Station, Hazaribag. Six of them were further selected on the basis of their resistance and susceptible pattern for virulence analysis and selective pattern study of Pi9 gene. The sequence analysis and phylogenetic study illustrated that such sequences are vastly homologous and clustered into two groups. All the blast resistance Pi9 alleles were grouped into one cluster, whereas Pi9 alleles of susceptible landraces formed another cluster even though these landraces have a low level of DNA polymorphisms. A total number of 136 polymorphic sites comprising of transitions, transversions, and insertion and deletions (InDels) were identified in the 2.9 kb sequence of Pi9 alleles. Lower variation in the form of mutations (77) (Transition + Transversion), and InDels (59) were observed in the Pi9 alleles isolated from rice landraces studied. The results showed that the Pi9 alleles of the selected rice landraces were less variable, suggesting that the rice landraces would have been exposed to less number of pathotypes across the country. The positive Tajima’s D (0.33580), P > 0.10 (not significant) was observed among the seven rice landraces, which suggests the balancing selection of Pi9 alleles. The value of synonymous substitution (-0.43337) was less than the non-synonymous substitution (0.78808). The greater non-synonymous substitution than the synonymous means that the coding region, mainly the leucine-rich repeat domain was under diversified selection. In this study, the Pi9 gene has been subjected to balancing selection with low nucleotide diversity which is different from the earlier reports, this may be because of the closeness of the rice landraces, cultivated in the same region, and under low pathotype pressure.

In Silico Approach in Bioremediation

Interdisciplinary investigation of processes involved in bioremediation is latest drift toward finding novel ways and schemes to improve the conventional treatment of toxic compounds with microorganisms. Though microorganisms are being genetically modified to increase their efficiency, but time and funds are always remains matter of concern when it comes to implement idea in a larger picture. In silico methods, include different mathematical models, modeling of metabolism, genomics, proteomics and biodegradation pathways which are being implemented in the bioremediation process for effectual outcome. Role of biological databases in building mathematical model for bioremediation. Role of docking process in the screening of best interaction of pollutant and its enzyme which degrades it. It reduces the samples to be tested in wet lab.

A Comprehensive Overview on Application of Bioinformatics and Computational Statistics in Rice Genomics Toward an Amalgamated Approach for Improving Acquaintance Base

Rice (Oryza sativa L.) is a major crop in the world and provides the staple food for over half of the world population. From thousands of years of cultivation and breeding to recent genomics and systems biology approach, rice has been the focus of agriculture and plant research. Modern scientific research depends on computer technology to organize and analyze large datasets. Rice informatics – a relatively new discipline – has been developing rapidly as a subdiscipline of bioinformatics. Rice informatics devotes to leveraging the power of nature’s experiment of breeding and evolution to extract key findings from sequence and experimental data. Recent advances in high-throughput genotyping and sequencing technologies have changed the landscape of data collection and its analysis by using friendly database access and information retrieval. It focuses on developing and applying database tools and computationally intensive techniques and statistical software (e.g., pattern recognition, data mining, machine learning algorithms, R-statistical, MATLAB, and visualization) which give the opportunity to quickly and efficiently study heap of genomics information, chemical structure, and model generation study. Over recent years, various newly emerged diseases to rice varieties have an increasing concern to agriculturists and pathologists. The establishments of International Rice Information System, Rice Genome Research Project, Integrated Rice Genome Explorer, and Rice Proteome Databases are important initiatives for rice improvement using in silico software (e.g., homology modeling using SWISS Model, Modeler, and Autodock); the recent ongoing research on rice protein and its role in metabolic pathways works is being done around the world. Rice informatics has already started showing its profound impact on agricultural research and developments.