Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance

Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t

Regulation of High-Temperature Stress Response by Small RNAs

Temperature extremes constitute one of the most common environmental stresses that adversely affect the growth and development of plants. Transcriptional regulation of temperature stress responses, particularly involving protein-coding gene networks, has been intensively studied in recent years. High-throughput sequencing technologies enabled the detection of a great number of small RNAs that have been found to change during and following temperature stress. The precise molecular action of some of these has been elucidated in detail. In the present chapter, we summarize the current understanding of small RNA-mediated modulation of high- temperature stress-regulatory pathways including basal stress responses, acclimation, and thermo-memory. We gather evidence that suggests that small RNA network changes, involving multiple upregulated and downregulated small RNAs, balance the trade-off between growth/development and stress responses, in order to ensure successful adaptation. We highlight specific characteristics of small RNA-based tem- perature stress regulation in crop plants. Finally, we explore the perspectives of the use of small RNAs in breeding to improve stress tolerance, which may be relevant for agriculture in the near future

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Not AvailableRNA interference (RNAi) is a mechanism of small RNA-guided regulation of gene expression in which small RNAs inhibit the expression of genes with complementary nucleotide sequences. RNAi has emerged as a powerful modality for battling challenging viruses and provides a natural defense against viral pathogens. In plants, RNAi has been successfully used to express cognate dsRNAs for viral transcripts in order to initiate the process of viral gene silencing. Despite the wide applicability of RNAi for achieving viral resistance, there are some challenges and constraints that must to be addressed to develop RNAi as a more effective tool for virus resistance. The present review provides an update on different approaches of using RNAi for virus resistance development in various crop plants. The factors influencing RNAi-mediated virus resistance and the major constraints are also discussed in detail.Not Availabl

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Not AvailableRice tungro virus disease is one of the most destructive diseases that cause extensive damage to the rice crop. To elucidate the multiplication behaviour of Rice tungro bacilliform virus (RTBV), real-time Polymerase chain reaction (PCR) experiments were performed on rice and insect vector green leafhopper (GLH). SYBR green chemistry-based real-time PCR assay for the quantification of RTBV was developed. A standard curve using plasmid DNA was constructed to determine the absolute quantity of RTBV genome copies in different plant tissues and GLH vector. Here, 6.309 × 104, 7.943 × 105, 3.162 × 106 and 3.162 × 103 RTBV genome copies per ng of total DNA were estimated in root, shoot, leaf and panicles, respectively, on virus-infected rice cultivar TN1. In addition, 5.011 × 103 copies of virus in an individual GLH were quantified. Also, RTBV was quantified at different time interval after inoculation. The real-time assay was performed with five different RTBV isolates that showed differential accumulation pattern of virus isolates in a same host. These results provide new insight into the biology of the economically important interaction between rice, GLH and RTBV.Not Availabl

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Not AvailableAmong the micronutrients, iron (Fe) and zinc (Zn) mineral deficiencies are the most common and widespread, afflicting more than half of the human population. Improving both Fe and Zn concentration and their bioavailability in food grains will assure major health benefits. Recent advancements in genomics and genome editing bring new possibilities for targeted research. Next-generation sequencing technologies are allowing the mass sequencing of genomes and transcriptomes, which facilitates the discovery of new genes and regulatory sequences. These can help improve our knowledge of gene function and regulation associated with Fe and Zn metabolism in crops. The key genes can then be used for biofortification of micronutrients through breeding or transgenic approaches. Small noncoding microRNAs (miRNAs) have the potential to provide more effective means to engineer improved Fe and Zn in food crops. Conventional plant breeding can thus be integrated with forward or reverse genomic approaches and high throughput methods to help in rice biofortification. In this chapter, we have described the genomics of micronutirents biofortification in rice. Recent advances in QTL (quantitative traits loci) mapping, noncoding miRNAs, and epigenetics of high Fe and Zn traits in rice have been deliberated. Conventional and recent approaches including transgenic and genome editing for genome engineering to enhance Fe and Zn of rice grain have also been elucidated.Not Availabl

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Not AvailableAims To test if microRNAs are involved in iron (Fe) homeostasis in Oryza sativa. Methods Recombinant inbred lines (RILs) of rice with contrasting levels of iron in seeds (high iron line HL, low iron line LL) and parent Swarna were grown in Fe sufficient ( + Fe) and deficient (−Fe) environment. miRNAs whose target genes underlie the QTLs mapped for iron concentration (mapped in our previous study) were identified using bioinformatics. The expression analysis of these miRNAs and their targets along with few other miRNAs involved in nutrient homeostasis was done in root and shoot tissue. Real time PCR was used to study the relative expression of miRNAs and their target genes. Results Out of nine miRNAs used in this study, 7 miRNAs-miR156, 168, 172, 162, 167, 171, and 398 showed down-regulation under Fe deficiency in root and shoot of high iron line when compared with Fe sufficient condition. Further, most of the miRNAs showed down-regulation while their target genes showed up-regulation under Fe deficiency in roots of all three genotypes (HL, LL and Swarna) suggesting roots are more responsive to Fe deficiency. Important role of miRNAs in iron homeostasis was analyzed by comparing the expression of these miRNAs in HL, LL and Swarna under + Fe and –Fe. Conclusion MicroRNAs showed differential expression in + Fe and –Fe environment. Further, their expression is more effectively regulated in root under Fe deficiency. This indicates that miRNAs might be playing regulatory roles in iron homeostasis in rice. This study suggests that Fe deficiency responsive miRNAs are involved in cross talk between other nutrients stress.Not Availabl

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Not AvailableRNA interference (RNAi) is a homology-dependent gene silencing technology that is initiated by double stranded RNA (dsRNA). A multitude of small RNAs accumulate in plant tissues, although heterogeneous in size, sequence, genomic distribution, biogenesis, and action, most of these molecules mediate repressive gene regulation through RNA silencing. Micro and small interfering RNAs represent small RNA families that are recognized as critical regulatory species across the eukaryotes. Besides their roles in developmental patterning and maintenance of genome integrity, small RNAs are also integral components of plant responses to adverse environmental conditions, including biotic stress. Recent studies broaden the role of RNAi, and many successful examples have described the application of RNAi for engineering plant resistance against a range of prokaryotic and eukaryotic organisms. Expression of dsRNA directed against suitable pathogen and insect genes in transgenic plants showed protection against pests, opening the way for a new generation of pest and disease resistant crops. Here, current knowledge on the uptake mechanisms of dsRNA in plant pests and the potential of RNAi to control pest and pathogen is described. Concerns regarding further research on dsRNA uptake mechanisms and the promising application possibilities for RNAi in pest and disease management have been discussed. Further, the progress of RNAi-based transgenic plant resistance against eukaryotic pests, as well as future challenges and prospects are addressed.Not Availabl

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Not AvailableRice is a staple food crop, which ensures the calorie requirement of half of the world’s population. With the continued increase in population, rice will play a key role in achieving the food security. However, in the constantly shrinking scenario of rice fields, the necessity of these extra grains of rice must be met by reducing the yield loss due to various abiotic and biotic stresses. The adverse effects of climate impact both quality and quantity of rice production. One of the most desirable applications of CRISPR/Cas technology would be to develop climate smart rice crop to sustain and enhance its productivity in the changing environment. In this review, we analyze the desirable phenotypes and responsible genetic factors, which can be utilized to develop tolerance against major abiotic stresses imposed by climate change through genome engineering. The possibility of utilizing the information from wild resources to engineer the corresponding alleles of cultivated rice has been presented. We have also shed light on available resources for generating genome edited rice lines. The CRISPR/Cas mediated genome editing strategies for engineering of novel genes were proposed to create a plant phenotype, which can face the adversities of climate change. Further, challenges of off-targets and undesirable phenotype were discussed.Not Availabl

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Not AvailableCrop improvement is a continuous process in agriculture which ensures ample supply of food, fodder and fiber to burgeoning world population. Despite tremendous success in plant breeding and transgenesis to improve the yield-related traits, there have been several limitations primarily with the specificity in genetic modifications and incompatibility of host species. Because of this, new breeding techniques (NBTs) are gaining worldwide attention for crop improvement programs. Among the NBTs, genome editing (GE) using site-directed nucleases (SDNs) is an important and potential technique that overcomes limitations associated with classical breeding and transgenesis. These SDNs specifically target a compatible region in the gene/genome. The meganucleases (MgN), zinc finger nucleases (ZFN), transcription activator-like effectors nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated endonuclease (Cas) are being successfully employed for GE. These can be used for desired or targeted modifications of the native endogenous gene(s) or targeted insertion of cis/trans elements in the genomes of recipient organisms. Applications of these techniques appear to be endless ever since their discovery and several modifications in original technologies have further brought precision and accuracy in these methods. In this review, we present an overview of GE using SDNs with an emphasis on CRISPR/Cas system, their advantages, limitations and also practical considerations while designing experiments have been discussed. The review also emphasizes on the possible applications of CRISPR for improving economic traits in crop plants.Not Availabl