The response to drought stress in rice could also be an advanced development involving several functionally interconnected genes unfold throughout the order. Natural phenomenon Analysis permits the analysis of the expression of thousands of genes in an extremely extra comprehensive and holistic suggests that, providing a world image of changes occurring inside the transcriptome of varied components of the plant beneath stress conditions. Expression analysis results is accustomed establish candidate genes for specific drought tolerance-related traits or physiological mechanisms associated with stress-induced adaptive processes [ 38 , 46 , 47 ].
In rice, several efforts were created to grasp the differential expression of genes under drought stress by transcription identification pattern RT-PCR and microarray technologies [ 48 ] distributed microarray analysis of rice panicles selected from a drought stressed plant and reported up-regulation of the many stressinduced genes like GTP-binding molecule 3, sugar synthase-6, heat shock cognate molecule, deoxyribonucleic acid repair molecule, reductase, zinc finger molecule, protein depolymerizing issue, and polysaccharide esterase [ 49 ] far-famed sixty 2 drought-inducible genes in 2-week-old drought-stressed rice seedlings.
Widespread rice landrace N22 Nagina could also be a natural different for lots of molecular characterization work because of its drought tolerance. A drought-induced DNA library was made of N22 and transcription identification was performed, acknowledged stress-related genes were far-famed, and, pattern this knowledge, candidate genes were deduced for drought QTLs [ 50 ].
In another study pattern N22, ESTs were generated from drought-stressed rice seedlings; most of the stress-induced genes were related to primary metabolic pathways, transcription, and conjointly the interpretation methodology [ 51 ].
Differential expression analysis of upland and lowland rice cultivars victimization cDNA-AFLP unconcealed that quite eight of the entire genes clothed were upregulated by drought stress in each cultivars. Fifty-seven and thirty-eight genes were specifically expressed in upland and lowland cultivars, severally. Among the differentially expressed genes, genes for cell rescue, drought defense, signal transduction, nucleotides, organic compound biogenesis, and genes for plant growth and development were specifically expressed in upland rice, whereas genes for macromolecule and ester degradation were specific to lowland rice cultivars [ 52 ].
The spatial temporal expression patterns of two-component system TCS genes in rice underneath drought stress showed a differential expression pattern in varied organs underneath stress . Reportable genes and signal pathways concerned within the anatomical and morphological developments of rice roots, notably for crown root initiation underneath drought stress [ 56 ]. Out of those, four transcripts were mapped inside the QTLs for root growth underneath water deficit.
In another study, [ 57 ] discovered differentially expressed genes in leaves and roots of upland rice and lowland rice. Combining our data of genes concerned in growth and development, reconciling mechanisms with genes that are differentially expressed underneath drought may facilitate determine necessary target traits for drought resistance.
The differentially expressed genes also can function candidate genes for additional characterization and for allele-morph mining. Pyrimidine methylation and demethylation by DNA methyltransferases are epigenetic mechanisms adopted by the upper organisms in response to worry. It causes differential regulation of organic phenomenon through either silencing or over [ 59 , 60 ]. There are reports demonstrating that DNA methylation-regulated organic phenomenon could be a response to drought stress.
A recent study exploring the genome-wide DNA methylation standing of 2 rice cultivars DK and IR64 with totally different tolerance of drought disclosed important variations within the methylation patterns between the 2 genomes [ 32 ]. Methylation and demethylation changes were elicited underneath drought conditions during a biological process and tissue-specific manner and that they accounted for twelve. Notably, seventieth of the drought-induced methylation changes were reversed once recovery, and twenty nine remained dateless [ 32 ].
Changes in methylation pattern in rice cultivars were reported by [ 61 ]. These observations recommend that DNA methylation changes play a task within the response of rice to dehydration conditions in all probability by activating or deactivating stress-responsive genes and resulting in adaptation to drought conditions. To date, many drought-responsive microRNAs are known in plants. In rice additionally, small polymer regulated drought response has been reported [ 38 , 62 ]. Plants react to drought stress by accumulating various metabolic compounds such as proline, glycine-betain, pinitol, carinitine, mannitol, sorbitol, polyols, trehalose, sucrose, oligosaccharides, and fructans in large quantities [ 63 ].
These are chemically dissimilar compounds; they keep the surface of the proteins hydrated, resulting in decreased water potential and facilitating continuous water movement, which might contribute to sustaining physiological processes such as stomatal opening, photosynthesis, and expansion of cell growth. The role of metabolites in drought tolerance has been thoroughly reviewed in earlier reports [ 64 , 65 ]. Cytosine methylation and demethylation by DNA methyl-transferases are epigenetic mechanisms adopted by the higher organisms in response to stress.
It causes differential regulation of gene expression through either silencing or over [ 60 , 61 ]. There are reports demonstrating that DNA methylationregulated gene expression is a response to drought stress. A recent study exploring the genome-wide DNA methylation status of two rice cultivars DK and IR64 with different tolerance of drought revealed significant differences in the methylation patterns between the two genomes [ 66 ].
Methylation and demethylation changes were induced under drought conditions in a developmental and tissue-specific manner and they accounted for Changes in methylation pattern in rice cultivars were reported by [ 32 ]. These observations suggest that DNA methylation changes play a role in the response of rice to dehydration conditions probably by activating or deactivating stress-responsive genes and leading to adaptation to drought conditions.
Michael Kohn Lab research on conservation genomics
To date, hundreds of droughtresponsive microRNAs have been identified in plants. In rice also, micro RNA regulated drought response has been reported [ 38 , 39 ]. Direct and indirect genetic transformation techniques e. These techniques proved to be very efficient in past few decades. Large numbers of candidate genes were observed against drought stress which was directly involved in post transcriptional modification, signal cascades and metabolite triggering Yang et al. Genetic engineering was found efficient technique that allows gene pyramiding for biotic and abiotic stresses.
Cattivelli et al. Transcription analysis enables gene expression for specific environmental stress especially for drought at any chronological crop stage. Genetic expression of MAP kinase related genes were found in drought stress Agrawal et al. Rice genome modified with such gene pyramiding protocol would be better adapted to new environment under drought. Overall efforts interpreted that proper genetic resource and techniques would be very effective for gene expression under stress. Durability and stable performance of genetic assembly of any specie is key factor for breeder.
Transcriptional factor along with specific genes have been incorporated in rice genome for durable and stable expression of protein under various type of seasonal fluctuates.
Transgenic rice germplasm has been widely evaluated invitro condition for better result it is needed to be evaluated in environmental condition. Hence transgenic approaches are preferred over traditional breeding program which is very laborious and time consuming. Genetic engineering is novel breeding technique widely used along the world to combat the global warming specially drought. It is needed that genetic engineering in rice would be very selective and appropriable method especially for drought stress Bhatnagar-Mathur et al.
Water is important component for Food security yet it is scarce resource in the world [ 67 ]. Water scarcity limit the agricultural growth worldwide. It is urgent need to develop a drought tolerant variety to produce quality food for the growing population . Rice is staple food along the worldwide which feed three billion population, depending upon daily dietary needs [ 2 ]. Rice crop is severely affected by water deficiency which significantly reduces per hectare production.
Rainfed rice yield is reduced by drought stress approximately 23 million hectare worldwide [ 3 ]. Rice crop is highly sensitive to water scarcity but during flowering stage, it was observed that the water stress cause economic loss on large scale. The ability of rice plant to stand in water scarcity condition is important for production of rice during drought season [ 5 , 6 ].
Breeder must develop rice varieties suitable for water deficit conditions. Recently several research programs have been introduced to develop drought tolerance rice cultivars utilizing multidiscipline approaches. Thus, it is imperious for breeders to develop cultivars of high yielding and drought tolerant. Genetic variability and durability of drought tolerance genes are novel approach for the stable production of rice against drought. Screening of these lines and introgressed to cultivated germplasm is highly demanding objective for development of drought tolerance rice variety.
But this process required time, cost and human capital. Research has been accomplished to develop drought tolerance rice variety in past few decades. Maximum production with sufficient adoptability of cultivar under drought condition is prerequisites for the initiation of breeding program [ 10 ]. Cultivated rice has two wild species named as O. Breeding of rice crop can be modified by utilizing bioinformatics and genomic tools which had been widely used in rice genome. Genetic engineering and MAS proved to be latest and innovative breeding strategy to evaluated genetic architecture of drought tolerance genes in rice.
By utilizing these strategies rice production would be increased under drought conditions. This review will benefits the scientist to develop drought tolerance rice cultivar by understanding the genetic and genomics application of innovative research tools in breeding programs. For drought tolerance, breeding efforts in rice have clearly revealed that a multidisciplinary approach is necessary.
Utilizing Standard approach to study the physiological basis of drought tolerance helps to determine the specific anatomical and morphological diversity, and pathways. Selection for donor parents above mention variation and approaches proved to be useful in molecular and traditional breeding program for drought tolerance [ 7 ]. A transgenic method allows the manipulation of drought-tolerant genes from different sources [ 70 - 75 ]. Through breeding procedures after the evaluation of transgenic plants and gene incorporation, these genes can be transferred to other genetic database . Functional genomic study may be very crucial in future crop improvement.
Breeder can only utilized these technologies when reasonable variation and integration is observed in rice germplasm. Drought tolerance trait is very complex genetic character which is main cause of drought tolerance rice germplasm However drought stress and its mitigation strategies were explored in last few years. Genetic variability for specific trait is key factor to start a breeding program. Genetically and physiological screening of rice germplasm for grain yield, QTLs, genomic marker and MAS would be very effective to develop drought resistant rice cultivar.
There are several Quantitative trait loci for Rice yield under drought have been transformed and would be utilized in future research. Advancement in functional genomics significantly helps to evaluate various molecular pathways and genetic resource participated in drought tolerance. Rice genome can be edited for drought tolerance and genetic pyramiding of drought responsive genes would be revolutionize rice productivity. Drought tolerance variety of rice can be developed through genetic engineering techniques. Sign up for our newsletter to receive the latest updates.
We respect your privacy and will never share your email address with anyone else. Peer Review Process. Advertise with us. Refer a Friend. Osnato et al. The trascriptional activity of MYB4 was also tested on several cold tolerance genes such as paf93 and pt 59 of barley and des90 of tomato. Rice gene Analogues The comparative genomics has established the genomic relationship between different members of Poaceae. The genomes of different cereals have been found to have a conserved gene content and order with minor translocational and mutational variations Goff et al.
Genomics thus helps in identification of different versions of rice genes from other species and genera. Such analysis will help in identification of orthologous genes in other cereals with similar sequence and function to those in rice but with markedly different phenotype. Such genes can be introduced into rice to produce novel phenotypes. This is especially important in case of resistance breeding where transfer of genes from related species is quite easy. A very important consideration in this regard is that since gene order is highly conserved among cereals and there is great synteny, the genes transferred from one cereal to another will do well because of similar genetic background.
Germplasm Mining Rice genome is believed to contain some genes. The structural and functional analysis of such a large number of genes is a long term endavour. But recent advances in high throughput gene expression studies involving microarray and gene chips will go a long way in identifying genes and assigning function to them. These studies will help in functional analysis of rice genome in spatial and temporal aspects, i. The practical aspects for a plant breeder would be to look for allelic variants Gene tilling in rice germplasm which confer superior phenotype.
Such an approach will be quite useful in backcrossing for alein introgression from exotic cultivars. Genomics and Hybrid Rice Hybrid rice breeding has been a driving force for rice improvement with substantial increase in grain yield especially in China.
One of the major limitations is narrow genetic base of restorer lines which decrease possibility of selecting optimal parental lines for hybrid combinations. It is very tedious to transfer restorer genes in elite genetic background by conventional breeding. This can be overcome by transgenic approach using several restorer genes like Rf-1, Rf-2 and Rf-3 for WA wild abortive system.
Recently some genes conditioning TGMS have been identified which will help in popularizing two-line approach of hybrid rice production. Poor grain quality sometimes is a major concern in hybrid rice breeding. Genomics helps in identifying and cloning such genes which affect grain quality in rice. Chinese Rice Functional Genomis Programme has objectively targeted such genes and has identified and cloned several genes by map-based cloning.
Continued success of our endeavour to exploit heetrosis will depend on our ability to apply genome manipulations. The primary areas of application of genomics for hybrid rice will be. Genomics and Rice Ideotypes Ideotype breeding in rice aims at arriving at a predetermined phenottypic expression for designing high yielding cultivars with good grain quality. Such an approach can be greatly facilitated by genomics by discovery of genes conditioning plant growth and developmental traits such as tillering, fertility and plant architecture.
Less unproductive tillers or Monoculm plant has been an important consideration in rice ideotype. A rice gene called Monoculm-1 MOC-1 has been recently cloned. The MOC-1 mutants are usually monoculm without tillers due to defect in formation of tiller buds. MOC-1 encodes a putative nuclear protein mainly expressed in auxiliary buds and promotes their outgrowth. Recently another gene governing feeding quality of rice culm BC-1 Brittle culm-1 has been cloned by map-based cloning. The BC-1 gene reduces cellulose content of culm which is a desirable nutritive change because ruminants do not possess any cellulase enzymes in their rumens.
Rice is unique in the sense that it is not only the model cereal for genomic research but also an important staple food. The global resources can be coherently integrated to achieve goals. The information generated by genomics will not only help in improvement of rice but also other cereals because of great synteny in gene order.
Genomics offers tremendous opportunities to scientists for innovation and also policy makers to put in place a coherent international effort in this regard. The population of rice eaters is anticipated to double upto , thus we need to produce more rice within the limitations of declining resource base. The understanding rice genome, besides being a major landmark in plant biotechnology will bring us one step further towards our goal of producing more rice with less land, less water and less chemicals.
Thus the future of genomics in rice improvement is undoubtedly promising. Subscribe Today. Science Alert. All Rights Reserved. Research Article. Genomics in Rice Improvement. Parvez Sofi and A. Similar Articles in this Journal. Search in Google Scholar. How to cite this article: Parvez Sofi and A. Trag , Asian Journal of Biochemistry, 1: DOI: Structural genomics: which studies the organization of genes in genomes and the structure of all proteins encoded by DNA sequences.
Functional genomics: Which studies the function and interaction of genes because of such organization, their effect and expression in time and space and explains why and how a given gene behaves in a certain manner under certain situations. Functional genomics also studies protein functions of an organism Proteomics. Comparative genomics: Which studies the synteny relationships between genomes of related organisms for possible gene exploration and transfer within related groups.
The size of genome has a great bearing on the nature of cloning vector to be used. Relatively higher total recombination distance in genome cM as against cM maize and Barley cM. Relatively lower proportion of kilobases per recombination unit cM as against maize and barley. This ratio is an indicator of how precisely a target gene can be located in terms of physical distance through linkage mapping techniques.
The smaller ratio means more precision. This is all the more important in map-based cloning i. Relatively lower amount of repetitive DNA. The compact nature of rice genome provides distinct advantage in gene isolation and genome sequencing as against other cereal crops. Large number of EST database is available in rice facilitating a quick identification of genes of interest Shimamoto and Kyozuka, Rice is amenable to manipulations in tissue culture techniques.
Transformation protocols for development of transgenics have been well standardized. Several rice lines have been developed in which genes are tagged by insertion elements Greco et al. Synteny relationships of rice genome with other cereals Sorrells et al. Genome size in terms of chromosome number 1n , base pairs Mb and total recombinational map length cM of some plant sp. Features of rice genome as per different versions of draft sequence Goff et al.
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