Advances in understanding salt tolerance in rice Ganie, Showkat Ahmad; Molla, Kutubuddin Ali; Henry, Robert J. ...
Theoretical and applied genetics,
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132, Številka:
4
Journal Article
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This review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics.
Salinity is one of ...the major constraints in rice cultivation globally. Traditionally, rice is a glycophyte except for a few genotypes that have been widely used in salinity tolerance breeding of rice. Both seedling and reproductive stages of rice are considered to be the salt-susceptible stages; however, research efforts have been biased towards improving the understanding of seedling-stage salt tolerance. An extensive literature survey indicated that there have been very few attempts to develop reproductive stage-specific salt tolerance in rice probably due to the lack of salt-tolerant phenotypes at the reproductive stage. Recently, the role of DNA methylation, genome duplication and codon usage bias in salinity tolerance of rice have been studied. Furthermore, the study of exogenous salt stress alleviants in rice has opened up another potential avenue for understanding and improving its salt tolerance. There is a need to not only generate additional genomic resources in the form of salt-responsive QTLs and molecular markers and to characterize the genes and their upstream regulatory regions, but also to use them to gain deep insights into the mechanisms useful for developing tolerant varieties. We analysed the genomic locations of diverse salt-responsive genomic resources and found that rice chromosomes 1–6 possess the majority of these salinity-responsive genomic resources. The review presents a comprehensive overview of the recent research on rice salt tolerance in the areas of genomics, proteomics, metabolomics and chemical genomics, which should help in understanding the molecular basis of salinity tolerance and its more effective improvement in rice.
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant ...breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.
Traffic flow prediction is an essential part of the intelligent transport system. This is the accurate estimation of traffic flow in a given region at a particular interval of time in the future. The ...study of traffic forecasting is useful in mitigating congestion and make safer and cost-efficient travel. While traditional models use shallow networks, there has been an exponential growth in the number of vehicles in recent times and these traditional machine learning models fail to work in current scenarios. In our paper, we review some of the latest works in deep learning for traffic flow prediction. Many deep learning architectures include Convolutional Neural Network (CNN), Recurrent Neural Network (RNN), Long Short-Term Memory (LSTM), Restricted Boltzmann Machines (RBM), and Stacked Auto Encoder (SAE). These deep learning models use multiple layers to extract higher level of features from raw input progressively. The latest deep learning models developed to tackle this very problem are reviewed and due to the complexity of transport networks, this review gives the reader information about how various factors influence these models and what models work best in different scenarios.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, ...genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
Small cardamom (
Maton), the queen of spices, is the third most expensive spice in the world after saffron and vanilla, valued highly for its aroma and taste. This perennial herbaceous plant is a ...native of coastal parts of Southern India and displays a significant amount of morphological diversity. Its genetic potential has not been exploited due to lack of genomic resources limiting our understanding of the genome and important metabolic pathways which give it the economic advantage in the spice industry. Here, we report upon the
assembled, draft whole genome sequence of cardamom variety, Njallani Green Gold. We used a hybrid assembly strategy using the reads from the Oxford Nanopore, Illumina and 10x Genomics GemCode sequencing chemistries. The assembled genome length was 1.06 Gb (gigabases) which is close to the estimated genome size of cardamom. More than 75% of the genome was captured in 8000 scaffolds with a N50 of 0.15 Mb. The genome appears to have a high repeat content and 68055 gene models were predicted. The genome is close to
species and displays an expansion and contraction in different gene families. The draft assembly was used for
mining of simple sequence repeats (SSRs). A total of 2,50,571 SSRs were identified of which 2,18,270 were perfect SSRs and 32,301 were compound SSRs. Among the perfect SSRs, trinucleotides were most abundant (1,25,329) and hexanucleotide repeats appear least (2,380). From the 2,50,571 SSRs mined, 2,27,808 primer pairs were designed based on flanking sequence information. Wet lab validation was performed for 246 SSR loci and based on their amplification profiles, 60 SSR markers were used for diversity analysis of a set of 60 diverse cardamom accessions. The average number of alleles detected per locus were 14.57 with a minimum of 4 and maximum of 30 alleles. Population structure analysis revealed the presence of high degree of admixtures which could primarily be due to cross-pollination prevalent in this species. The SSR markers identified would help in the development of gene or trait-linked markers which can be subsequently used for marker-assisted breeding for crop improvement in cardamom. The information on utilization of the SSR loci for generation of markers has been developed into a public database, 'cardamomSSRdb' that is freely available for use by the cardamom community.
Sesame seed is a reservoir of nutritional components with numerous beneficial effects along with health promotion in humans. The bioactive components present in the seed include vital minerals, ...vitamins, phytosterols, polyunsaturated fatty acids, tocopherols and unique class of lignans such as sesamin and sesamolin. The presence of phenylpropanoid compounds namely lignans along with tocopherols and phytosterols provide defense mechanism against reactive oxygen species and increases keeping quality of oil by preventing oxidative rancidity. In this article, we have reviewed the nutraceutical, pharmacological, traditional and industrial value of sesame seeds with respect to bioactive components that hold high antioxidant value. Valuable information on superior functional components of sesame will strongly promote the use of sesame seeds in the daily diet world-wide. In spite of huge repertoire of sesame germplasm collection, limited research efforts on the use of conventional and biotechnological methodologies have resulted in minimal success in developing nutritionally superior cultivars. In consequence, value addition efforts in sesame would enable development of genotypes with high antioxidant activity and subsequently prevention of free radical related diseases. Modification of bioactive components in sesame would enable production of stabilized sesame oil with enhanced shelf life and better market value.
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•Bougainvillea, an omnipresent ornamental is cultivated in highly diverse conditions.•Novel SSR markers were identified from genomic DNA sequences of cultivar Shubhra.•33 out of 175 ...SSRs characterised were highly polymorphic with gene diversity of 0.13 to 0.91.•SSRs identified here were useful to distinguish the 125 bougainvillea cultivars analysed.
Novel microsatellite markers were developed to investigate the genetic diversity and DNA fingerprinting of bougainvillea cultivars. Total of 175 SSRs were designed from over 50,000 SSRs identified in the whole genome sequence data, 33 highly polymorphic markers were identified. These selected SSRs produced a total of 165 alleles with 2 (BOUG-3 and BOUG-50) to 9 (BOUG-69) alleles per loci with an average of 5 alleles per locus. The overall size of the amplified products ranged from 90 bp (BOUG-51 and BOUG-81) to 320 bp (BOUG-162). The gene diversity per locus ranged from 0.13 to 0.91 with a mean of 0.71. Primer BOUG-73 and BOUG-124 exhibited highest gene diversity with greater number of alleles. The mean Nei's genetic diversity index was 0.678 with range of 0.134 (BOUG-77) to 0.958 (BOUG-69). The UPGMA based dendrogram divided the cultivars into seven major clusters. Clustering pattern was more distinct for bract types and variegated cultivars which were also confirmed by PCA scatter plot diagram. The pair-wise genetic distance estimates ranged from 0.089 to 0.86 with an average of 0.56. Each of the 125 cultivar profiled had unique marker profile indicating that the SSR markers identified are useful for identification and differentiation of bougainvillea cultivars. These informative markers identified from the study will be of great utility to assess the genetic diversity, understanding the population structure and in marker assisted breeding for improvement of bougainvillea.
Wireless sensor networks have been considered as an emerging technology for numerous applications of cyber-physical systems. These applications often require the deployment of sensor nodes in various ...anisotropic fields. Localization in anisotropic fields is a challenge because of the factors such as non-line of sight communications, irregularities of terrains, and network holes. Traditional localization techniques, when applied to anisotropic or irregular fields, result in colossal location estimation errors. To improve location estimations, this paper presents a comparative analysis of available localization techniques based on taxonomy framework. A detailed discussion on the importance of localization of sensor nodes in irregular fields from the reported real-life applications is presented along with challenges faced by existing localization techniques. Further, taxonomy based on techniques adopted by localization methods to address the effects of irregular fields on location estimations is reported. Finally, using the designed taxonomy framework, a comparative analysis of different localization techniques addressing irregularities and the directions towards the development of an optimal localization technique is addressed.
A germplasm collection of 33 entries comprising 22 sesame (Sesamum indicum L.) cultivars, 4 landraces of S. mulayanum and 7 other accessions of 4 wild species were analyzed for the fatty acid ...compositions of their seed oil. The entries varied widely in their fatty acid compositions. The percentage content of oleic, linoleic, palmitic and erucic acids ranged between 36.7-52.4, 30.4-51.6, 9.1-14.8 and 0.0-8.0, respectively. Linolenic and arachidonic acids were the minor constituents but varied widely in wild species. Oleic and linoleic were the major fatty acids with mean values of 45.9 and 40.5%, respectively and the mean of their combined values was 86.4%. The polyunsaturated fatty acid (PUFA) compositions ranged from 30.9 to 52.5% showing high variation in PUFA in the germplasm. Linoleic acid content was very high in one landrace (47.8) and one accession each of three wild species, S. mulayanum (49.3), S. malabaricum (48.2) and S. radiatum (51.6%). Use of fatty acid ratios to estimate the efficiency of biosynthetic pathways resulted in high oleic and low linoleic desaturation ratios and consequently high linoleic and very low linolenic acid contents in seed oil. The results of this study provided useful background information on the germplasm and also identified a few accessions having high linoleic acid which can be used for developing cultivars with desirable fatty acid compositions.
Use of space-based spectral information with weather inputs for wheat yield modeling by empirical and crop simulation models is reviewed and extended with enhanced spectral modeling approach for ...districts in central Punjab. The study uses multi-date and multi-year MODIS data at 250m resolution to both identify wheat crop and develop temporal spectral Enhanced Vegetation Index (EVI) profile for 2001-2019 period. Recently developed high resolution (12km) gridded temperature data from NCMRWF, namely India Monsoon Data Assimilation and Analysis (IMDAA) has been used for computing district-level average of daily (AV) and night-time (NT) temperatures. Multiple linear regression analysis with statistical tests on significance of coefficients for various inputs is used to investigate significance of various input parameters in yield models on multi-district data set. Results identify both area under spectral profile (AS-EVI) and mean peak value (PK-EVI) have significant control on yield. Individual district-level trend based yield (YT) is a significant coefficient in the multi-district models. Model performance is significantly improved by the inclusion of phase-specific temperatures and at specific post-flowering phases the night temperature figured in best models. Significance of the results in development of spatially resolved yields for applications like yield forecast, crop insurance and climate change studies is discussed.
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