Cytogenomics and Mutagenomics in Plant Functional Biology and Breeding
01 Jan 2015-pp 113-156
TL;DR: The functionality of mutagenomics is greatly enhanced due to integration of classical mutagenesis with modern “omics” technology through the development of desirable diploid mutants, recombinant inbred lines, and aneuploid and polyploid lines as effective cytogenetic tools, utilizable in genome mapping and analysis.
Abstract: One of the most important breakthroughs in the history of genetics and plant breeding was the development of plant cytology and experimental mutagenesis, which later brought about plant cytogenetics and mutation breeding and now they have entered in functional biology era with the unprecedented development of plant molecular cytogenetics, genetics, and functional genomics. Application of cell biology particularly chromosome biology in the fields of plant genome structure and function has ushered the development of plant cytogenomics. Development of advanced technology like DNA base-specific fluorescence banding, GISH, and FISH-based chromosome painting has greatly facilitated the identification, localization, and mapping of chromosome-specific markers in plants, which is of high importance in plant molecular systematics, species identification, detection of hybrid nature, alien chromosomes and chromosomal aberrations, analysis of somaclonal variations, and diversity analysis. The dynamism of chromatin architecture and cell cycle, representing chromosome functional biology, is another important part of plant cytogenomics. On the other hand, mutagenomics is defined as applied mutation breeding, in which genomic information and tools are utilized in the designing of breeding strategies, screening, selection and verification/authentication of natural and induced mutants, and the utilization of desirable mutations in the breeding processes. Considerable progress has been made in recent times in breeding of cereals, legumes, oil seeds, vegetables, horticultural crops, spices and condiments, fiber-yielding plants, and medicinal and aromatic plants for diverse types of desirable agronomic and functional traits including disease and abiotic stress resistance/tolerance; herbicide resistance; lowering of anti-nutritional factors; enhancement of proteins, minerals, vitamins, essential amino acids, flavonoids, antioxidants, and dietary fibers; enrichment of soil nutrition; enhancement of ornamental, medicinal, and aromatic values; and development of functional and therapeutic foods and other diverse traits related to nutritional quality and high yield. This can be found in a mutant population which carries variant forms of potentially each and every gene present in a particular genome. The functionality of mutagenomics is greatly enhanced due to integration of classical mutagenesis with modern “omics” technology through the development of desirable diploid mutants, recombinant inbred lines, and aneuploid and polyploid lines as effective cytogenetic tools, utilizable in genome mapping and analysis. Functional sets of aneuploid tools are now available in different edible plants, through which several morphological, biochemical, and molecular traits/markers have been assigned on definite chromosomes to construct linkage maps. Recently, induced mutations showing alterations in antioxidant defense response have been identified and tested against diverse types of abiotic stresses to reveal intrinsic cellular and metabolic events toward sensitivity of seed plants to salinity, drought, metal toxicity, and other stresses. These mutations are giving vital inputs, which can be used in formulating effective breeding strategies in different agroclimatic conditions. Mutagenized population has revealed altered pattern of genome response and can also be exploited in enhancing production of natural plant products like antioxidants and flavonoids. Furthermore, these large mutant populations have the potential in reverse genetics approach by employing various techniques, particularly “Targeting Induced Local Lesions in Genomics (TILLING)” technology to better understand gene functions through high-throughput mutation screening, and have been successfully used in major crop plants along with model plant Arabidopsis. The development of mutagenomic approach, thus, provides a cost-effective, clean, and easy-to-use functional tool to increase the genetic diversity and in utilization of this diversity in plant molecular mutation breeding through modern genomic methods.
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TL;DR: In this paper, the authors used colchicine solution for induction of polyploidy in grass pea (Lathyrus sativus L.) variety BioR-231 using apical shoot tip treatment of young seedlings.
Abstract: Abstract Induction of polyploidy was successfully achieved in grass pea (Lathyrus sativus L.) variety BioR-231 using 0.10% (eight hours three days), 0.20% (six hours two days and eight hours two days), 0.30% (eight hours one day) and 0.40% (six hours one day) colchicine solution by apical shoot tip treatment of young seedlings. Compared to diploid variety the tetraploid plants were morphologically distinguished by luxuriant vegetative growth showing broader and thicker leafl ets and stipules, fl attened stems, increased number of branches, enhanced length of tendril as well as peduncle, delayed fl owering and reduced pollen fertility. Number of sto-mata decreased but its size increased signifi cantly in tetraploids. Presence of 7II and 7–7 separation at meiosis-I were the usual feature in diploids (2n=2x=14) while occurrences of 28 chromosomes in different combinations of multivalents, bivalents and univalents at metaphase-I and unequal separation of chromosomes toward the spindle poles, bridge formation, laggard at anaphase-I distinguished tetraploid (2n=4x=28) from diploid plants, cytogenetically. All these meiotic irregularities through the formation of unbalanced gametes have been ascribed for pollen sterility and reduced seed yield in tetraploid plants. Nature of origin, morphology and formation of trivalent as well as quadrivalent indicated autopolyploid nature of present tetraploids in grass pea. Occurrence of majority pairing as bivalents has also been discussed.
26 citations
TL;DR: In this paper , the authors discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt, which is a major fungal disease caused by fusarium oxysporum f. sp. ciceris (FOC).
Abstract: Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.
5 citations
Journal Article•
TL;DR: Analysis of pattern of chromosomal ring formation at meiosis I in the F1 progeny of crosses between RT-7 and six previously detected RT lines suggested that the two mutations, distichous pedicel and tendril-less leaf, which assorted independently in N/N plants, were integrated on a single chromosome by a reciprocal translocation inRT-7 line.
Abstract: Grass pea (Lathyrus sativus L.) is a crop with 2n = 2x = 14 chromosomes. Two variants were isolated from 250 Gy gamma ray treated M2 progenies of variety BioL-203: (i) two pedicels per peduncle (distichous pedicel); and (ii) complete absence of tendril in leaf (tendril-less). Occurrence of quadrivalents at meiosis I and partial pollen sterility (48.50%) indicated that the plants were heterozygous for a reciprocal translocation (RT), and were tentatively designated as RT-7. It transmitted at an average of 44% in the progeny, and along with normal fertile plants (N/N), produced trisomic plants (5.76%) with association of five chromosomes in selfed and intercrossed progenies. Test of independence of this newly found translocation was performed by analyzing the pattern of chromosomal ring formation at meiosis I in the F1 progeny of crosses between RT-7 and six previously detected RT lines. Presence of a ring of six chromosomes in F1 plants indicates that the two translocations have one chromosome in common in crosses between RT-7 and RT-2, RT-3, RT-5 and RT-6, but possessed two different chromosomes in RT-7 × RT-1 and in RT-7 × RT-4. The two mutant traits assorted independently in F2 and back cross progenies of N/N plants. However, a strong deviation of segregation of four phenotypes derived from N/N × RT-7 from normal F2 and back cross ratios revealed tight linkages among translocation breakpoint, distichous pedicel and tendril-less leaf. The results suggested that the two mutations, distichous pedicel and tendril-less leaf, which assorted independently in N/N plants, were integrated on a single chromosome by a reciprocal translocation in RT-7 line.
2 citations
TL;DR: In this article , the authors performed a comprehensive association analysis of genome-wide methylation sequencing, transcriptome sequencing, and histone H3K9me3 modification in RGSV-infested as well as noninfested rice leaves, and the levels of all three cytosine contexts (CG, CHG and CHH) were found to be slightly lower in rice leaves than in normal rice leaves.
Abstract: Rice grassy stunt virus (RGSV), a typical negative single-stranded RNA virus, invades rice and generates several disease signs, including dwarfing, tillering, and sterility. Previous research has revealed that RGSV-encoded proteins can force the host’s ubiquitin-proteasome system to utilize them for viral pathogenesis. However, most of the studies were limited to a single omics level and lacked multidimensional data collection and correlation analysis on the mechanisms of RGSV-rice interactions. Here, we performed a comprehensive association analysis of genome-wide methylation sequencing, transcriptome sequencing, and histone H3K9me3 modification in RGSV-infested as well as non-infested rice leaves, and the levels of all three cytosine contexts (CG, CHG and CHH) were found to be slightly lower in RGSV-infected rice leaves than in normal rice. Large proportions of DMRs were distributed in the promoter and intergenic regions, and most DMRs were enriched in the CHH context, where the number of CHH hypo-DMRs was almost twice as high as that of hyper-DMRs. Among the genes with down-regulated expression and hypermethylation, we analyzed and identified 11 transcripts involved in fertility, plant height and tillering, and among the transcribed up-regulated and hypermethylated genes, we excavated 7 transcripts related to fertility, plant height and tillering. By analyzing the changes of histone H3K9me3 modification before and after virus infestation, we found that the distribution of H3K9me3 modification in the whole rice genome was prevalent, mainly concentrated in the gene promoter and gene body regions, which was distinctly different from the characteristics of animals. Combined with transcriptomic data, H3K9me3 mark was found to favor targeting highly expressed genes. After RGSV infection, H3K9me3 modifications in several regions of CTK and BR hormone signaling-related genes were altered, providing important targets for subsequent studies.
TL;DR: A review of the effect of waterlogging in plants, signaling (calcium, reactive oxygen species, nitric oxide, hormones), and adaptive responses is provided in this paper .
Abstract: Soil flooding has emerged as a serious threat to modern agriculture due to the rapid global warming and climate change, resulting in catastrophic crop damage and yield losses. The most detrimental effects of waterlogging in plants are hypoxia, decreased nutrient uptake, photosynthesis inhibition, energy crisis, and microbiome alterations, all of which result in plant death. Although significant advancement has been made in mitigating waterlogging stress, it remains largely enigmatic how plants perceive flood signals and translate them for their adaptive responses at a molecular level. With the advent of multiomics, there has been significant progress in understanding and decoding the intricacy of how plants respond to different stressors which have paved the way towards the development of climate-resistant smart crops. In this review, we have provided the overview of the effect of waterlogging in plants, signaling (calcium, reactive oxygen species, nitric oxide, hormones), and adaptive responses. Secondly, we discussed an insight into past, present, and future prospects of waterlogging tolerance focusing on conventional breeding, transgenic, multiomics, and gene-editing approaches. In addition, we have also highlighted the importance of panomics for developing waterlogging-tolerant cultivars. Furthermore, we have discussed the role of high-throughput phenotyping in the screening of complex waterlogging-tolerant traits. Finally, we addressed the current challenges and future perspectives of waterlogging signal perception and transduction in plants, which warrants future investigation.
References
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TL;DR: Phenomics should be recognized and pursued as an independent discipline to enable the development and adoption of high-throughput and high-dimensional phenotyping.
Abstract: A key goal of biology is to understand phenotypic characteristics, such as health, disease and evolutionary fitness. Phenotypic variation is produced through a complex web of interactions between genotype and environment, and such a 'genotype-phenotype' map is inaccessible without the detailed phenotypic data that allow these interactions to be studied. Despite this need, our ability to characterize phenomes - the full set of phenotypes of an individual - lags behind our ability to characterize genomes. Phenomics should be recognized and pursued as an independent discipline to enable the development and adoption of high-throughput and high-dimensional phenotyping.
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TL;DR: This work cloned FRI and analyzed the molecular basis of the allelic variation at the FRIGIDA locus, finding that loss-of-function mutations at FRI have provided the basis for the evolution of many early-flowering ecotypes.
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Abstract: Activation of cell division in the root apical meristem after germination is essential for postembryonic root development. Arabidopsis plants homozygous for a mutation in the ROOT MERISTEMLESS1 (RML1) gene are unable to establish an active postembryonic meristem in the root apex. This mutation abolishes cell division in the root but not in the shoot. We report the molecular cloning of the RML1 gene, which encodes the first enzyme of glutathione (GSH) biosynthesis, γ-glutamylcysteine synthetase, and which is allelic to CADMIUM SENSITIVE2. The phenotype of the rml1 mutant, which was also evident in the roots of wild-type Arabidopsis and tobacco treated with an inhibitor of GSH biosynthesis, could be relieved by applying GSH to rml1 seedlings. By using a synchronized tobacco cell suspension culture, we showed that the G1-to-S phase transition requires an adequate level of GSH. These observations suggest the existence of a GSH-dependent developmental pathway essential for initiation and maintenance of cell division during postembryonic root development.
575 citations
TL;DR: Induced mutations will continue to have an increasing role in creating crop varieties with traits such as modified oil, protein and starch quality, enhanced uptake of specific metals, deeper rooting system, and resistance to drought, diseases and salinity as a major component of the environmentally sustainable agriculture.
Abstract: During the past seventy years, worldwide more than 2250 varieties have been released that have been derived either as direct mutants or from their progenies Induction of mutations with radiation has been the most frequently used method for directly developed mutant varieties The prime strategy in mutation-based breeding has been to upgrade the well-adapted plant varieties by altering one or two major traits, which limit their productivity or enhance their quality value In this paper, the global impact of mutation-derived varieties on food production and quality enhancement is presented In addition, the economic contribution of the selected mutant varieties of rice, barley, cotton, groundnut, pulses, sunflower, rapeseed and Japanese pear is discussed In several mutation-derived varieties, the changed traits have resulted in synergistic effect on increasing the yield and quality of the crop, improving agronomic inputs, crop rotation, and consumer acceptance In contrast to the currently protected plant varieties or germplasm and increasing restrictions on their use, the induced mutants have been freely available for plant breeding Many mutants have made transnational impact on increasing yield and quality of several seed-propagated crops Induced mutations will continue to have an increasing role in creating crop varieties with traits such as modified oil, protein and starch quality, enhanced uptake of specific metals, deeper rooting system, and resistance to drought, diseases and salinity as a major component of the environmentally sustainable agriculture Future research on induced mutations would also be important in the functional genomics of many food crops
561 citations