To address this, as mentioned above, the Arabidopsis plant research community has developed a vision of sequencing a larger number of Arabidopsis genotype accessions, including various ecotypic and experimental population samples. The 1KP sample list consists of entries [ 51 ] broadly grouped by phylogenetically angiosperm, non-flowering, and green algae species and by application agriculture, medicine, biochemistry, and extremophytes.
Most of these species have been sequenced for the first time Table 1. Ultimately, the obtained genomic sequence data will be used to analyze the phylogenetic, taxonomic, and evolutionary relationships of plant species, to study plant speciation, and to determine the timing of gene duplications during speciation events [ 35 , 52 ].
Key aims and expertise
However, the biggest limitation is associated with sequencing only transcriptomes rather targeting the whole genome, which limits obtaining many non-coding and repetitive portions of genomes. The results should not only accelerate crop improvement and boost the agricultural and medicine production worldwide but also help to understand the basics of plant life, evolution, speciation, and plant adaptations to the extreme environments in the era of global climate change and technological advancements. Source: Ref. In this book, we have presented several chapters targeting to review and discuss the strategies for sequencing and assembly challenges by Deschamps and Llaca , new-generation sequencing platforms for comparative genomics of cereal crops by Sikhakhane et al.
These chapters describe the current advances and future needs on these topics. At present, the reference genomes for many agricultural plants including specialty crops have been sequenced, as reviewed by Michael and VanBuren [ 32 ], which created a new paradigm for modern crop breeding. Crop breeding, which is powered and enriched by molecular markers, genetic linkage maps, QTL mapping, association mapping, and marker-assisted selection methods in the past century [ 37 , 53 ], has now greatly accelerated and become ever productive and efficient in the plant genomics era [ 26 ].
This is due to the 1 availability of large-scale transcriptome and whole-genome reference sequences [ 32 ]; 2 high-throughput SNP marker collection and cost-effective, automated, and high-throughput genotyping platforms HTP and technologies e. The biggest driving force for genomics-assisted crop breeding in the plant genomics era has been the inexpensive sequencing and re-sequencing opportunity for population individuals of genetic crosses and breeding lines.
Tackling Plant Meiosis: From Model Research to Crop Improvement.
This helps to precisely identify and link genetic variations to the phenotypic expressions, taking into account the rare and private allelic variations that are abundant in crop line population or germplasm resources [ 26 , 53 , 54 ]. Furthermore, the availability of SNP marker collections and automated genotyping platforms provided a better genome converge to perform genome-wide genotype-to-phenotype associations GWAS [ 11 , 37 ].
Also, when whole-genome sequences are not available and SNP markers are present in a limited number, the breeders using GBS and HTS platforms can readily genotype their mapping population and can provide genomic selections for the targeted crops of interest [ 23 , 26 , 54 ]. Although it was first applied for animal breeding [ 55 ], recently genomic selection has been successfully applied to a number of plant species [ 56 — 62 ], including studies using GBS in the context of genomic selection [ 26 ].
Several chapters in this book have covered the advances toward plant resistance genomics and molecular breeding against bacterial diseases in ryegrasses see the chapter by Dr. The availability of genome sequences and a large number of SNP marker collections also provided the analysis of copy number variations CNVs in crop genomes, and their links to the key traits have greatly enhanced the crop improvement programs [ 11 , 22 , 23 , 26 , 37 ].
Furthermore, although challenges are evident, the opportunity provided by post-genome sequencing advances has help to integrate and enrich genomic selection with key proteome and metabolome markers. This significantly fostered and powered up the breeding of complex traits [ 22 ] of crops. Because of high-throughput genome analysis, it is possible to date that many plant compounds, including herbicides, growth regulators and phytohormones, elicitors, low molecular metabolites e.
Crop improvement is also greatly impacted by novel transgenomics and genome editing technologies developed as a result of plant genome characterization and understanding in the era of plant genomics. In the past two decades, a variety of novel transgenomics technologies have been developed to replace or enrich the traditional transgenesis-based genetic engineering and plant molecular biotechnology [ 65 ].
These novel transgenomics technologies including genome-editing tools,the latter also referred to as genome editing with engineered nucleases GEEN , are widely developed and utilized to investigate the gene function and apply to solve problems in medicine and agriculture. They are become methods of choice for major functional genomics and biotechnological studies [ 67 ]. For a detailed description of RNAi, readers are suggested to read a chapter by Ricano-Rodriguez et al.
The potential application of RNA-mediated gene silencing methods for crop improvement, including RNAi in plant biotechnology, is huge and the technology has already generated many successful examples in a wide range of technical, food, and horticulture crops. The examples include A. The revolutionizing advances made in the past three decades in plant genomics and its sub-disciplines provided a mass of novel opportunities with easy-solution applications and high-throughput, cost-effective, and time-effective technologies.
However, it also piled up challenging grand tasks ahead for current genomics and post-genomics era. Several chapters of this book have discussed some aspects of these challenges, and I tried to briefly summarize some of them here. However, the first current and future task ahead is to extend such large-scale, multiple accession genome sequencing initiatives for each priority agricultural and specialty crop species including their wild relatives and ancestor-like genome representatives.
Although it sounds largely ambitious, this task will be mandatory and important for the next plant genome sequencing phase.
This is especially needed for polyploidy crops [ 24 , 32 , 37 ] because the sequencing of many polyploids and their subgenomes would increase our understanding of the complexity of polypoidy, gene silencing, epigenetics, and biased retention and expression of genes after polyploidization [ 24 , 95 — 97 ]. Furthermore, it also helps to discover all natural variations and lost genes during crop domestication that should be useful to restore the key agriculturally important traits in the future.
Results would be useful for plant evolutionary, speciation and taxonomy studies.
TILLING for Mutations in Model Plants and Crops
There are ongoing planning and targets toward this goal, and it should not cause much trouble in the land of experiences gained and inexpensive high-throughput sequencing technologies [ 1 , 27 , 32 ]. Although high-throughput DNA sequencing instrumentation exists and keeps evolving to better versions year-to-year, the consequent task is still to improve the sequence length that would solve many incorrect sequence sites and genome assembly challenges that plant genomics faces currently [ 1 , 32 ].
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Some of the currently ongoing efforts and possible solution with the advent of third-generation sequencing platforms and genome assembly tools and methodologies highlighted herein have been discussed by several book chapters in this book. There is an urgent need to develop more efficient bioinformatics platforms to handle plant genome data due to challenges, specificities, complexities, and sizes of currently available and future sequenced plant genomes mentioned herein [ 1 , 98 ].
Funding this aspect of plant genomics and bioinformatics research is a necessary key step [ 1 ] for future advances on this task ahead. Furthermore, the most important current and future post-genomics grand task ahead is to link the sequence variation s with phenotype s , trait expression, and epigenetic and adaptive features of plants to their living environment and extreme conditions.
The successful completion of this task will require the combined approaches of genomics with bioinformatics, proteomics, metabolomics, phenomics, genomic selections, genetical genomics, reverse genomics, system biology, etc. This also requires the integration of all available genomic and phenotypic data to identify key networks that also require downstream effort of integration of specific networks to networks of other systems in order to connect heterogeneous data [ 29 ].
There is a need to use molecular phenotyping i. All these will help to minimize the current challenges with improved crop line development costs through efficient breeding [ 11 , 22 , 23 , 26 ]. These particular grand tasks further highlight a need for extended effort and work on the development of inexpensive high-throughput plant phenotyping [ 25 , 26 ] and plant proteome and metabolome profiling tools and instrumentation [ 27 , 28 ] by utilizing small amount single-cell-derived samples [ 27 — 29 ].
A parallel grand task to the above-outlined needs is to have concentrated efforts on the timely application of novel transgenomics and genome-editing tools for all types of plants and to optimize it for routine large- and short-scale biotechnology industry usage. There are grandest tasks to 1 utilize the complex effects of plant developmental genes e.
In addition, there are needs to 3 identify the appropriate choice of plant tissues for genome editing, 4 reduce or eliminate side effects and off-target toxicity and mutagenesis of application of novel genome modification technologies, and 5 develop reliable screens for the detection of edited genome samples [ 99 ]. Therefore, this is one of the most important grand tasks ahead in the front of plant sciences research community in the era of plant genomics and post-genomics.
Importantly, they are required to have a capability to utilize modern computing and instrumentation platforms and bioinformatics knowledge [ 29 ]. For instance, there is a huge need for a new generation of molecular breeders [ ] with full knowledge and appreciation of conventional plant breeding aspects including the understanding of agrotechnology methodologies, genetic diversity of crop germplasm, and randomized multi-environmental field trails.
These breeders also need to have abilities to handle, work, and utilize the sequenced genomes, high-throughput genotyping, and phenotyping platforms. This is a bottleneck for plant genomics at present, which requires urgent awareness, attention, and investment. Thus, in the past three decades, plant genomics has evolved from the enrichment and advances made in conventional genetics and breeding, molecular biology, molecular genetics, molecular breeding, and molecular biotechnology in the land of high-throughput DNA sequencing technologies powering the plant research community to sequence and understand the genetic compositions, structures, architectures, and functions of full plant genomes.
The technological and instrumentation advancements as well as the desire and need to feed the increasing human population, overcome biosecurity issues, and sustain agricultural production in the era of global climate change, the societal globalization, and technological advancements have been the main driving forces for plant genomics development. To date, more than plant genomes including a large number of crops as well as flowering, non-flowering, crop wild relative, model and non-model, and specialty plants have been fully sequenced. As a result, it expanded our knowledge and understanding of many aspects of plant biology, genetics, breeding, and crop evolution and domestication, which contributed to the development of analytical and breeding tools, resulting in accelerated crop improvement programs.
To look even deeper scales, more than Arabidopsis accessions from various eco-geographic origin and experimental populations have been fully sequenced, which will equip plant researchers with better analysis tools and help in tagging and exploiting the biologically meaningful variations. All of these successes have significantly accelerated crop improvement using novel genomic selections and new-generation genome-editing and manipulation technologies.
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- Technique using plant's own DNA could produce crops that are more resistant to drought and disease.
- Model grasses hold key to crop improvement!
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These advances, briefly highlighted herein, also have generated a number of grand challenges and mandatory tasks ahead in plant genomics and post-genomics era. There are many tasks ahead for the plant genomics community, which require more collaborations, integrated approaches, better computing capacity and analytical tools, accelerated training and education of well-qualified researchers, and larger investments.
In this book, the authors tried to highlight some updates on current plant genomics efforts with future perspectives. We trust that the next phase of plant genomics efforts and development will be more exciting and help to solve current and future issues in front of humanity. I also thank Dr. Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution 3. Help us write another book on this subject and reach those readers. Login to your personal dashboard for more detailed statistics on your publications.
Edited by Ibrokhim Y. By Thandeka N. We are IntechOpen, the world's leading publisher of Open Access books. Built by scientists, for scientists. Our readership spans scientists, professors, researchers, librarians, and students, as well as business professionals. Downloaded: Abstract Historically, unintentional plant selection and subsequent crop domestication, coupled with the need and desire to get more food and feed products, have resulted in the continuous development of plant breeding and genetics efforts.
Introduction The Plant Kingdom is a key of the food chain in our planet. Genome of plants and crop species 2. Challenges and advantages Compared to other eukaryotic systems, plant genomes are more complex, which create challenges to study its DNA compositions. Table 1. Crop improvement in the genomics and post-genomics era 3. Genomics-assisted selection or genomic selection At present, the reference genomes for many agricultural plants including specialty crops have been sequenced, as reviewed by Michael and VanBuren [ 32 ], which created a new paradigm for modern crop breeding.
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