Advances in Bioscience and Biotechnology
Vol.3 No.4(2012), Article ID:21870,8 pages DOI:10.4236/abb.2012.34054

Genomics of crop plant genetic resources

Arun Prabhu Dhanapal1,2

1Plant Genetic Resources, Scuola Superiore Sant’ Anna, Rome, Italy

2Division of Plant Sciences, University of Missouri, Columbia, USA


Received 15 May 2012; revised 25 June 2012; accepted 6 July 2012

Keywords: Crop plant genetic resources; genomics; next generation sequencing (NGS)


Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. Primarily studies were based on model species, although it now enhances the transferability of information to crops and related species. With the tremendous outbreak of new high-throughput technologies like next-generation sequencing (NGS) and reduction in their costs are bringing many more plants within the range of genome and transcriptome level analysis. The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the crop plant genetic resources to accelerate crop improvement. The future of crop improvement will be centred on comparisons of individual crop plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here I review the importance of crop plant genetic resources and insights that have been emerged in recent years.


Plants have always been the most important resource as food for humankind and feed for animals. The cultivation of plants species are often regarded as the starting point of modern civilization, which is some 10,000 years ago. Humans began domesticating crops as a food source in different era of civilizations. Among the available wild germplasms of plant species, the best adapted one are preferably selected for cultivation and utilization, but this also had led to a decline in the genetic diversity of the crops. Land races and traditional varieties have been replaced by less diverse modern cultivars and hybrids. In order to face the challenging demand of agricultural production with the rapid growing population and with the alarming climate change, the need for the utilization of wild relatives and underutilized crops (orphan crops) are in necessity today. Although wild ancestors have continued to persist in regions where domestication took place, there is a permanent risk of loss of the genetic variability of cultivated plants and their wild relatives in response to changing environmental conditions and cultural practices [1]. Enhancement and synergistic innovations are fundamentally important in addressing these needs for the improvement of agricultural productivity and sustainability across a broad front - food safety and security, diet and health, environmental safety and novel crops are some area of new opportunities in plant science [2]. The need to preserve and use plant genetic resources is well recognized, and the prospect of dwindling plant genetic diversity, coupled with increased demands on these resources has made them a topic of global discussion [3].

With the tremendous outbreak of new high-throughput technologies and reduction in their costs are bringing many more crops, trees and orphan plant genomes within range of analysis [4] Today entire sequence of complete crop plant genomes and transcriptomes can be well considered a newly developed genetic resource, for the information it provides on plant functions and allows us in discovering the genes from the wild species that correspond to specific phenotypes [3]. Availability of rapid techniques and the introduction of NGS and their advancement over recent years, one could foresee the very good chances of deciphering the genetic mechanism involved in novel complex traits [5] and thereby will help us dissecting the genetic variability of the selected genetic resources, their characterization and conservation, and in generating increased value for collections of crop genetics resources. Collecting rapid and accurate phenotypes in crop plants is a hindrance to integrating genomics with crop improvement, and advancement in informatics are needed to put these tools in the hands of the scientists on the ground [6].


Plant genetic resources are the most important components of agrobiodiversity. They include primitive forms of cultivated crop species and land-races, modern cultivars, obsolete cultivars, breeding lines and genetic stocks and related wild species. The introgression of genes that reduced plant height and increased disease and viral resistance in wheat provided the foundation for the “Green Revolution” and demonstrated the tremendous impact that genetic resources can have on crop production [7]. Food production and security depend on the wise use and conservation of agricultural biodiversity and genetic resources [8]. Even though several thousands of plant species are globally available only few are in use (Table 1). Since importance have been given to relatively small number of crop species for global food security, it is particularly important that their genetic diversity is conserved effectively and managed wisely. So far, only a small part of the total genetic variability has been characterized and used for crop breeding purposes.


Genetic resources provide basic material for selection and improvement through breeding to ensure food security needs of world’s rapidly rising population. All aspects related to genetic resources (collection, conservation, evaluation, management and utilization) are however, needed to be done eminently. Molecular technique has proved useful in a number of ways to improve the conservation and management of PGR [9]. Molecular markers help in verification of accession identity and genetic contamination [10-12] and also been used to identify ecogeographic races within the domesticated or wild gene pools of crop species [13]. Presently, existing biotechnological approaches to overcome challenges for effective utilization and enhancement of crop genetic resources include embryo rescue and somatic hybridization [14,15]. The ability to store and exchange healthy

Table 1. Total number of plant species.

Germplasm is fundamental objective for effective conservation and use of crop genetic resources.


Genomics, the study of an organism’s entire genome is the new field of study to enhance the use of crop genetic resources. Today genomic technology has been applied in gene identification laying good foundation for functional genomics research and to aid us in understanding the gene expression and biological activity, genomics initiatives are focused on fundamental elements of plant biology with regard to growth, development, reproduction, photosynthesis and responses to environmental conditions and pathogens.

Cereal genomics potentially carries the strength to shape the future of agriculture and its sustainability [16]. The better prediction of the phenotype that a particular genotype will produce is a primary goal of genomicsbased breeding. Analysis of the crop genomes architecture and their expressed components are now possible with the development in crop genomics, and subsequently leads to an increase in our knowledge of the genes that are linked to key agronomically important complex traits particularly in major crop species. DNA-based molecular markers have played a pivotal role in detecting the genetic variation available in germplasm collections and breeding lines. Various sets of diverse molecular markers have been developed for many major crop species and are being used extensively for the development of saturated molecular, genetic and physical maps and for the identification of genes or quantitative trait loci (QTL) controlling traits of economic importance through marker assisted selection (MAS) [17,18]. Together with MAS other approaches like association mapping [19], functional genomics [20], genetical genomics [21], allele mining [17], Targeting Induced Local Lesions in Genomes (TILLING) and Eco Type TILLING (EcoTILLING) [22] have been available from past decade.

Development in cereal genomics would play key role in crop improvement in two general ways. First, a better understanding of the biological mechanisms can lead to new or improved screening methods for selecting superior genotypes more efficiently. Second, new knowledge can improve the decision-making process for more efficient breeding strategies [17]. These advances and development will provide opportunity for efficient transfer of information systems from model species and major crops to orphan crops [23]


Comparative genomics, promised to identify the functional elements in a genome based on the assumption that these elements are preferentially conserved through evolutionary time [24]. It has taken advantage of evolutionary signature that has been acted on the genome to understand the function and evolution across different crop species. With the availability of whole-genome sequences of crops and plant species, as well as other genomic resources (e.g. microarray methods, expressed sequence tag (EST) libraries, high throughput resequencing technologies), have extended the comparative method to encompass the evolution of genome structure and function [25,26].

Rapid progress in crop genomics is making possible to undertake detailed structural and functional comparisons of genes involved in various biological processes among important crops and other plant species. This flow of research was promising and would provide important information for future work on the evolution of higher crop plants. Comparisons at varying levels of evolutionary divergence are likely to reveal functional regions characteristic of different plant groups, Moreover intraspecific genomic approaches have been shown to be useful in predicting functional sequence motifs [27]. Since significant genomic colinearity has been reported in cereal species [28] the comparative genomics approach using bioinformatics tools might therefore provide an opportunity for efficient transfer of information from model species and major crops to minor and orphan crops, and particularly crops such as pearl millet, small millets and tef that are often considered orphan crops for poor genomic research shelter, and these crops are regionally or locally important for nutrition and income, particularly in developing countries [23,27,29].


Plant translational genomics, a challenge faced by the plant genomics research to develop applications in crop plants which imply the translation of gene functions from a model to a crop species. Candidate gene approach (CGA) renown as a tool for translational genomics has been considered for successful application in crops with determined factors such as the type of crop, the complexity of the trait and the type of genes involved. The CGA is based on the assumption that genes with a proven or predicted function in a “model” species (functional candidate genes) or genes that are co-localized with a traitlocus (positional candidate genes) could control a similar function or trait in an arbitrary crop of interest (target crop) [30]. Studying the sequence variation among alleles (paralogs and orthologs) of candidate genes may provide conserved sequence motifs or conserved SNPs associated with a trait [31]. The extrapolations of gene function from a model crop to a more distant species have been well discussed [32,33].


In recent years crop genomics based research has been providing the means to uncover the genetic basis of crop characteristics with significance to human life and health. Crop-plant genome research integrated with human genome analysis, nutritional science and medicine constitutes a novel discipline of research in support of human welfare [34,35]. This existing new multidisciplinary approach is called nutrigenomics. This approach focuses on the highly complex interplay between human genetic predisposition and nutrition, in regard to both, food nutritional quality and disease prevention [36]. Strong priorities are now to focus on the genes that determine characteristics supporting the production of crops in an environmentally, friendly and sustainable manner. Millions of poor children in the world particularly in semiarid tropics of Asia and Africa suffer from vitamin A deficiency, which causes blindness, and reduces the bioavailability of other important dietary micro-nutrients, including iron that were important for human health. This serious public health problem is addressed by genetically increasing the levels of pro-vitamin A (primarily green and yellow vegetables) in dietary staples like rice, maize, sorghum, and pearl millet. Besides the genes that control the accumulation of bulk nutrients, efforts are taken to uncover the genes that determine the content of valuable compounds such as potential pharmaceuticals, health promoting pro-biotics, flavor and fragrance compounds, protectants, biocides, fine chemicals, etc. The rapid development and innovations in crop plant genomics are expected to provide newer knowledge in these areas and will open up ways for targeted crop improvement, both through the direct use of natural genetic diversity and via genetic engineering [36].


Revolution in DNA sequencing technology has brought down the cost of DNA sequencing and made the sequencing of an increased number of genomes both feasible and cost effective [37]. The first plant genome Arabidopsis was completely sequenced in December 2000, and it was the third complete genome of a higher eukaryote and further studies were carried in recent years on Arabidposis thaliana and Arabidopsis lyrata [38,39].

Subsequently after Arabidopsis, several other cropplants have been sequenced [38-64] (Table 2). Genomes of other crop plant species like Tomato (Solanum lycopersicum), monkey flower (Mimulus guttatus), rose gum tree (Eucalyptus grandis) Cassava (Manihot esculenta), Peaches (Prunus persica), Columbine (Aquilegia

Table 2. Genome sequencing of crop plants.

sp.) and Foxtail Millet (Setaria italica) are still not yet completely published. These genomes reveals numerous species-specific details, including genome size, gene number, patterns of sequence duplication, a catalog of transposable elements, and syntenic relationships. To understand the complex instructions contained in all these raw sequence information of the plant genome, largescale functional genomics projects are required. Progress towards a complete understanding of gene regulatory networks shared among many crop plants is important for improving cultivated species and for understanding plant evolution.


Sanger dideoxy sequencing [65] and its modifications dominated the DNA sequencing field for nearly 30 years and in the past 10 years the length of Sanger sequence reads has increased from 450 bases to more than 1 kb [37]

Currently, with the rapid demand, novel innovations at the technological perspectives are being made and the important innovation was the introduction of Next-Generation Sequencing (NGS).

The term NGS is used to collectively describe technologies other than Sanger sequencing that have the potential to sequence the human genome in coming years for US $1000 [66] and such technologies are either already commercially available [67]. Present manufacturers of sequencing machine are constantly increasing sequence output in terms of number of reads (bp-base pair), increasing read length, as well as working to improve read quality [4,68,69].


A greater challenge for sequence storage and management is solved by redundant data being generated by the new sequencing technologies. Several tools offer various levels of sophistication and simplicity for accessing the reference genome sequences available, genome viewers had been developed to allow users for visualization and assessment of data through common browsers such as EnsEMBL [70-72], Gbrowse and the University of California, Santa Cruz genome browser [73]. The International Nucleotide Sequence Databases consisting of GenBank [74], the DNA Databank of Japan (DDBJ) [75], and European Molecular Biological Laboratory (EMBL) [76] has been the principle repositories for DNA sequence data. The collection of large volumes of structured phenotypic data and its integration with the abundant genome data will add dimensions and challenges for the storage, management, and visualization of this information. Generation of new online servers like cloud computing and Galaxy has allowed researchers to perform comparative biology at an unprecedented level, providing insights into the foundations of life and the evolutionary processes that shape biological processes [77-79].


Crop evolution under domestication has led increased productivity of crop species, but at the same time has narrowed their genetic basis. Fortunately, wild relatives of crop plants exhibit vast genetic diversity for adaptation to stressful environments such as frost, drought and high salt and metal. Genomics is a brand new science that promises to revolutionize genetics, plant breeding and biotechnology using molecular characterization, transcript profiling and cloning of whole genomes to understand the structure, function and evolution of genes as well as to answer fundamental biological questions. Combining comprehensive sequence information with knowledge of the morphological and physiological diversity of crop plant and well-understood phylogeny promises to answer many questions about crop genome evolution and function.

Applications of genome resequencing, high-density genetic markers and a new generation of experimental designs that more readily relate mutational diversity to agronomic phenotypes, comparative genomics will become increasingly relevant to crop improvement. A combination of Genome Wide Association Studies (GWASs) and next-generation-mapping populations will improve our ability to connect phenotypes and genotypes, and genomic selection can take advantage of this data for rapid selection and breeding. The combination of these approaches with the promise of improved genomic technologies provides an opportunity for comparative genomics to apply our understanding of the past to the future of crop improvement.


I thank Shalini Narasimhan for helping me in editing and finalizing this manuscript.


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