Sequencing for the cream of the crop

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Nature Biotechnology (Impact Factor: 41.51). 02/2011; 29(2):138-9. DOI: 10.1038/nbt.1756
Source: PubMed


Sequencing technologies are poised to transform conventional strategies for crop improvement.

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    • "This might be particularly true for polyploid crops in which assignment of genic SNPs to specific homologous loci can often be more reliable using haplotype-oriented sequencing data than on array platforms. Furthermore, because they can theoretically access novel allelic variants in genetically diverse association panels, NGS-based genotyping methods (see Davey et al. 2011 for a comprehensive review) have a potential advantage over array-based SNP screening methods that only survey known alleles in a given panel of SNPs (Chia and Ware 2011). Use of SNPs discovered by genomic resequencing for GWAS was shown by Huang et al. (2010) to be highly effective for uncovering genes involved in important agronomic traits in rice. "
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    ABSTRACT: Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.
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    ABSTRACT: Changes in climate and urbanisation rapidly affecting human livelihood are particularly threatening to developing nations in tropical regions. Food production crises have focused the global development agenda on agricultural research, a proven approach for increasing crop yield. A few crops benefit from private investment, but improvement of most crops will rely on limited public funding that must be deployed strategically, pushing forward both proven approaches and new ideas. Why not invest in beans? More than 300 million people rely on this crop, considered to be the most important grain legume for human consumption. Yet the yield of beans, especially in poor regions or marginal soils, is reduced by abiotic stresses such as phosphorus deficiency, aluminum toxicity and especially drought. Is it possible to assemble resources, including genetic diversity in beans, breeding expertise, genomic information and tools, and physiological insight to generate rapid progress in developing new lines of beans more tolerant to abiotic stress? A workshop to address this question was held in November 2010 at the International Center for Tropical Agriculture (CIAT) in Colombia. The resulting 'call to action' is presented in this issue which also includes research papers focused on tolerance of beans to stress.
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    ABSTRACT: World's population has crossed 6.5 billion with majority of human beings living in developing or under developing countries. Clearly, food security in such countries will be a primary concern over the next few decades. However, options for increased food production to meet this population pressure are limited because most arable land is already under cultivation, and in many areas land use cannot be further intensified without a risk to the long-term productivity. Agricultural land use has been especially intense in recent years because of rapid urbanization and increasing environmental pollution. The ultimate need is to use newer technologies which could help us to curb this food insecurity. Biotechnology is globally recognized as a rapidly emerging, complex and far reaching new technology. It has revolutionized all the fields of life. Recent discoveries and technical innovations in the field of genomics and biotechnology are revealing the full complement of genes in crops, the ability to define genetic variation and use DNA markers to follow chromosome segments with known functions through breeding programmes are leading to new efficiencies in breeding. The ability to isolate and redesign genes and transfer them into different plants also offers the breeder solutions to several key limitations. The convergence of advances in biology-genomics, proteomics, bioinformatics and information technologies is driving the emergence of a new bio-economy. By the usage of this technology we have achieved remarkable success in increasing crop productivity, improving crop quality as well as overcoming food shortage. Additionally the genetically engineered crops have shown a remarkable potential to tackle some of the world's most challenging socioeconomic problems which are more prevalent in the developing world than in the industrialized nations. © 2012 Springer Science+Business Media B.V. All rights reserved.
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